Zirconium 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:
Zirconium Binding Sites:
The binding sites of Zirconium 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 Zirconium atom.
In total 3 binding sites of Zirconium 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 Zirconium binding site number:
1;
2;
3;
Zirconium binding site 1 out
of 3 in 6gnl
Go back to
Zirconium Binding Sites List in 6gnl
Zirconium binding site 1 out
of 3 in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
![](/pictures/ZR/pdb/gn/6gnl-ZR-sphere_01.jpg) Mono view
![](/pictures/ZR/pdb/gn/6gnl-ZR-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zirconium with other atoms in the Zr 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:Zr201
b:23.0
occ:0.29
|
ZR1
|
A:ZKG201
|
0.0
|
23.0
|
0.3
|
O77
|
A:ZKG201
|
2.2
|
23.0
|
0.3
|
O76
|
A:ZKG201
|
2.2
|
23.0
|
0.3
|
O75
|
A:ZKG201
|
2.2
|
23.0
|
0.3
|
O78
|
A:ZKG201
|
2.2
|
23.0
|
0.3
|
O61
|
A:ZKG201
|
3.1
|
23.0
|
0.3
|
W18
|
A:ZKG201
|
3.7
|
23.0
|
0.3
|
O
|
A:HOH301
|
3.7
|
34.9
|
0.7
|
W17
|
A:ZKG201
|
3.7
|
23.0
|
0.3
|
W13
|
A:ZKG201
|
3.8
|
23.0
|
0.3
|
W12
|
A:ZKG201
|
3.9
|
23.0
|
0.3
|
O55
|
A:ZKG201
|
4.0
|
23.0
|
0.3
|
O41
|
A:ZKG201
|
4.0
|
23.0
|
0.3
|
P2
|
A:ZKG201
|
4.0
|
23.0
|
0.3
|
O57
|
A:ZKG201
|
4.2
|
23.0
|
0.3
|
O53
|
A:ZKG201
|
4.2
|
23.0
|
0.3
|
O59
|
A:ZKG201
|
4.3
|
23.0
|
0.3
|
O60
|
A:ZKG201
|
4.3
|
23.0
|
0.3
|
O46
|
A:ZKG201
|
4.6
|
23.0
|
0.3
|
O42
|
A:ZKG201
|
4.6
|
23.0
|
0.3
|
O45
|
A:ZKG201
|
4.7
|
23.0
|
0.3
|
O40
|
A:ZKG201
|
4.7
|
23.0
|
0.3
|
O54
|
A:ZKG201
|
4.9
|
23.0
|
0.3
|
O56
|
A:ZKG201
|
4.9
|
23.0
|
0.3
|
|
Zirconium binding site 2 out
of 3 in 6gnl
Go back to
Zirconium Binding Sites List in 6gnl
Zirconium binding site 2 out
of 3 in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
![](/pictures/ZR/pdb/gn/6gnl-ZR-sphere_02.jpg) Mono view
![](/pictures/ZR/pdb/gn/6gnl-ZR-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zirconium with other atoms in the Zr 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:Zr202
b:27.7
occ:0.15
|
ZR1
|
A:ZKG202
|
0.0
|
27.7
|
0.1
|
ZR1
|
A:ZKG202
|
0.8
|
27.7
|
0.2
|
O75
|
A:ZKG202
|
1.6
|
27.7
|
0.2
|
OD1
|
A:ASN65
|
2.0
|
25.9
|
1.0
|
O78
|
A:ZKG202
|
2.1
|
27.7
|
0.2
|
O76
|
A:ZKG202
|
2.2
|
27.7
|
0.1
|
O77
|
A:ZKG202
|
2.2
|
27.7
|
0.1
|
O75
|
A:ZKG202
|
2.2
|
27.7
|
0.1
|
O78
|
