Chlorine in PDB 3se9: Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Protein crystallography data
The structure of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120, PDB code: 3se9
was solved by
P.D.Kwong,
T.Zhou,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.73 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.804,
66.476,
237.305,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
23.3
|
Chlorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Chlorine atom in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
(pdb code 3se9). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 18 binding sites of Chlorine where determined in the
Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120, PDB code: 3se9:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Chlorine binding site 1 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 1 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1013
b:65.2
occ:1.00
|
OG1
|
G:THR388
|
2.6
|
44.6
|
1.0
|
HB3
|
G:PRO363
|
2.6
|
55.9
|
1.0
|
O
|
G:HOH8
|
2.7
|
26.6
|
1.0
|
O
|
G:HOH585
|
2.7
|
54.3
|
1.0
|
O
|
G:HOH32
|
2.8
|
28.6
|
1.0
|
HG1
|
G:THR388
|
3.0
|
53.6
|
1.0
|
HD2
|
G:PRO364
|
3.2
|
36.6
|
1.0
|
H
|
G:THR388
|
3.4
|
36.6
|
1.0
|
HA
|
G:THR388
|
3.4
|
40.8
|
1.0
|
CB
|
G:PRO363
|
3.6
|
46.6
|
1.0
|
OD1
|
G:ASN386
|
3.6
|
38.8
|
1.0
|
N
|
G:THR388
|
3.6
|
30.5
|
1.0
|
H
|
G:THR387
|
3.7
|
41.2
|
1.0
|
CB
|
G:THR388
|
3.7
|
43.2
|
1.0
|
HB2
|
G:PRO363
|
3.8
|
55.9
|
1.0
|
CA
|
G:THR388
|
3.8
|
34.0
|
1.0
|
N2
|
G:NAG886
|
3.9
|
40.0
|
1.0
|
CD
|
G:PRO364
|
4.0
|
30.5
|
1.0
|
HD3
|
G:PRO364
|
4.1
|
36.6
|
1.0
|
C1
|
G:NAG886
|
4.1
|
38.3
|
1.0
|
HA
|
G:PRO363
|
4.2
|
47.8
|
1.0
|
CG
|
G:ASN386
|
4.2
|
41.7
|
1.0
|
HB
|
G:THR388
|
4.2
|
51.8
|
1.0
|
N
|
G:THR387
|
4.3
|
34.3
|
1.0
|
O
|
G:THR372
|
4.3
|
32.3
|
1.0
|
HG3
|
G:PRO363
|
4.4
|
58.7
|
1.0
|
C
|
G:THR387
|
4.4
|
43.8
|
1.0
|
ND2
|
G:ASN386
|
4.4
|
43.0
|
1.0
|
OG1
|
G:THR387
|
4.4
|
36.9
|
1.0
|
CA
|
G:PRO363
|
4.5
|
39.8
|
1.0
|
CG
|
G:PRO363
|
4.5
|
48.9
|
1.0
|
C2
|
G:NAG886
|
4.6
|
43.4
|
1.0
|
HA
|
G:ASN386
|
4.6
|
35.4
|
1.0
|
HG22
|
G:THR388
|
4.7
|
60.6
|
1.0
|
HG2
|
G:PRO363
|
4.7
|
58.7
|
1.0
|
C8
|
G:NAG886
|
4.8
|
56.1
|
1.0
|
O
|
G:HOH691
|
4.8
|
36.7
|
1.0
|
C7
|
G:NAG886
|
4.8
|
53.4
|
1.0
|
CG2
|
G:THR388
|
4.8
|
50.5
|
1.0
|
HD21
|
G:ASN386
|
4.8
|
51.6
|
1.0
|
CA
|
G:THR387
|
4.8
|
32.7
|
1.0
|
HG2
|
G:PRO364
|
4.9
|
40.0
|
1.0
|
N
|
G:PRO364
|
4.9
|
33.8
|
1.0
|
HG1
|
G:THR387
|
5.0
|
44.3
|
1.0
|
|
Chlorine binding site 2 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 2 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1014
b:69.9
occ:1.00
|
O
|
G:HOH605
|
2.6
|
31.7
|
1.0
|
O
|
G:HOH547
|
3.0
|
42.0
|
1.0
|
HB1
|
G:ALA58
|
3.5
|
40.3
|
1.0
|
HA
|
G:THR71
|
3.6
|
41.0
|
1.0
|
O
|
G:ALA58
|
3.7
|
38.6
|
1.0
|
HA
|
G:PRO76
|
3.8
|
48.5
|
1.0
|
H
|
G:ALA58
|
4.1
|
43.3
|
1.0
|
O
|
G:SER56
|
4.1
|
34.3
|
1.0
|
HG3
|
G:PRO76
|
4.1
|
58.6
|
1.0
|
N
|
G:ALA58
|
4.4
|
36.0
|
1.0
|
HG1
|
G:THR71
|
4.4
|
43.1
|
1.0
|
CB
|
G:ALA58
|
4.4
|
33.6
|
1.0
|
O
|
G:VAL75
|
4.4
|
41.8
|
1.0
|
N
|
G:PRO76
|
4.4
|
43.0
|
1.0
|
O
|
G:CYS74
|
4.4
|
42.5
|
1.0
|
C
|
G:VAL75
|
4.4
|
37.1
|
1.0
|
C
|
G:ALA58
|
4.5
|
34.7
|
1.0
|
CA
|
G:PRO76
|
4.5
|
40.4
|
1.0
|
OG
|
G:SER56
|
4.5
|
38.8
|
1.0
|
HD3
|
G:PRO76
|
4.6
|
48.8
|
1.0
|
CA
|
G:THR71
|
4.6
|
34.1
|
1.0
|
O
|
G:ALA70
|
4.6
|
33.2
|
1.0
|
HG21
|
G:THR71
|
4.6
|
40.5
|
1.0
|
CA
|
G:ALA58
|
4.6
|
35.5
|
1.0
|
HA
|
G:ASP57
|
4.8
|
55.4
|
1.0
|
HA
|
G:VAL75
|
4.8
|
44.9
|
1.0
|
CG
|
G:PRO76
|
4.8
|
48.8
|
1.0
|
O
|
G:HOH635
|
4.8
|
45.0
|
1.0
|
HG
|
G:SER56
|
4.8
|
46.6
|
1.0
|
C
|
G:SER56
|
4.9
|
36.4
|
1.0
|
CD
|
G:PRO76
|
4.9
|
40.7
|
1.0
|
H
|
G:SER56
|
4.9
|
37.3
|
1.0
|
HB3
|
G:ALA58
|
4.9
|
40.3
|
1.0
|
HB2
|
G:ALA58
|
4.9
|
40.3
|
1.0
|
O
|
G:THR71
|
5.0
|
31.1
|
1.0
|
C
|
G:ASP57
|
5.0
|
43.2
|
1.0
|
HB2
|
G:CYS74
|
5.0
|
39.5
|
1.0
|
|
Chlorine binding site 3 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 3 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1015
b:76.5
occ:1.00
|
H
|
G:LEU277
|
2.3
|
40.4
|
1.0
|
HA
|
G:ASN276
|
3.0
|
47.7
|
1.0
|
C3
|
G:GOL1007
|
3.1
|
70.8
|
1.0
|
HB2
|
G:LEU277
|
3.1
|
49.3
|
1.0
|
N
|
G:LEU277
|
3.1
|
33.6
|
1.0
|
C8
|
G:NAG734
|
3.2
|
44.6
|
1.0
|
HG
|
G:LEU277
|
3.3
|
52.4
|
1.0
|
C1
|
G:GOL1007
|
3.5
|
77.9
|
1.0
|
N2
|
G:NAG734
|
3.6
|
38.0
|
1.0
|
C7
|
G:NAG734
|
3.7
|
48.3
