Chlorine in PDB 6gnl: Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
Enzymatic activity of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
All present enzymatic activity of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl):
3.2.1.17;
Protein crystallography data
The structure of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl), PDB code: 6gnl
was solved by
L.Vandebroek,
L.Van Meervelt,
T.N.Parac-Vogt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.85 /
1.23
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.701,
77.701,
37.866,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.8 /
17.1
|
Other elements in 6gnl:
The structure of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl) also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
(pdb code 6gnl). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the
Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl), PDB code: 6gnl:
Jump to Chlorine binding site number:
1;
2;
3;
Chlorine binding site 1 out
of 3 in 6gnl
Go back to
Chlorine Binding Sites List in 6gnl
Chlorine binding site 1 out
of 3 in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl203
b:18.4
occ:1.00
|
H
|
A:GLY26
|
2.4
|
13.8
|
1.0
|
O
|
A:HOH400
|
2.5
|
30.3
|
1.0
|
HG
|
A:SER24
|
2.8
|
19.1
|
1.0
|
HA
|
A:GLN121
|
2.8
|
21.0
|
1.0
|
HA3
|
A:GLY26
|
2.9
|
13.6
|
1.0
|
HB2
|
A:SER24
|
2.9
|
17.6
|
1.0
|
OG
|
A:SER24
|
3.0
|
15.9
|
1.0
|
N
|
A:GLY26
|
3.2
|
11.5
|
1.0
|
HG23
|
A:VAL120
|
3.4
|
18.3
|
1.0
|
CB
|
A:SER24
|
3.5
|
14.6
|
1.0
|
HB2
|
A:GLN121
|
3.5
|
26.4
|
1.0
|
CA
|
A:GLY26
|
3.5
|
11.3
|
1.0
|
O
|
A:HOH439
|
3.5
|
36.9
|
1.0
|
HD11
|
A:ILE124
|
3.6
|
27.4
|
1.0
|
CA
|
A:GLN121
|
3.6
|
17.5
|
1.0
|
HG2
|
A:GLN121
|
3.6
|
31.2
|
1.0
|
HG12
|
A:ILE124
|
3.7
|
24.8
|
1.0
|
HD13
|
A:ILE124
|
3.8
|
27.4
|
1.0
|
CB
|
A:GLN121
|
3.9
|
22.0
|
1.0
|
N
|
A:GLN121
|
3.9
|
15.6
|
1.0
|
CD1
|
A:ILE124
|
4.1
|
22.9
|
1.0
|
HB3
|
A:SER24
|
4.1
|
17.6
|
1.0
|
H
|
A:LEU25
|
4.1
|
15.0
|
1.0
|
HA2
|
A:GLY26
|
4.1
|
13.6
|
1.0
|
H
|
A:ASN27
|
4.2
|
12.8
|
1.0
|
CG
|
A:GLN121
|
4.2
|
26.0
|
1.0
|
N
|
A:LEU25
|
4.2
|
12.5
|
1.0
|
H
|
A:GLN121
|
4.2
|
18.8
|
1.0
|
C
|
A:VAL120
|
4.3
|
14.0
|
1.0
|
HB3
|
A:LEU25
|
4.3
|
14.8
|
1.0
|
CG2
|
A:VAL120
|
4.3
|
15.3
|
1.0
|
O
|
A:VAL120
|
4.3
|
13.8
|
1.0
|
C
|
A:LEU25
|
4.4
|
11.9
|
1.0
|
C
|
A:SER24
|
4.4
|
12.2
|
1.0
|
CG1
|
A:ILE124
|
4.4
|
20.6
|
1.0
|
HG3
|
A:GLN121
|
4.4
|
31.2
|
1.0
|
C
|
A:GLY26
|
4.6
|
10.8
|
1.0
|
HG21
|
A:VAL120
|
4.6
|
18.3
|
1.0
|
CA
|
A:SER24
|
4.6
|
12.7
|
1.0
|
N
|
A:ASN27
|
4.7
|
10.7
|
1.0
|
CA
|
A:LEU25
|
4.8
|
12.1
|
1.0
|
C
|
A:GLN121
|
4.8
|
16.1
|
1.0
|
HB
|
A:VAL120
|
4.8
|
17.4
|
1.0
|
HB3
|
A:GLN121
|
4.8
|
26.4
|
1.0
|
O
|
A:SER24
|
4.9
|
12.7
|
1.0
|
HG22
|
A:VAL120
|
4.9
|
18.3
|
1.0
|
HG13
|
A:ILE124
|
4.9
|
24.8
|
1.0
|
HD12
|
A:ILE124
|
5.0
|
27.4
|
1.0
|
HG23
|
A:ILE124
|
5.0
|
21.9
|
1.0
|
|
Chlorine binding site 2 out
of 3 in 6gnl
Go back to
Chlorine Binding Sites List in 6gnl
Chlorine binding site 2 out
of 3 in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl204
b:20.4
occ:0.67
|
H
|
A:ILE88
|
2.5
|
18.4
|
1.0
|
HG12
|
A:ILE88
|
2.7
|
17.9
|
1.0
|
HA
|
A:ASP87
|
3.0
|
22.3
|
1.0
|
O
|
A:HOH305
|
3.1
|
30.8
|
1.0
|
HH22
|
A:ARG14
|
3.3
|
29.0
|
1.0
|
HE2
|
A:HIS15
|
3.3
|
25.4
|
1.0
|
HZ
|
A:PHE3
|
3.3
|
16.5
|
1.0
|
N
|
A:ILE88
|
3.3
|
15.3
|
1.0
|
HB1
|
A:ALA11
|
3.4
|
16.8
|
1.0
|
HG23
|
A:ILE88
|
3.5
|
18.4
|
1.0
|
CG1
|
A:ILE88
|
3.6
|
14.9
|
1.0
|
HH21
|
A:ARG14
|
3.8
|
29.0
|
1.0
|
NH2
|
A:ARG14
|
3.9
|
24.1
|
1.0
|
CA
|
A:ASP87
|
3.9
|
18.6
|
1.0
|
O
|
A:HOH357
|
3.9
|
31.7
|
1.0
|
HB2
|
A:ALA11
|
4.0
|
16.8
|
1.0
|
HG13
|
A:ILE88
|
4.0
|
17.9
|
1.0
|
NE2
|
A:HIS15
|
4.1
|
21.2
|
1.0
|
C
|
A:ASP87
|
4.1
|
16.7
|
1.0
|
CB
|
A:ALA11
|
4.1
|
14.0
|
1.0
|
OD1
|
A:ASP87
|
4.1
|
23.6
|
1.0
|
O
|
A:SER86
|
4.1
|
21.0
|
1.0
|
CZ
|
A:PHE3
|
4.2
|
13.8
|
1.0
|
CB
|
A:ILE88
|
4.3
|
13.7
|
1.0
|
HE2
|
A:PHE3
|
4.3
|
17.0
|
1.0
|
CG2
|
A:ILE88
|
4.3
|
15.4
|
1.0
|
HD2
|
A:HIS15
|
4.3
|
25.1
|
1.0
|
CA
|
A:ILE88
|
4.3
|
13.8
|
1.0
|
H
|
A:THR89
|
4.5
|
16.9
|
1.0
|
HD11
|
A:ILE88
|
4.6
|
18.8
|
1.0
|
CD1
|
A:ILE88
|
4.6
|
15.7
|
1.0
|
HD13
|
A:ILE88
|
4.6
|
18.8
|
1.0
|
CD2
|
A:HIS15
|
4.6
|
20.9
|
1.0
|
HB3
|
A:ALA11
|
4.6
|
16.8
|
1.0
|
HG21
|
A:ILE88
|
4.7
|
18.4
|
1.0
|
CG
|
A:ASP87
|
4.7
|
23.8
|
1.0
|
CE2
|
A:PHE3
|
4.7
|
14.1
|
1.0
|
HG1
|
A:THR89
|
4.8
|
22.1
|
1.0
|
CB
|
A:ASP87
|
4.8
|
20.8
|
1.0
|
N
|
A:ASP87
|
4.9
|
17.6
|
1.0
|
C
|
A:SER86
|
5.0
|
19.1
|
1.0
|
N
|
A:THR89
|
5.0
|
14.1
|
1.0
|
|
Chlorine binding site 3 out
of 3 in 6gnl
Go back to
Chlorine Binding Sites List in 6gnl
Chlorine binding site 3 out
of 3 in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl205
b:15.1
occ:1.00
|
HH
|
A:TYR23
|
2.4
|
14.1
|
1.0
|
OH
|
A:TYR23
|
3.0
|
11.7
|
1.0
|
HE2
|
A:TYR23
|
3.2
|
13.6
|
1.0
|
O
|
A:HOH356
|
3.3
|
15.8
|
1.0
|
HA3
|
A:GLY104
|
3.3
|
13.1
|
1.0
|
CZ
|
A:TYR23
|
3.7
|
10.7
|
1.0
|
CE2
|
A:TYR23
|
3.7
|
11.3
|
1.0
|
HA2
|
A:GLY104
|
4.0
|
13.1
|
1.0
|
CA
|
A:GLY104
|
4.1
|
10.9
|
1.0
|
O
|
A:ARG21
|
4.6
|
14.7
|
1.0
|
N
|
A:GLY104
|
4.6
|
11.5
|
1.0
|
H
|
A:MET105
|
4.8
|
11.8
|
1.0
|
H
|
A:GLY104
|
4.8
|
13.8
|
1.0
|
HB3
|
A:ARG21
|
4.9
|
22.8
|
1.0
|
CE1
|
A:TYR23
|
4.9
|
11.1
|
1.0
|
CD2
|
A:TYR23
|
4.9
|
11.1
|
1.0
|
|
Reference:
L.Vandebroek,
L.Van Meervelt,
T.N.Parac-Vogt.
Direct Observation of the Zrivinteraction with the Carboxamide Bond in A Noncovalent Complex Between Hen Egg White Lysozyme and A Zr-Substituted Keggin Polyoxometalate. Acta Crystallogr C Struct V. 74 1348 2018CHEM.
ISSN: ESSN 2053-2296
PubMed: 30398187
DOI: 10.1107/S2053229618010690
Page generated: Sun Jul 28 00:02:25 2024
|