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:

Tungsten (W) 33 atoms
Zirconium (Zr) 3 atoms

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: Sat Dec 12 13:02:10 2020

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