|
1.0
|
C2
|
G:GOL1007
|
3.7
|
70.4
|
1.0
|
CA
|
G:ASN276
|
3.8
|
39.8
|
1.0
|
CB
|
G:LEU277
|
3.8
|
41.1
|
1.0
|
O
|
G:HOH507
|
3.8
|
41.3
|
1.0
|
O
|
G:SER274
|
3.9
|
29.8
|
1.0
|
HB3
|
G:SER274
|
3.9
|
37.0
|
1.0
|
O
|
G:HOH503
|
3.9
|
67.7
|
1.0
|
C
|
G:ASN276
|
4.0
|
40.1
|
1.0
|
O2
|
G:GOL1007
|
4.0
|
55.8
|
1.0
|
CG
|
G:LEU277
|
4.0
|
43.7
|
1.0
|
O3
|
G:GOL1007
|
4.0
|
62.4
|
1.0
|
O3
|
G:NAG734
|
4.0
|
42.3
|
1.0
|
CA
|
G:LEU277
|
4.1
|
38.6
|
1.0
|
HD11
|
G:LEU277
|
4.2
|
54.6
|
1.0
|
N
|
G:ASN276
|
4.2
|
31.9
|
1.0
|
O1
|
G:GOL1007
|
4.5
|
90.9
|
1.0
|
O
|
G:GLU275
|
4.5
|
33.4
|
1.0
|
C
|
G:GLU275
|
4.5
|
38.4
|
1.0
|
C3
|
G:NAG734
|
4.5
|
43.1
|
1.0
|
HA
|
G:LEU277
|
4.5
|
46.3
|
1.0
|
H
|
G:ASN276
|
4.6
|
38.3
|
1.0
|
O7
|
G:NAG734
|
4.6
|
42.8
|
1.0
|
C
|
G:SER274
|
4.6
|
33.1
|
1.0
|
C2
|
G:NAG734
|
4.6
|
41.5
|
1.0
|
CD1
|
G:LEU277
|
4.7
|
45.5
|
1.0
|
HB3
|
G:LEU277
|
4.7
|
49.3
|
1.0
|
CB
|
G:SER274
|
4.8
|
30.9
|
1.0
|
H
|
G:THR278
|
4.8
|
35.9
|
1.0
|
OG
|
G:SER274
|
5.0
|
32.2
|
1.0
|
H
|
G:SER274
|
5.0
|
42.7
|
1.0
|
|
Chlorine binding site 4 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 4 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1016
b:83.8
occ:1.00
|
HE22
|
G:GLN428
|
2.2
|
40.2
|
1.0
|
HG2
|
G:GLN428
|
2.5
|
41.8
|
1.0
|
HB2
|
G:ASP113
|
2.6
|
48.3
|
1.0
|
HG23
|
G:ILE109
|
2.9
|
40.0
|
1.0
|
O
|
G:ILE109
|
3.0
|
31.2
|
1.0
|
NE2
|
G:GLN428
|
3.0
|
33.5
|
1.0
|
HA
|
G:ASP113
|
3.2
|
46.0
|
1.0
|
CB
|
G:ASP113
|
3.4
|
40.3
|
1.0
|
CG
|
G:GLN428
|
3.4
|
34.9
|
1.0
|
H
|
G:ASP113
|
3.4
|
45.7
|
1.0
|
N
|
G:ASP113
|
3.5
|
38.1
|
1.0
|
O
|
G:HOH595
|
3.5
|
42.6
|
1.0
|
CA
|
G:ASP113
|
3.5
|
38.3
|
1.0
|
OD1
|
G:ASP113
|
3.5
|
66.6
|
1.0
|
HE21
|
G:GLN428
|
3.6
|
40.2
|
1.0
|
HB2
|
G:TRP112
|
3.6
|
37.2
|
1.0
|
HG22
|
G:ILE109
|
3.6
|
40.0
|
1.0
|
CG2
|
G:ILE109
|
3.7
|
33.3
|
1.0
|
CD
|
G:GLN428
|
3.7
|
40.2
|
1.0
|
HA
|
G:ILE109
|
3.7
|
30.6
|
1.0
|
C
|
G:ILE109
|
3.9
|
32.6
|
1.0
|
CG
|
G:ASP113
|
3.9
|
59.9
|
1.0
|
HG3
|
G:GLN428
|
4.0
|
41.8
|
1.0
|
HB3
|
G:TRP112
|
4.0
|
37.2
|
1.0
|
O
|
G:HOH552
|
4.0
|
30.8
|
1.0
|
C
|
G:TRP112
|
4.1
|
38.6
|
1.0
|
HB3
|
G:ASP113
|
4.2
|
48.3
|
1.0
|
HB3
|
G:GLN428
|
4.2
|
44.1
|
1.0
|
CB
|
G:TRP112
|
4.2
|
31.0
|
1.0
|
CA
|
G:ILE109
|
4.2
|
25.5
|
1.0
|
HG21
|
G:ILE109
|
4.3
|
40.0
|
1.0
|
CB
|
G:GLN428
|
4.3
|
36.7
|
1.0
|
HB2
|
G:GLN428
|
4.5
|
44.1
|
1.0
|
CB
|
G:ILE109
|
4.5
|
30.6
|
1.0
|
HG12
|
G:ILE109
|
4.6
|
36.1
|
1.0
|
O
|
G:TRP112
|
4.6
|
40.6
|
1.0
|
CA
|
G:TRP112
|
4.7
|
30.4
|
1.0
|
HG1
|
G:THR430
|
4.8
|
47.8
|
1.0
|
OE1
|
G:GLN428
|
4.9
|
32.0
|
1.0
|
H
|
G:TRP112
|
4.9
|
40.1
|
1.0
|
|
Chlorine binding site 5 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 5 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1017
b:68.1
occ:1.00
|
H
|
G:GLY250
|
2.5
|
40.9
|
1.0
|
HB2
|
G:HIS249
|
2.8
|
42.8
|
1.0
|
HE1
|
G:HIS216
|
3.1
|
50.2
|
1.0
|
HA
|
G:HIS249
|
3.3
|
46.9
|
1.0
|
N
|
G:GLY250
|
3.4
|
34.0
|
1.0
|
CB
|
G:HIS249
|
3.6
|
35.6
|
1.0
|
CA
|
G:HIS249
|
3.8
|
39.1
|
1.0
|
CE1
|
G:HIS216
|
3.9
|
41.9
|
1.0
|
HB3
|
G:HIS249
|
4.0
|
42.8
|
1.0
|
O
|
G:HOH164
|
4.1
|
41.9
|
1.0
|
HA3
|
G:GLY250
|
4.1
|
35.6
|
1.0
|
C
|
G:HIS249
|
4.1
|
34.5
|
1.0
|
CA
|
G:GLY250
|
4.3
|
29.6
|
1.0
|
HD2
|
G:HIS249
|
4.6
|
46.4
|
1.0
|
HD1
|
G:HIS216
|
4.7
|
42.7
|
1.0
|
ND1
|
G:HIS216
|
4.7
|
35.6
|
1.0
|
CG
|
G:HIS249
|
4.7
|
35.8
|
1.0
|
NE2
|
G:HIS216
|
4.8
|
41.9
|
1.0
|
HE2
|
G:HIS216
|
4.8
|
50.3
|
1.0
|
|
Chlorine binding site 6 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 6 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1019
b:77.8
occ:1.00
|
HD1
|
G:HIS72
|
2.5
|
58.1
|
1.0
|
HB3
|
G:HIS72
|
2.9
|
47.0
|
1.0
|
HD1
|
G:TRP69
|
3.0
|
38.3
|
1.0
|
HA
|
G:TRP69
|
3.0
|
36.9
|
1.0
|
CD1
|
G:TRP69
|
3.1
|
31.9
|
1.0
|
ND1
|
G:HIS72
|
3.2
|
48.5
|
1.0
|
O
|
G:HOH602
|
3.2
|
33.7
|
1.0
|
O
|
G:TRP69
|
3.4
|
29.2
|
1.0
|
HB2
|
G:ALA73
|
3.5
|
41.0
|
1.0
|
NE1
|
G:TRP69
|
3.6
|
34.9
|
1.0
|
OE1
|
G:GLN114
|
3.6
|
57.7
|
1.0
|
HE1
|
G:TRP69
|
3.7
|
41.8
|
1.0
|
CB
|
G:HIS72
|
3.7
|
39.2
|
1.0
|
CG
|
G:TRP69
|
3.7
|
32.6
|
1.0
|
CG
|
G:HIS72
|
3.8
|
47.5
|
1.0
|
CA
|
G:TRP69
|
3.8
|
30.8
|
1.0
|
HE21
|
G:GLN114
|
3.8
|
54.4
|
1.0
|
H
|
G:ALA73
|
4.0
|
45.2
|
1.0
|
C
|
G:TRP69
|
4.0
|
27.4
|
1.0
|
O
|
G:HOH628
|
4.0
|
34.3
|
1.0
|
HB2
|
G:HIS72
|
4.2
|
47.0
|
1.0
|
CE1
|
G:HIS72
|
4.2
|
44.9
|
1.0
|
CD
|
G:GLN114
|
4.3
|
54.5