A:ZKG202
|
2.2
|
27.7
|
0.1
|
O76
|
A:ZKG202
|
2.4
|
27.7
|
0.2
|
O77
|
A:ZKG202
|
2.8
|
27.7
|
0.2
|
O
|
A:HOH302
|
2.9
|
16.0
|
0.7
|
O61
|
A:ZKG202
|
3.1
|
27.7
|
0.2
|
CG
|
A:ASN65
|
3.2
|
20.6
|
1.0
|
O61
|
A:ZKG202
|
3.2
|
27.7
|
0.1
|
W12
|
A:ZKG202
|
3.2
|
27.7
|
0.2
|
HB3
|
A:ASN65
|
3.5
|
19.8
|
1.0
|
W18
|
A:ZKG202
|
3.6
|
27.7
|
0.2
|
O41
|
A:ZKG202
|
3.7
|
27.7
|
0.2
|
W18
|
A:ZKG202
|
3.8
|
27.7
|
0.1
|
HB3
|
A:PRO79
|
3.8
|
20.1
|
1.0
|
O57
|
A:ZKG202
|
3.8
|
27.7
|
0.2
|
W17
|
A:ZKG202
|
3.8
|
27.7
|
0.1
|
W13
|
A:ZKG202
|
3.8
|
27.7
|
0.1
|
W12
|
A:ZKG202
|
3.8
|
27.7
|
0.1
|
CB
|
A:ASN65
|
3.9
|
16.5
|
1.0
|
W13
|
A:ZKG202
|
3.9
|
27.7
|
0.2
|
O40
|
A:ZKG202
|
4.0
|
27.7
|
0.2
|
P2
|
A:ZKG202
|
4.0
|
27.7
|
0.2
|
O46
|
A:ZKG202
|
4.0
|
27.7
|
0.2
|
O41
|
A:ZKG202
|
4.0
|
27.7
|
0.1
|
O59
|
A:ZKG202
|
4.0
|
27.7
|
0.2
|
O55
|
A:ZKG202
|
4.1
|
27.7
|
0.1
|
O
|
A:ASN65
|
4.1
|
13.2
|
1.0
|
HA
|
A:PRO79
|
4.2
|
18.4
|
1.0
|
W17
|
A:ZKG202
|
4.2
|
27.7
|
0.2
|
P2
|
A:ZKG202
|
4.2
|
27.7
|
0.1
|
ND2
|
A:ASN65
|
4.2
|
19.4
|
1.0
|
O55
|
A:ZKG202
|
4.2
|
27.7
|
0.2
|
HD21
|
A:ASN65
|
4.3
|
23.3
|
1.0
|
O53
|
A:ZKG202
|
4.3
|
27.7
|
0.1
|
O57
|
A:ZKG202
|
4.4
|
27.7
|
0.1
|
O60
|
A:ZKG202
|
4.4
|
27.7
|
0.2
|
O59
|
A:ZKG202
|
4.5
|
27.7
|
0.1
|
O60
|
A:ZKG202
|
4.5
|
27.7
|
0.1
|
C
|
A:ASN65
|
4.5
|
13.4
|
1.0
|
O42
|
A:ZKG202
|
4.6
|
27.7
|
0.1
|
HB2
|
A:ASN65
|
4.6
|
19.8
|
1.0
|
O40
|
A:ZKG202
|
4.7
|
27.7
|
0.1
|
CB
|
A:PRO79
|
4.7
|
16.8
|
1.0
|
O53
|
A:ZKG202
|
4.7
|
27.7
|
0.2
|
O45
|
A:ZKG202
|
4.7
|
27.7
|
0.1
|
O42
|
A:ZKG202
|
4.8
|
27.7
|
0.2
|
O46
|
A:ZKG202
|
4.8
|
27.7
|
0.1
|
O56
|
A:ZKG202
|
4.8
|
27.7
|
0.2
|
W19
|
A:ZKG202
|
4.8
|
27.7
|
0.2
|
CA
|
A:PRO79
|
4.9
|
15.3
|
1.0
|
CA
|
A:ASN65
|
4.9
|
14.3
|
1.0
|
H
|
A:GLY67
|
4.9
|
17.5
|
1.0
|
O56
|
A:ZKG202
|
4.9
|
27.7
|
0.1
|
HD22
|
A:ASN65
|
5.0
|
23.3
|
1.0
|
O54
|
A:ZKG202
|
5.0
|
27.7
|
0.1
|
|
Zirconium binding site 3 out
of 3 in 6gnl
Go back to
Zirconium Binding Sites List in 6gnl
Zirconium binding site 3 out
of 3 in the Zr(IV)-Substituted Keggin Directly Binding to the Side Chain of Hen Egg-White Lysozyme (Hewl)
![](/pictures/ZR/pdb/gn/6gnl-ZR-sphere_03.jpg) Mono view
![](/pictures/ZR/pdb/gn/6gnl-ZR-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zirconium with other atoms in the Zr 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:Zr202
