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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:

Tungsten (W) 33 atoms
Chlorine (Cl) 3 atoms

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)


Mono view


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)


Mono view


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)


Mono view


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

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