Zinc in PDB 6lj5: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145, PDB code: 6lj5 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) 24.39 / 1.26
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.785, 60.015, 42.321, 90.00, 98.48, 90.00
R / Rfree (%) 13.5 / 16.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145 (pdb code 6lj5). 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 WSS04145, PDB code: 6lj5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6lj5

Go back to Zinc Binding Sites List in 6lj5
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145


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 WSS04145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:14.4
occ:1.00
NE2 A:HIS189 2.0 15.0 1.0
ND1 A:HIS122 2.0 12.5 1.0
NE2 A:HIS120 2.1 12.7 1.0
S1 A:EF0402 2.3 17.1 1.0
CE1 A:HIS189 2.9 16.6 1.0
CE1 A:HIS122 3.0 14.1 1.0
CE1 A:HIS120 3.0 13.0 1.0
CD2 A:HIS189 3.0 14.6 1.0
CD2 A:HIS120 3.0 12.6 1.0
CG A:HIS122 3.1 12.5 1.0
C8 A:EF0402 3.2 18.2 1.0
CB A:HIS122 3.4 12.3 1.0
ZN A:ZN404 3.7 15.4 1.0
SG A:CYS208 4.0 14.8 0.9
CB A:CYS208 4.1 16.2 1.0
ND1 A:HIS189 4.1 17.7 1.0
ND1 A:HIS120 4.1 14.1 1.0
OD1 A:ASP124 4.1 13.0 1.0
NE2 A:HIS122 4.1 16.0 1.0
CG A:HIS189 4.1 16.3 1.0
CD2 A:HIS122 4.2 14.7 1.0
CG A:HIS120 4.2 12.5 1.0
CG2 A:THR190 4.4 17.8 1.0
C7 A:EF0402 4.7 24.4 1.0
OD2 A:ASP124 4.8 14.9 1.0
CA A:HIS122 4.9 11.4 1.0
CG A:ASP124 4.9 12.5 1.0

Zinc binding site 2 out of 2 in 6lj5

Go back to Zinc Binding Sites List in 6lj5
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04145


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 WSS04145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:15.4
occ:1.00
OD2 A:ASP124 1.9 14.9 1.0
NE2 A:HIS250 2.1 14.4 1.0
SG A:CYS208 2.3 14.8 0.9
S1 A:EF0402 2.3 17.1 1.0
CG A:ASP124 3.0 12.5 1.0
CE1 A:HIS250 3.0 15.3 1.0
CD2 A:HIS250 3.1 15.0 1.0
OD1 A:ASP124 3.2 13.0 1.0
C8 A:EF0402 3.4 18.2 1.0
CB A:CYS208 3.4 16.2 1.0
ZN A:ZN403 3.7 14.4 1.0
C7 A:EF0402 3.9 24.4 1.0
ND1 A:HIS250 4.1 15.6 1.0
CG A:HIS250 4.2 15.7 1.0
CB A:ASP124 4.3 11.5 1.0
CB A:SER249 4.3 14.0 1.0
C1 A:EF0402 4.5 37.4 1.0
NE2 A:HIS189 4.5 15.0 1.0
CE1 A:HIS120 4.5 13.0 1.0
NE2 A:HIS120 4.6 12.7 1.0
C2 A:EF0402 4.6 40.2 1.0
OG A:SER249 4.6 13.4 1.0
CA A:CYS208 4.6 16.3 1.0
C6 A:EF0402 4.7 31.0 1.0
O A:HOH537 4.7 48.8 1.0
CE1 A:HIS189 4.8 16.6 1.0
CE A:LYS125 4.9 14.6 1.0
N1 A:EF0402 4.9 56.1 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: Wed Dec 16 12:15:35 2020

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