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Zinc in PDB 3nzk: Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor

Enzymatic activity of Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor

All present enzymatic activity of Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor:
3.5.1.33;

Protein crystallography data

The structure of Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor, PDB code: 3nzk was solved by K.E.Cole, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.49 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.812, 47.614, 68.410, 74.53, 87.87, 68.98
R / Rfree (%) 16.7 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor (pdb code 3nzk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor, PDB code: 3nzk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3nzk

Go back to Zinc Binding Sites List in 3nzk
Zinc binding site 1 out of 2 in the Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:16.7
occ:1.00
O22 A:C90501 2.1 16.5 0.5
O22 A:C90501 2.1 16.6 0.5
OD1 A:ASP242 2.1 14.4 1.0
NE2 A:HIS79 2.1 14.3 1.0
NE2 A:HIS238 2.2 12.9 1.0
O24 A:C90501 2.2 16.3 0.5
O24 A:C90501 2.2 16.3 0.5
OD2 A:ASP242 2.6 16.8 1.0
CG A:ASP242 2.7 12.5 1.0
C22 A:C90501 2.8 21.2 0.5
C22 A:C90501 2.8 21.2 0.5
N23 A:C90501 2.9 20.8 0.5
N23 A:C90501 2.9 20.8 0.5
CD2 A:HIS79 3.0 11.6 1.0
CD2 A:HIS238 3.1 15.5 1.0
CE1 A:HIS238 3.2 12.5 1.0
CE1 A:HIS79 3.2 13.8 1.0
OG1 A:THR191 4.1 17.3 1.0
CG A:GLU78 4.1 18.3 1.0
CB A:ASP242 4.2 12.1 1.0
CG A:HIS79 4.2 10.2 1.0
C18 A:C90501 4.2 18.1 0.5
ND1 A:HIS238 4.2 12.8 1.0
C18 A:C90501 4.2 18.1 0.5
CG A:HIS238 4.2 11.6 1.0
ND1 A:HIS79 4.2 13.1 1.0
O20 A:C90501 4.3 29.3 0.5
CB A:THR191 4.3 16.5 1.0
O20 A:C90501 4.3 29.3 0.5
OE2 A:GLU78 4.4 19.8 1.0
CE1 A:HIS265 4.6 19.3 1.0
C19 A:C90501 4.7 23.9 0.5
C19 A:C90501 4.7 23.9 0.5
CD A:GLU78 4.8 16.1 1.0
CA A:THR191 4.8 14.4 1.0
CA A:ASP242 4.8 10.8 1.0
O A:HIS238 4.8 13.5 1.0
NE2 A:HIS265 4.9 19.3 1.0
N17 A:C90501 5.0 17.9 0.5

Zinc binding site 2 out of 2 in 3nzk

Go back to Zinc Binding Sites List in 3nzk
Zinc binding site 2 out of 2 in the Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Lpxc From Yersinia Enterocolitica Complexed with CHIR090 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:18.5
occ:1.00
OD1 B:ASP242 2.1 15.7 1.0
O22 B:C90501 2.1 18.9 0.5
O22 B:C90501 2.1 18.9 0.5
NE2 B:HIS79 2.1 14.7 1.0
NE2 B:HIS238 2.1 12.5 1.0
O24 B:C90501 2.3 19.6 0.5
O24 B:C90501 2.3 19.6 0.5
OD2 B:ASP242 2.7 17.8 1.0
CG B:ASP242 2.7 17.9 1.0
C22 B:C90501 2.8 20.7 0.5
C22 B:C90501 2.9 20.7 0.5
N23 B:C90501 2.9 21.0 0.5
N23 B:C90501 2.9 21.0 0.5
CD2 B:HIS79 3.1 15.1 1.0
CE1 B:HIS238 3.1 16.1 1.0
CD2 B:HIS238 3.1 13.9 1.0
CE1 B:HIS79 3.2 12.2 1.0
OG1 B:THR191 4.0 14.6 1.0
CG B:GLU78 4.1 20.4 1.0
ND1 B:HIS238 4.2 12.8 1.0
CB B:ASP242 4.2 9.9 1.0
CG B:HIS79 4.2 12.7 1.0
CG B:HIS238 4.2 12.6 1.0
ND1 B:HIS79 4.2 11.1 1.0
C18 B:C90501 4.3 16.6 0.5
O20 B:C90501 4.3 33.0 0.5
C18 B:C90501 4.3 16.6 0.5
CB B:THR191 4.3 14.6 1.0
O20 B:C90501 4.3 32.7 0.5
OE2 B:GLU78 4.3 26.6 1.0
CE1 B:HIS265 4.6 20.7 1.0
NE2 B:HIS265 4.8 23.7 1.0
CD B:GLU78 4.8 22.1 1.0
CA B:ASP242 4.8 15.9 1.0
CA B:THR191 4.9 11.8 1.0
C19 B:C90501 4.9 25.2 0.5
C19 B:C90501 4.9 25.2 0.5
O B:HIS238 4.9 12.0 1.0

Reference:

K.E.Cole, S.G.Gattis, H.D.Angell, C.A.Fierke, D.W.Christianson. Structure of the Metal-Dependent Deacetylase Lpxc From Yersinia Enterocolitica Complexed with the Potent Inhibitor Chir-090 . Biochemistry V. 50 258 2010.
ISSN: ISSN 0006-2960
PubMed: 21171638
DOI: 10.1021/BI101622A
Page generated: Wed Dec 16 04:39:31 2020

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