Chlorine in PDB 8pob: Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3:
3.2.1.17;
Protein crystallography data
The structure of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3, PDB code: 8pob
was solved by
Z.Alsalman,
E.Girard,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.70 /
1.74
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.404,
77.404,
37.602,
90,
90,
90
|
R / Rfree (%)
|
18 /
22.8
|
Other elements in 8pob:
The structure of Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
(pdb code 8pob). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3, PDB code: 8pob:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 8pob
Go back to
Chlorine Binding Sites List in 8pob
Chlorine binding site 1 out
of 6 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
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 Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl204
b:34.6
occ:1.00
|
H
|
A:THR69
|
2.4
|
31.7
|
1.0
|
HG
|
A:SER72
|
3.0
|
45.2
|
1.0
|
O
|
A:HOH349
|
3.1
|
26.2
|
1.0
|
O
|
A:HOH397
|
3.1
|
40.6
|
1.0
|
O
|
A:HOH389
|
3.1
|
35.9
|
1.0
|
HA2
|
A:GLY67
|
3.2
|
30.4
|
1.0
|
H
|
A:GLY67
|
3.2
|
36.3
|
1.0
|
N
|
A:THR69
|
3.2
|
26.6
|
1.0
|
O
|
A:THR69
|
3.3
|
30.5
|
1.0
|
O
|
A:HOH318
|
3.4
|
40.3
|
1.0
|
C
|
A:GLY67
|
3.5
|
44.5
|
1.0
|
OD1
|
A:ASN65
|
3.5
|
30.6
|
1.0
|
H
|
A:ARG68
|
3.6
|
34.2
|
1.0
|
N
|
A:ARG68
|
3.6
|
28.7
|
1.0
|
CA
|
A:GLY67
|
3.6
|
25.4
|
1.0
|
OG
|
A:SER72
|
3.6
|
37.8
|
1.0
|
HB
|
A:THR69
|
3.6
|
29.5
|
1.0
|
C
|
A:THR69
|
3.7
|
28.7
|
1.0
|
N
|
A:GLY67
|
3.7
|
30.4
|
1.0
|
CA
|
A:THR69
|
3.9
|
28.6
|
1.0
|
O
|
A:HOH360
|
4.0
|
29.8
|
1.0
|
O
|
A:GLY67
|
4.1
|
33.5
|
1.0
|
H
|
A:ASP66
|
4.2
|
34.6
|
1.0
|
OD1
|
A:ASP66
|
4.2
|
25.7
|
1.0
|
CB
|
A:THR69
|
4.2
|
24.7
|
1.0
|
C
|
A:ARG68
|
4.2
|
26.9
|
1.0
|
CA
|
A:ARG68
|
4.3
|
35.6
|
1.0
|
HA
|
A:PRO70
|
4.4
|
44.1
|
1.0
|
HA
|
A:ARG68
|
4.4
|
42.6
|
1.0
|
N
|
A:PRO70
|
4.5
|
34.2
|
1.0
|
HA3
|
A:GLY67
|
4.5
|
30.4
|
1.0
|
H
|
A:SER72
|
4.6
|
41.8
|
1.0
|
NA
|
A:NA210
|
4.6
|
28.0
|
1.0
|
O
|
A:HOH409
|
4.6
|
36.0
|
1.0
|
CG
|
A:ASN65
|
4.7
|
27.2
|
1.0
|
C
|
A:ASP66
|
4.8
|
25.7
|
1.0
|
HA
|
A:THR69
|
4.8
|
34.2
|
1.0
|
N
|
A:ASP66
|
4.8
|
29.0
|
1.0
|
OG1
|
A:THR69
|
4.9
|
25.8
|
1.0
|
CB
|
A:SER72
|
4.9
|
41.0
|
1.0
|
CA
|
A:PRO70
|
4.9
|
36.9
|
1.0
|
HA
|
A:ASN65
|
4.9
|
30.2
|
1.0
|
CL
|
A:CL208
|
5.0
|
50.5
|
0.5
|
|
Chlorine binding site 2 out
of 6 in 8pob
Go back to
Chlorine Binding Sites List in 8pob
Chlorine binding site 2 out
of 6 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
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 Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl205
b:41.5
occ:1.00
|
OH
|
A:TYR23
|
2.8
|
29.0
|
1.0
|
HH
|
A:TYR23
|
3.2
|
34.7
|
1.0
|
HE2
|
A:TYR23
|
3.3
|
35.6
|
1.0
|
HA3
|
A:GLY104
|
3.5
|
29.6
|
1.0
|
CZ
|
A:TYR23
|
3.6
|
28.9
|
1.0
|
O
|
A:HOH352
|
3.6
|
39.3
|
1.0
|
CE2
|
A:TYR23
|
3.7
|
29.8
|
1.0
|
HA2
|
A:GLY104
|
4.3
|
29.6
|
1.0
|
CA
|
A:GLY104
|
4.3
|
24.8
|
1.0
|
O
|
A:ARG21
|
4.6
|
34.2
|
1.0
|
H
|
A:MET105
|
4.7
|
32.1
|
1.0
|
CE1
|
A:TYR23
|
4.7
|
31.8
|
1.0
|
O
|
A:HOH407
|
4.7
|
47.9
|
1.0
|
CD2
|
A:TYR23
|
4.9
|
30.2
|
1.0
|
HE1
|
A:TYR23
|
5.0
|
38.0
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 8pob
Go back to
Chlorine Binding Sites List in 8pob
Chlorine binding site 3 out
of 6 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
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 Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl206
b:39.2
occ:1.00
|
H
|
A:GLY26
|
2.4
|
33.0
|
1.0
|
HG
|
A:SER24
|
2.6
|
38.4
|
1.0
|
HA
|
A:GLN121
|
2.7
|
46.9
|
1.0
|
HB2
|
A:SER24
|
2.9
|
39.7
|
1.0
|
HA3
|
A:GLY26
|
2.9
|
31.7
|
1.0
|
OG
|
A:SER24
|
2.9
|
32.1
|
1.0
|
N
|
A:GLY26
|
3.1
|
27.7
|
1.0
|
HD13
|
A:ILE124
|
3.3
|
54.6
|
1.0
|
HD11
|
A:ILE124
|
3.4
|
54.6
|
1.0
|
CB
|
A:SER24
|
3.4
|
33.2
|
1.0
|
HG22
|
A:VAL120
|
3.5
|
34.8
|
1.0
|
CA
|
A:GLY26
|
3.5
|
26.5
|
1.0
|
CA
|
A:GLN121
|
3.6
|
39.2
|
1.0
|
HB2
|
A:GLN121
|
3.7
|
50.5
|
1.0
|
HG2
|
A:GLN121
|
3.7
|
76.0
|
1.0
|
CD1
|
A:ILE124
|
3.8
|
45.7
|
1.0
|
HG12
|
A:ILE124
|
3.8
|
53.4
|
1.0
|
CB
|
A:GLN121
|
4.0
|
42.2
|
1.0
|
N
|
A:GLN121
|
4.0
|
37.2
|
1.0
|
HB3
|
A:SER24
|
4.0
|
39.7
|
1.0
|
H
|
A:LEU25
|
4.0
|
29.7
|
1.0
|
N
|
A:LEU25
|
4.1
|
24.9
|
1.0
|
H
|
A:ASN27
|
4.1
|
32.7
|
1.0
|
HG21
|
A:VAL120
|
4.2
|
34.8
|
1.0
|
HA2
|
A:GLY26
|
4.2
|
31.7
|
1.0
|
O
|
A:VAL120
|
4.2
|
30.3
|
1.0
|
C
|
A:SER24
|
4.2
|
31.4
|
1.0
|
CG2
|
A:VAL120
|
4.3
|
29.2
|
1.0
|
CG
|
A:GLN121
|
4.3
|
63.5
|
1.0
|
C
|
A:VAL120
|
4.3
|
32.1
|
1.0
|
C
|
A:LEU25
|
4.3
|
29.4
|
1.0
|
CG1
|
A:ILE124
|
4.3
|
44.6
|
1.0
|
HB3
|
A:LEU25
|
4.4
|
31.5
|
1.0
|
H
|
A:GLN121
|
4.4
|
44.5
|
1.0
|
CA
|
A:SER24
|
4.5
|
32.8
|
1.0
|
C
|
A:GLY26
|
4.5
|
24.8
|
1.0
|
N
|
A:ASN27
|
4.6
|
27.4
|
1.0
|
HD12
|
A:ILE124
|
4.6
|
54.6
|
1.0
|
HG3
|
A:GLN121
|
4.6
|
76.0
|
1.0
|
O
|
A:SER24
|
4.7
|
29.9
|
1.0
|
HG22
|
A:ILE124
|
4.7
|
43.4
|
1.0
|
CA
|
A:LEU25
|
4.7
|
24.7
|
1.0
|
C
|
A:GLN121
|
4.7
|
33.6
|
1.0
|
HB
|
A:VAL120
|
4.8
|
39.0
|
1.0
|
HD22
|
A:ASN27
|
4.9
|
37.7
|
1.0
|
HG13
|
A:ILE124
|
4.9
|
53.4
|
1.0
|
O
|
A:GLN121
|
4.9
|
37.6
|
1.0
|
HB3
|
A:GLN121
|
5.0
|
50.5
|
1.0
|
HG23
|
A:VAL120
|
5.0
|
34.8
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 8pob
Go back to
Chlorine Binding Sites List in 8pob
Chlorine binding site 4 out
of 6 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
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 Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl207
b:36.5
occ:0.70
|
H
|
A:ILE88
|
2.5
|
32.8
|
1.0
|
HG12
|
A:ILE88
|
2.8
|
35.8
|
1.0
|
HH22
|
A:ARG14
|
2.9
|
61.6
|
0.6
|
HA
|
A:ASP87
|
2.9
|
44.4
|
1.0
|
HE1
|
A:HIS15
|
3.1
|
52.3
|
1.0
|
N
|
A:ILE88
|
3.3
|
27.4
|
1.0
|
HH21
|
A:ARG14
|
3.4
|
61.1
|
0.4
|
O
|
A:HOH356
|
3.4
|
48.4
|
1.0
|
HZ
|
A:PHE3
|
3.4
|
39.1
|
1.0
|
HG22
|
A:ILE88
|
3.5
|
40.6
|
1.0
|
HH22
|
A:ARG14
|
3.5
|
61.1
|
0.4
|
HB1
|
A:ALA11
|
3.5
|
42.7
|
1.0
|
OD1
|
A:ASP87
|
3.5
|
76.2
|
1.0
|
NH2
|
A:ARG14
|
3.6
|
51.4
|
0.6
|
CG1
|
A:ILE88
|
3.7
|
29.9
|
1.0
|
NH2
|
A:ARG14
|
3.8
|
51.1
|
0.4
|
CA
|
A:ASP87
|
3.8
|
37.2
|
1.0
|
HH21
|
A:ARG14
|
3.9
|
61.6
|
0.6
|
CE1
|
A:HIS15
|
3.9
|
43.7
|
1.0
|
C
|
A:ASP87
|
4.1
|
32.5
|
1.0
|
O
|
A:SER86
|
4.2
|
37.8
|
1.0
|
HH12
|
A:ARG14
|
4.2
|
68.3
|
0.6
|
CG
|
A:ASP87
|
4.2
|
48.0
|
1.0
|
HG13
|
A:ILE88
|
4.2
|
35.8
|
1.0
|
CG2
|
A:ILE88
|
4.3
|
34.0
|
1.0
|
HB2
|
A:ALA11
|
4.3
|
42.7
|
1.0
|
CB
|
A:ILE88
|
4.3
|
31.5
|
1.0
|
CZ
|
A:PHE3
|
4.3
|
32.7
|
1.0
|
HD13
|
A:ILE88
|
4.3
|
39.1
|
1.0
|
CB
|
A:ALA11
|
4.3
|
35.7
|
1.0
|
CA
|
A:ILE88
|
4.4
|
31.2
|
1.0
|
CD1
|
A:ILE88
|
4.5
|
32.8
|
1.0
|
CB
|
A:ASP87
|
4.5
|
32.5
|
1.0
|
HD11
|
A:ILE88
|
4.5
|
39.1
|
1.0
|
HE2
|
A:PHE3
|
4.5
|
34.7
|
1.0
|
H
|
A:THR89
|
4.6
|
32.8
|
1.0
|
CZ
|
A:ARG14
|
4.6
|
59.7
|
0.6
|
HB2
|
A:ASP87
|
4.6
|
38.8
|
1.0
|
NH1
|
A:ARG14
|
4.7
|
57.0
|
0.6
|
ND1
|
A:HIS15
|
4.7
|
45.9
|
1.0
|
HZ3
|
A:LYS1
|
4.8
|
64.3
|
1.0
|
HG23
|
A:ILE88
|
4.8
|
40.6
|
1.0
|
N
|
A:ASP87
|
4.8
|
36.0
|
1.0
|
HB3
|
A:ALA11
|
4.9
|
42.7
|
1.0
|
NE2
|
A:HIS15
|
4.9
|
50.1
|
1.0
|
CE2
|
A:PHE3
|
4.9
|
29.0
|
1.0
|
HG21
|
A:ILE88
|
4.9
|
40.6
|
1.0
|
C
|
A:SER86
|
4.9
|
37.7
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 8pob
Go back to
Chlorine Binding Sites List in 8pob
Chlorine binding site 5 out
of 6 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
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 Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl208
b:50.5
occ:0.50
|
H
|
A:GLY71
|
2.0
|
40.0
|
1.0
|
N
|
A:GLY71
|
2.9
|
33.4
|
1.0
|
O
|
A:HOH389
|
2.9
|
35.9
|
1.0
|
HA
|
A:PRO70
|
3.1
|
44.1
|
1.0
|
HA2
|
A:GLY71
|
3.4
|
38.5
|
1.0
|
O
|
A:HOH397
|
3.5
|
40.6
|
1.0
|
CA
|
A:GLY71
|
3.7
|
32.2
|
1.0
|
C
|
A:PRO70
|
3.8
|
32.4
|
1.0
|
H
|
A:SER72
|
3.8
|
41.8
|
1.0
|
CA
|
A:PRO70
|
3.8
|
36.9
|
1.0
|
O
|
A:HOH409
|
4.2
|
36.0
|
1.0
|
N
|
A:SER72
|
4.3
|
35.0
|
1.0
|
C
|
A:GLY71
|
4.4
|
39.2
|
1.0
|
HB3
|
A:PRO70
|
4.4
|
51.1
|
1.0
|
HA3
|
A:GLY71
|
4.5
|
38.5
|
1.0
|
O
|
A:THR69
|
4.5
|
30.5
|
1.0
|
CB
|
A:PRO70
|
4.7
|
42.8
|
1.0
|
O
|
A:SER72
|
4.9
|
35.9
|
1.0
|
N
|
A:PRO70
|
4.9
|
34.2
|
1.0
|
O
|
A:PRO70
|
4.9
|
42.4
|
1.0
|
CL
|
A:CL204
|
5.0
|
34.6
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 8pob
Go back to
Chlorine Binding Sites List in 8pob
Chlorine binding site 6 out
of 6 in the Crystal Structure of Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3
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 Hen Egg White Lysozyme Co-Crystallized with 10 Mm TBXO4-SO3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl209
b:31.8
occ:0.50
|
H
|
A:ASN59
|
2.4
|
29.7
|
1.0
|
HA
|
A:ILE58
|
2.7
|
27.8
|
1.0
|
HD13
|
A:ILE98
|
3.0
|
30.1
|
1.0
|
N
|
A:ASN59
|
3.0
|
24.9
|
1.0
|
HB2
|
A:ASN59
|
3.0
|
39.2
|
1.0
|
HD1
|
A:TRP63
|
3.1
|
29.2
|
1.0
|
HB3
|
A:ASN59
|
3.1
|
39.2
|
1.0
|
CB
|
A:ASN59
|
3.4
|
32.8
|
1.0
|
CD1
|
A:TRP63
|
3.6
|
24.5
|
1.0
|
CA
|
A:ILE58
|
3.6
|
23.3
|
1.0
|
HG23
|
A:ILE58
|
3.6
|
34.8
|
1.0
|
HE1
|
A:TRP63
|
3.6
|
31.8
|
1.0
|
C
|
A:ILE58
|
3.8
|
25.3
|
1.0
|
CA
|
A:ASN59
|
3.8
|
23.6
|
1.0
|
O
|
A:GLN57
|
3.8
|
24.8
|
1.0
|
NE1
|
A:TRP63
|
3.9
|
26.7
|
1.0
|
CD1
|
A:ILE98
|
3.9
|
25.2
|
1.0
|
HD12
|
A:ILE98
|
4.1
|
30.1
|
1.0
|
HG21
|
A:ILE98
|
4.1
|
30.6
|
1.0
|
HG12
|
A:ILE58
|
4.2
|
37.0
|
1.0
|
O
|
A:HOH361
|
4.2
|
42.1
|
1.0
|
HD11
|
A:ILE98
|
4.4
|
30.1
|
1.0
|
CG2
|
A:ILE58
|
4.5
|
29.1
|
1.0
|
CB
|
A:ILE58
|
4.5
|
29.7
|
1.0
|
HA
|
A:ASN59
|
4.5
|
28.1
|
1.0
|
N
|
A:ILE58
|
4.5
|
24.9
|
1.0
|
C
|
A:GLN57
|
4.6
|
25.1
|
1.0
|
CG
|
A:TRP63
|
4.6
|
24.7
|
1.0
|
HG12
|
A:ILE98
|
4.6
|
30.8
|
1.0
|
O
|
A:ASN59
|
4.7
|
33.4
|
1.0
|
HD22
|
A:ASN59
|
4.8
|
65.3
|
1.0
|
HG23
|
A:ILE98
|
4.8
|
30.6
|
1.0
|
HE1
|
A:TRP108
|
4.8
|
31.5
|
1.0
|
C
|
A:ASN59
|
4.8
|
27.2
|
1.0
|
CG1
|
A:ILE58
|
4.8
|
31.0
|
1.0
|
CG
|
A:ASN59
|
4.9
|
36.2
|
1.0
|
CG2
|
A:ILE98
|
4.9
|
25.6
|
1.0
|
CG1
|
A:ILE98
|
4.9
|
25.8
|
1.0
|
HG22
|
A:ILE58
|
4.9
|
34.8
|
1.0
|
HB1
|
A:ALA107
|
4.9
|
45.5
|
1.0
|
HB2
|
A:TRP63
|
4.9
|
30.4
|
1.0
|
O
|
A:ILE58
|
4.9
|
26.3
|
1.0
|
NE1
|
A:TRP108
|
5.0
|
26.4
|
1.0
|
CE2
|
A:TRP63
|
5.0
|
27.9
|
1.0
|
|
Reference:
A.Roux,
Z.Alsalman,
T.Jiang,
J.C.Mulatier,
D.Pitrat,
E.Dumont,
F.Riobe,
N.Gillet,
E.Girard,
O.Maury.
Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network. Chemistry 00900 2024.
ISSN: ISSN 0947-6539
PubMed: 38738452
DOI: 10.1002/CHEM.202400900
Page generated: Tue Jul 30 11:38:00 2024
|