Atomistry » Zinc » PDB 6l6e-6lj4 » 6liz
Atomistry »
  Zinc »
    PDB 6l6e-6lj4 »
      6liz »

Zinc in PDB 6liz: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120, PDB code: 6liz was solved by H.Zhang, G.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.741, 59.953, 42.264, 90.00, 98.51, 90.00
R / Rfree (%) 17.1 / 18.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120 (pdb code 6liz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120, PDB code: 6liz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6liz

Go back to Zinc Binding Sites List in 6liz
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.0
occ:1.00
ND1 A:HIS122 2.0 17.8 1.0
NE2 A:HIS120 2.0 17.8 1.0
NE2 A:HIS189 2.0 18.8 1.0
S1 A:EEO303 2.3 18.3 1.0
CE1 A:HIS122 2.9 19.1 1.0
CD2 A:HIS120 3.0 16.0 1.0
CE1 A:HIS189 3.0 20.1 1.0
CE1 A:HIS120 3.0 17.4 1.0
CG A:HIS122 3.0 17.4 1.0
CD2 A:HIS189 3.0 19.5 1.0
C2 A:EEO303 3.3 19.6 1.0
CB A:HIS122 3.4 15.8 1.0
ZN A:ZN302 3.7 16.7 1.0
NE2 A:HIS122 4.1 20.6 1.0
CB A:CYS208 4.1 20.8 1.0
SG A:CYS208 4.1 17.8 1.0
ND1 A:HIS189 4.1 21.5 1.0
ND1 A:HIS120 4.1 17.0 1.0
CD2 A:HIS122 4.1 18.8 1.0
CG A:HIS120 4.1 15.8 1.0
CG A:HIS189 4.2 20.1 1.0
OD1 A:ASP124 4.2 17.2 1.0
CG2 A:THR190 4.4 21.0 1.0
C10 A:EEO303 4.7 20.8 1.0
CA A:HIS122 4.9 14.9 1.0
OD2 A:ASP124 4.9 18.1 1.0
CG A:ASP124 5.0 16.2 1.0

Zinc binding site 2 out of 2 in 6liz

Go back to Zinc Binding Sites List in 6liz
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02120 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:16.7
occ:1.00
OD2 A:ASP124 1.9 18.1 1.0
NE2 A:HIS250 2.1 19.6 1.0
SG A:CYS208 2.3 17.8 1.0
S1 A:EEO303 2.3 18.3 1.0
CG A:ASP124 2.9 16.2 1.0
CE1 A:HIS250 3.0 20.2 1.0
CD2 A:HIS250 3.1 18.8 1.0
OD1 A:ASP124 3.2 17.2 1.0
C2 A:EEO303 3.3 19.6 1.0
CB A:CYS208 3.4 20.8 1.0
ZN A:ZN301 3.7 17.0 1.0
C10 A:EEO303 3.9 20.8 1.0
ND1 A:HIS250 4.1 20.3 1.0
CG A:HIS250 4.2 20.1 1.0
CB A:ASP124 4.2 15.2 1.0
C5 A:EEO303 4.3 37.0 1.0
CB A:SER249 4.3 19.0 1.0
CE1 A:HIS120 4.5 17.4 1.0
NE2 A:HIS120 4.5 17.8 1.0
NE2 A:HIS189 4.6 18.8 1.0
OG A:SER249 4.6 18.2 1.0
CA A:CYS208 4.6 19.6 1.0
CE1 A:HIS189 4.8 20.1 1.0
C9 A:EEO303 4.8 33.0 1.0
CE A:LYS125 4.8 16.0 1.0
N1 A:EEO303 5.0 34.5 1.0
CD A:LYS125 5.0 16.3 1.0

Reference:

G.Ma, S.Wang, K.Wu, W.Zhang, A.Ahmad, Q.Hao, X.Lei, H.Zhang. Structure-Guided Optimization of D-Captopril For Discovery of Potent Ndm-1 Inhibitors Bioorg.Med.Chem. V. 29 2020.
ISSN: ESSN 1464-3391
DOI: 10.1016/J.BMC.2020.115902
Page generated: Tue Oct 29 02:36:21 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy