Chlorine in PDB 5w4q: Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
Protein crystallography data
The structure of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4q
was solved by
A.T.Gres,
K.A.Kirby,
S.G.Sarafianos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.03 /
2.29
|
Space group
|
P 6
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.055,
92.055,
58.253,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.6 /
24.5
|
Other elements in 5w4q:
The structure of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
(pdb code 5w4q). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the
Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4q:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Chlorine binding site 1 out
of 7 in 5w4q
Go back to
Chlorine Binding Sites List in 5w4q
Chlorine binding site 1 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl308
b:40.9
occ:0.95
|
O
|
A:GLY60
|
2.7
|
52.5
|
1.0
|
ND1
|
A:HIS62
|
3.6
|
57.9
|
1.0
|
CE1
|
A:HIS62
|
3.7
|
57.4
|
1.0
|
C
|
A:GLY60
|
3.9
|
53.5
|
1.0
|
O
|
A:HOH428
|
4.1
|
63.3
|
1.0
|
CG1
|
A:VAL27
|
4.2
|
58.5
|
1.0
|
CA
|
A:ALA28
|
4.3
|
56.1
|
1.0
|
N
|
A:GLY60
|
4.4
|
48.4
|
1.0
|
N
|
A:ALA28
|
4.6
|
52.5
|
1.0
|
CG1
|
A:VAL59
|
4.7
|
39.2
|
1.0
|
CA
|
A:GLY60
|
4.7
|
50.9
|
1.0
|
O
|
A:VAL27
|
4.7
|
45.2
|
1.0
|
CB
|
A:ALA28
|
4.7
|
55.2
|
1.0
|
C
|
A:VAL27
|
4.7
|
51.8
|
1.0
|
N
|
A:GLY61
|
4.8
|
52.8
|
1.0
|
CA
|
A:GLY61
|
4.9
|
50.4
|
1.0
|
CG
|
A:HIS62
|
4.9
|
56.7
|
1.0
|
C
|
A:GLY61
|
5.0
|
38.1
|
1.0
|
NE2
|
A:HIS62
|
5.0
|
57.8
|
1.0
|
|
Chlorine binding site 2 out
of 7 in 5w4q
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Chlorine Binding Sites List in 5w4q
Chlorine binding site 2 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl309
b:94.5
occ:1.00
|
O
|
A:HOH478
|
3.1
|
74.3
|
1.0
|
CL
|
A:CL311
|
3.6
|
96.4
|
1.0
|
CD1
|
A:ILE129
|
3.7
|
61.4
|
1.0
|
CG1
|
A:ILE129
|
4.2
|
62.1
|
1.0
|
CZ3
|
A:TRP80
|
4.3
|
62.4
|
1.0
|
CH2
|
A:TRP80
|
4.4
|
62.3
|
1.0
|
NH1
|
A:ARG132
|
4.9
|
74.5
|
1.0
|
CG
|
A:PRO125
|
4.9
|
59.0
|
1.0
|
CD
|
A:PRO125
|
5.0
|
62.1
|
1.0
|
|
Chlorine binding site 3 out
of 7 in 5w4q
Go back to
Chlorine Binding Sites List in 5w4q
Chlorine binding site 3 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl310
b:65.5
occ:1.00
|
O
|
A:HOH439
|
2.7
|
54.5
|
1.0
|
NH2
|
A:ARG173
|
3.3
|
47.5
|
1.0
|
O
|
A:HOH453
|
4.1
|
65.6
|
1.0
|
NE
|
A:ARG173
|
4.2
|
45.8
|
1.0
|
CZ
|
A:ARG173
|
4.2
|
46.3
|
1.0
|
CG
|
A:PRO38
|
4.3
|
51.5
|
1.0
|
CD
|
A:PRO38
|
4.4
|
44.6
|
1.0
|
CB
|
A:PRO38
|
4.6
|
48.8
|
1.0
|
|
Chlorine binding site 4 out
of 7 in 5w4q
Go back to
Chlorine Binding Sites List in 5w4q
Chlorine binding site 4 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl311
b:96.4
occ:1.00
|
CL
|
A:CL309
|
3.6
|
94.5
|
1.0
|
O
|
A:HOH440
|
3.8
|
45.3
|
1.0
|
CH2
|
A:TRP80
|
4.3
|
62.3
|
1.0
|
CG2
|
A:ILE124
|
4.5
|
72.5
|
1.0
|
CD
|
A:PRO125
|
4.7
|
62.1
|
1.0
|
|
Chlorine binding site 5 out
of 7 in 5w4q
Go back to
Chlorine Binding Sites List in 5w4q
Chlorine binding site 5 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl312
b:81.2
occ:1.00
|
O
|
A:HOH452
|
3.0
|
57.9
|
1.0
|
O
|
A:GLN219
|
3.7
|
92.5
|
1.0
|
O
|
A:HOH408
|
4.0
|
64.7
|
1.0
|
N
|
A:ARG162
|
4.0
|
45.1
|
1.0
|
CB
|
A:PRO160
|
4.0
|
53.5
|
1.0
|
N
|
A:PHE161
|
4.1
|
43.6
|
1.0
|
CB
|
A:ARG162
|
4.2
|
48.0
|
1.0
|
CA
|
A:GLN219
|
4.2
|
85.4
|
1.0
|
O
|
A:CYS218
|
4.3
|
67.7
|
1.0
|
C
|
A:GLN219
|
4.4
|
91.8
|
1.0
|
I
|
A:IOD303
|
4.4
|
62.6
|
0.6
|
CA
|
A:PRO160
|
4.5
|
50.2
|
1.0
|
C
|
A:PRO160
|
4.6
|
46.5
|
1.0
|
CA
|
A:ARG162
|
4.7
|
48.6
|
1.0
|
CA
|
A:PHE161
|
4.8
|
45.3
|
1.0
|
CB
|
A:PHE161
|
4.8
|
38.9
|
1.0
|
CG
|
A:GLN219
|
4.9
|
94.8
|
1.0
|
NE
|
A:ARG162
|
4.9
|
74.7
|
1.0
|
C
|
A:PHE161
|
4.9
|
45.4
|
1.0
|
|
Chlorine binding site 6 out
of 7 in 5w4q
Go back to
Chlorine Binding Sites List in 5w4q
Chlorine binding site 6 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl313
b:71.0
occ:1.00
|
O
|
A:HOH479
|
3.0
|
53.5
|
1.0
|
NH2
|
A:ARG167
|
3.3
|
51.2
|
1.0
|
CD
|
A:ARG167
|
3.6
|
48.6
|
1.0
|
CD1
|
A:ILE153
|
3.7
|
44.9
|
1.0
|
I
|
A:IOD307
|
3.8
|
88.2
|
0.4
|
CB
|
A:ARG167
|
4.1
|
46.7
|
1.0
|
CG2
|
A:THR148
|
4.2
|
74.8
|
1.0
|
CG
|
A:ARG167
|
4.2
|
51.8
|
1.0
|
CZ
|
A:ARG167
|
4.3
|
50.7
|
1.0
|
NE
|
A:ARG167
|
4.4
|
44.0
|
1.0
|
OG1
|
A:THR171
|
4.8
|
46.7
|
1.0
|
CB
|
A:THR148
|
5.0
|
73.1
|
1.0
|
|
Chlorine binding site 7 out
of 7 in 5w4q
Go back to
Chlorine Binding Sites List in 5w4q
Chlorine binding site 7 out
of 7 in the Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Structure of the R18A/E28A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl314
b:74.3
occ:1.00
|
O
|
A:HOH444
|
2.5
|
71.1
|
1.0
|
CB
|
A:ALA31
|
3.6
|
61.6
|
1.0
|
CD2
|
A:TYR145
|
3.8
|
54.3
|
1.0
|
CE2
|
A:TYR145
|
4.4
|
54.1
|
1.0
|
CD2
|
A:PHE32
|
4.5
|
57.3
|
1.0
|
CG
|
A:TYR145
|
4.7
|
56.4
|
1.0
|
N
|
A:PHE32
|
4.7
|
63.4
|
1.0
|
NE2
|
A:HIS62
|
4.8
|
57.8
|
1.0
|
CD2
|
A:HIS62
|
4.8
|
56.8
|
1.0
|
CB
|
A:TYR145
|
4.8
|
52.6
|
1.0
|
CA
|
A:ALA31
|
4.9
|
62.7
|
1.0
|
|
Reference:
P.Craveur,
A.T.Gres,
K.A.Kirby,
D.Liu,
J.A.Hammond,
Y.Deng,
S.Forli,
D.S.Goodsell,
J.R.Williamson,
S.G.Sarafianos,
A.J.Olson.
Novel Intersubunit Interaction Critical For Hiv-1 Core Assembly Defines A Potentially Targetable Inhibitor Binding Pocket. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 30862755
DOI: 10.1128/MBIO.02858-18
Page generated: Fri Jul 26 19:09:40 2024
|