b:27.7
occ:0.23
|
ZR1
|
A:ZKG202
|
0.0
|
27.7
|
0.2
|
ZR1
|
A:ZKG202
|
0.8
|
27.7
|
0.1
|
O78
|
A:ZKG202
|
1.5
|
27.7
|
0.1
|
OD1
|
A:ASN65
|
1.6
|
25.9
|
1.0
|
O77
|
A:ZKG202
|
2.2
|
27.7
|
0.2
|
O76
|
A:ZKG202
|
2.2
|
27.7
|
0.2
|
O75
|
A:ZKG202
|
2.2
|
27.7
|
0.2
|
O77
|
A:ZKG202
|
2.2
|
27.7
|
0.1
|
O78
|
A:ZKG202
|
2.2
|
27.7
|
0.2
|
O75
|
A:ZKG202
|
2.2
|
27.7
|
0.1
|
O
|
A:HOH302
|
2.7
|
16.0
|
0.7
|
CG
|
A:ASN65
|
2.7
|
20.6
|
1.0
|
O76
|
A:ZKG202
|
2.8
|
27.7
|
0.1
|
O61
|
A:ZKG202
|
3.0
|
27.7
|
0.1
|
O61
|
A:ZKG202
|
3.0
|
27.7
|
0.2
|
W18
|
A:ZKG202
|
3.1
|
27.7
|
0.1
|
HB3
|
A:ASN65
|
3.4
|
19.8
|
1.0
|
O55
|
A:ZKG202
|
3.6
|
27.7
|
0.1
|
CB
|
A:ASN65
|
3.6
|
16.5
|
1.0
|
W18
|
A:ZKG202
|
3.7
|
27.7
|
0.2
|
W17
|
A:ZKG202
|
3.7
|
27.7
|
0.1
|
ND2
|
A:ASN65
|
3.7
|
19.4
|
1.0
|
W17
|
A:ZKG202
|
3.7
|
27.7
|
0.2
|
HD21
|
A:ASN65
|
3.7
|
23.3
|
1.0
|
O57
|
A:ZKG202
|
3.8
|
27.7
|
0.1
|
W12
|
A:ZKG202
|
3.8
|
27.7
|
0.2
|
W13
|
A:ZKG202
|
3.8
|
27.7
|
0.2
|
O55
|
A:ZKG202
|
3.9
|
27.7
|
0.2
|
W12
|
A:ZKG202
|
3.9
|
27.7
|
0.1
|
O41
|
A:ZKG202
|
4.0
|
27.7
|
0.2
|
P2
|
A:ZKG202
|
4.0
|
27.7
|
0.2
|
O53
|
A:ZKG202
|
4.2
|
27.7
|
0.2
|
P2
|
A:ZKG202
|
4.2
|
27.7
|
0.1
|
O56
|
A:ZKG202
|
4.2
|
27.7
|
0.1
|
HB2
|
A:ASN65
|
4.2
|
19.8
|
1.0
|
O57
|
A:ZKG202
|
4.2
|
27.7
|
0.2
|
O
|
A:ASN65
|
4.3
|
13.2
|
1.0
|
O59
|
A:ZKG202
|
4.3
|
27.7
|
0.2
|
O60
|
A:ZKG202
|
4.3
|
27.7
|
0.2
|
O59
|
A:ZKG202
|
4.4
|
27.7
|
0.1
|
O41
|
A:ZKG202
|
4.4
|
27.7
|
0.1
|
W13
|
A:ZKG202
|
4.4
|
27.7
|
0.1
|
HD22
|
A:ASN65
|
4.5
|
23.3
|
1.0
|
O53
|
A:ZKG202
|
4.5
|
27.7
|
0.1
|
HB3
|
A:PRO79
|
4.5
|
20.1
|
1.0
|
O
|
A:HOH302
|
4.5
|
10.7
|
0.3
|
C
|
A:ASN65
|
4.5
|
13.4
|
1.0
|
O46
|
A:ZKG202
|
4.5
|
27.7
|
0.1
|
H
|
A:GLY67
|
4.6
|
17.5
|
1.0
|
O42
|
A:ZKG202
|
4.6
|
27.7
|
0.2
|
HA
|
A:PRO79
|
4.6
|
18.4
|
1.0
|
O40
|
A:ZKG202
|
4.6
|
27.7
|
0.2
|
O45
|
A:ZKG202
|
4.6
|
27.7
|
0.2
|
O46
|
A:ZKG202
|
4.7
|
27.7
|
0.2
|
O60
|
A:ZKG202
|
4.7
|
27.7
|
0.1
|
CA
|
A:ASN65
|
4.8
|
14.3
|
1.0
|
HA2
|
A:GLY67
|
4.8
|
19.4
|
1.0
|
O40
|
A:ZKG202
|
4.8
|
27.7
|
0.1
|
N
|
A:GLY67
|
4.8
|
14.6
|
1.0
|
O54
|
A:ZKG202
|
4.9
|
27.7
|
0.1
|
O54
|
A:ZKG202
|
4.9
|
27.7
|
0.2
|
O56
|
A:ZKG202
|
4.9
|
27.7
|
0.2
|
O67
|
A:ZKG202
|
5.0
|
27.7
|
0.1
|
|
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: Wed Dec 16 14:05:34 2020
|