|
1.0
|
CB
|
G:TRP69
|
4.3
|
32.4
|
1.0
|
NE2
|
G:GLN114
|
4.3
|
45.4
|
1.0
|
CE2
|
G:TRP69
|
4.3
|
33.4
|
1.0
|
N
|
G:ALA73
|
4.3
|
37.6
|
1.0
|
CB
|
G:ALA73
|
4.4
|
34.2
|
1.0
|
CD2
|
G:TRP69
|
4.4
|
35.5
|
1.0
|
HE1
|
G:HIS72
|
4.5
|
53.9
|
1.0
|
HB2
|
G:TRP69
|
4.5
|
38.9
|
1.0
|
HB3
|
G:ALA73
|
4.6
|
41.0
|
1.0
|
H
|
G:HIS72
|
4.7
|
36.5
|
1.0
|
O
|
G:HOH128
|
4.7
|
25.3
|
1.0
|
O
|
G:VAL68
|
4.8
|
33.1
|
1.0
|
CA
|
G:HIS72
|
4.8
|
36.0
|
1.0
|
CA
|
G:ALA73
|
4.8
|
40.3
|
1.0
|
C
|
G:HIS72
|
4.9
|
37.1
|
1.0
|
HA
|
G:ALA73
|
4.9
|
48.3
|
1.0
|
N
|
G:TRP69
|
5.0
|
33.4
|
1.0
|
|
Chlorine binding site 7 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 7 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1022
b:78.5
occ:1.00
|
H
|
G:SER300
|
2.4
|
64.1
|
1.0
|
HA
|
G:PRO299
|
2.8
|
49.3
|
1.0
|
HG
|
G:SER300
|
3.0
|
75.1
|
1.0
|
HB3
|
G:PRO299
|
3.1
|
52.9
|
1.0
|
N
|
G:SER300
|
3.2
|
53.4
|
1.0
|
HG3
|
G:LYS442
|
3.2
|
68.2
|
1.0
|
HB2
|
G:LYS442
|
3.4
|
61.7
|
1.0
|
OG
|
G:SER300
|
3.4
|
62.6
|
1.0
|
CA
|
G:PRO299
|
3.5
|
41.1
|
1.0
|
HD2
|
G:LYS442
|
3.6
|
69.6
|
1.0
|
CB
|
G:PRO299
|
3.7
|
44.0
|
1.0
|
C
|
G:PRO299
|
3.8
|
43.1
|
1.0
|
CG
|
G:LYS442
|
3.9
|
56.8
|
1.0
|
HE3
|
G:LYS442
|
3.9
|
75.1
|
1.0
|
CB
|
G:LYS442
|
4.1
|
51.5
|
1.0
|
HA
|
G:LYS442
|
4.1
|
55.1
|
1.0
|
CD
|
G:LYS442
|
4.2
|
58.0
|
1.0
|
HB3
|
G:SER300
|
4.2
|
64.7
|
1.0
|
CB
|
G:SER300
|
4.2
|
53.9
|
1.0
|
CA
|
G:SER300
|
4.2
|
52.2
|
1.0
|
HB2
|
G:PRO299
|
4.3
|
52.9
|
1.0
|
HG21
|
G:THR297
|
4.4
|
54.9
|
1.0
|
O
|
G:SER300
|
4.6
|
49.5
|
1.0
|
CE
|
G:LYS442
|
4.6
|
62.6
|
1.0
|
CA
|
G:LYS442
|
4.6
|
45.9
|
1.0
|
HG3
|
G:PRO299
|
4.7
|
58.6
|
1.0
|
HG2
|
G:LYS442
|
4.8
|
68.2
|
1.0
|
N
|
G:PRO299
|
4.8
|
38.6
|
1.0
|
HG22
|
G:THR297
|
4.8
|
54.9
|
1.0
|
CG
|
G:PRO299
|
4.9
|
48.9
|
1.0
|
HB3
|
G:LYS442
|
4.9
|
61.7
|
1.0
|
C
|
G:SER300
|
4.9
|
51.9
|
1.0
|
CG2
|
G:THR297
|
5.0
|
45.8
|
1.0
|
HA
|
G:SER300
|
5.0
|
62.7
|
1.0
|
|
Chlorine binding site 8 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 8 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1027
b:70.6
occ:1.00
|
HE2
|
G:HIS352
|
2.0
|
59.5
|
1.0
|
H
|
G:ILE272
|
2.2
|
33.7
|
1.0
|
HZ3
|
G:LYS348
|
2.7
|
74.0
|
1.0
|
NE2
|
G:HIS352
|
2.8
|
49.6
|
1.0
|
O
|
G:HOH540
|
2.8
|
49.8
|
1.0
|
HA
|
G:ILE271
|
3.0
|
56.9
|
1.0
|
N
|
G:ILE272
|
3.0
|
28.1
|
1.0
|
HG12
|
G:ILE272
|
3.1
|
46.4
|
1.0
|
HB
|
G:ILE272
|
3.2
|
47.3
|
1.0
|
O
|
G:HOH636
|
3.4
|
42.5
|
1.0
|
HG23
|
G:ILE271
|
3.4
|
42.3
|
1.0
|
HE1
|
G:HIS352
|
3.5
|
62.8
|
1.0
|
NZ
|
G:LYS348
|
3.5
|
61.7
|
1.0
|
CE1
|
G:HIS352
|
3.5
|
52.3
|
1.0
|
HZ1
|
G:LYS348
|
3.6
|
74.0
|
1.0
|
HZ2
|
G:LYS348
|
3.8
|
74.0
|
1.0
|
CA
|
G:ILE271
|
3.8
|
47.4
|
1.0
|
CB
|
G:ILE272
|
3.8
|
39.4
|
1.0
|
HG3
|
G:LYS348
|
3.8
|
52.8
|
1.0
|
CG1
|
G:ILE272
|
3.9
|
38.7
|
1.0
|
C
|
G:ILE271
|
3.9
|
38.9
|
1.0
|
CA
|
G:ILE272
|
3.9
|
37.8
|
1.0
|
CD2
|
G:HIS352
|
3.9
|
46.4
|
1.0
|
O
|
G:ILE272
|
4.0
|
33.4
|
1.0
|
O
|
G:HOH682
|
4.0
|
48.0
|
1.0
|
HD2
|
G:HIS352
|
4.1
|
55.7
|
1.0
|
O
|
G:ILE270
|
4.2
|
44.1
|
1.0
|
HG13
|
G:ILE272
|
4.2
|
46.4
|
1.0
|
CG2
|
G:ILE271
|
4.2
|
35.3
|
1.0
|
HG22
|
G:ILE271
|
4.4
|
42.3
|
1.0
|
HG2
|
G:LYS348
|
4.4
|
52.8
|
1.0
|
HG12
|
G:ILE271
|
4.4
|
56.9
|
1.0
|
C
|
G:ILE272
|
4.4
|
36.0
|
1.0
|
CG
|
G:LYS348
|
4.5
|
44.0
|
1.0
|
CB
|
G:ILE271
|
4.5
|
39.8
|
1.0
|
HB3
|
G:ASN234
|
4.6
|
54.0
|
1.0
|
CE
|
G:LYS348
|
4.7
|
54.2
|
1.0
|
ND1
|
G:HIS352
|
4.7
|
54.5
|
1.0
|
HA
|
G:ILE272
|
4.8
|
45.3
|
1.0
|
HD2
|
G:LYS348
|
4.8
|
61.8
|
1.0
|
HB2
|
G:ASN234
|
4.9
|
54.0
|
1.0
|
CG1
|
G:ILE271
|
4.9
|
47.4
|
1.0
|
N
|
G:ILE271
|
4.9
|
31.4
|
1.0
|
HE3
|
G:LYS348
|
4.9
|
65.1
|
1.0
|
CD
|
G:LYS348
|
4.9
|
51.5
|
1.0
|
HG13
|
G:ILE271
|
4.9
|
56.9
|
1.0
|
C
|
G:ILE270
|
4.9
|
41.5
|
1.0
|
CG
|
G:HIS352
|
4.9
|
51.1
|
1.0
|
HG21
|
G:ILE271
|
5.0
|
42.3
|
1.0
|
|
Chlorine binding site 9 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 9 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl1028
b:59.5
occ:1.00
|
HB3
|
G:PHE53
|
3.3
|
45.1
|
1.0
|
HO2
|
G:GOL1005
|
3.5
|
40.5
|
1.0
|
HA
|
G:PHE53
|
3.6
|
30.4
|
1.0
|
O
|
G:HOH181
|
3.6
|
23.6
|
1.0
|
O
|
G:LEU52
|
3.7
|
27.9
|
1.0
|
HB2
|
G:PHE53
|
3.8
|
45.1
|
1.0
|
CB
|
G:PHE53
|
3.9
|
37.6
|
1.0
|
HG22
|
G:THR51
|
4.0
|
48.8
|
1.0
|
CA
|
G:PHE53
|
4.2
|
25.4
|
1.0
|
H12
|
G:GOL1005
|
4.4
|
34.2
|
1.0
|
HG21
|
G:THR51
|
4.4
|
48.8
|
1.0
|
O2
|
G:GOL1005
|
4.4
|
33.7
|
1.0
|
C
|
G:LEU52
|
4.6
|
33.5
|
1.0
|
CG2
|
G:THR51
|
4.6
|
40.7
|
1.0
|
N
|
G:PHE53
|
4.8
|
31.3
|
1.0
|
H32
|
G:GOL1005
|
4.8
|
25.0
|
1.0
|
HG23
|
G:THR51
|
4.9
|
48.8
|
1.0
|
|
Chlorine binding site 10 out
of 18 in 3se9
Go back to
Chlorine Binding Sites List in 3se9
Chlorine binding site 10 out
of 18 in the Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 10 of Crystal Structure of Broadly and Potently Neutralizing Antibody Vrc- PG04 in Complex with Hiv-1 GP120 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl1010
b:65.9
occ:1.00
|
H
|
H:ASP62
|
2.5
|
35.8
|
1.0
|
HD2
|
H:PRO61
|
2.6
|
50.1
|
1.0
|
O
|
H:HOH356
|
2.7
|
40.7
|
1.0
|
HB2
|
H:ASP62
|
2.8
|
48.0
|
1.0
|
HB2
|
H:SER60
|
2.9
|
42.8
|
1.0
|
N
|
H:ASP62
|
3.3
|
29.8
|
1.0
|
CD
|
H:PRO61
|
3.5
|
41.8
|
1.0
|
HB3
|
H:ASP62
|
3.5
|
48.0
|
1.0
|
HB2
|
H:PRO61
|
3.5
|
45.0
|
1.0
|
CB
|
H:ASP62
|
3.5
|
40.0
|
1.0
|
HG
|
H:SER60
|
3.7
|
40.4
|
1.0
|
CB
|
H:SER60
|
3.7
|
35.7
|
1.0
|
OG
|
H:SER60
|
3.9
|
33.6
|
1.0
|
HG2
|
H:PRO61
|
3.9
|
53.5
|
1.0
|
N
|
H:PRO61
|
3.9
|
36.7
|
1.0
|
CA
|
H:ASP62
|
4.0
|
37.7
|
1.0
|
CG
|
H:PRO61
|
4.1
|
44.6
|
1.0
|
CB
|
H:PRO61
|
4.1
|
37.5
|
1.0
|
HD3
|
H:PRO61
|
4.2
|
50.1
|
1.0
|
C
|
H:PRO61
|
4.3
|
32.9
|
1.0
|
HB3
|
H:SER60
|
4.4
|
42.8
|
1.0
|
CA
|
H:PRO61
|
4.4
|
32.9
|
1.0
|
HA
|
H:ASP62
|
4.4
|
45.3
|
1.0
|
C
|
H:SER60
|
4.5
|
34.7
|
1.0
|
CA
|
H:SER60
|
4.6
|
31.8
|
1.0
|
HA
|
H:SER60
|
4.7
|
38.1
|
1.0
|
CG
|
H:ASP62
|
4.8
|
42.9
|
1.0
|
H
|
H:PHE63
|
4.8
|
35.8
|
1.0
|
O
|
H:HOH364
|
4.9
|
56.9
|
1.0
|
|
Reference:
X.Wu,
T.Zhou,
J.Zhu,
B.Zhang,
I.Georgiev,
C.Wang,
X.Chen,
N.S.Longo,
M.Louder,
K.Mckee,
S.O'dell,
S.Perfetto,
S.D.Schmidt,
W.Shi,
L.Wu,
Y.Yang,
Z.Y.Yang,
Z.Yang,
Z.Zhang,
M.Bonsignori,
J.A.Crump,
S.H.Kapiga,
N.E.Sam,
B.F.Haynes,
M.Simek,
D.R.Burton,
W.C.Koff,
N.A.Doria-Rose,
M.Connors,
J.C.Mullikin,
G.J.Nabel,
M.Roederer,
L.Shapiro,
P.D.Kwong,
J.R.Mascola.
Focused Evolution of Hiv-1 Neutralizing Antibodies Revealed By Structures and Deep Sequencing. Science V. 333 1593 2011.
ISSN: ISSN 0036-8075
PubMed: 21835983
DOI: 10.1126/SCIENCE.1207532
Page generated: Sun Jul 21 04:23:50 2024
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