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Zinc in PDB 6lj1: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer

Enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer, PDB code: 6lj1 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 / 1.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.795, 59.210, 42.041, 90.00, 93.41, 90.00
R / Rfree (%) 14 / 16

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer (pdb code 6lj1). 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 WSS02127 Monomer, PDB code: 6lj1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6lj1

Go back to Zinc Binding Sites List in 6lj1
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer


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 WSS02127 Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:15.7
occ:1.00
OD2 A:ASP124 2.0 17.8 1.0
NE2 A:HIS250 2.1 16.6 1.0
SG A:CYS208 2.3 15.5 0.8
S1 A:EEX303 2.3 16.1 1.0
CG A:ASP124 3.0 16.3 1.0
CE1 A:HIS250 3.0 17.3 1.0
CD2 A:HIS250 3.1 16.5 1.0
OD1 A:ASP124 3.3 17.9 1.0
C13 A:EEX303 3.3 18.2 1.0
CB A:CYS208 3.4 16.2 1.0
ZN A:ZN302 3.7 16.0 1.0
C12 A:EEX303 3.8 20.5 1.0
ND1 A:HIS250 4.1 17.2 1.0
CG A:HIS250 4.2 17.1 1.0
CB A:SER249 4.2 16.8 1.0
CB A:ASP124 4.3 16.7 1.0
C8 A:EEX303 4.4 22.8 1.0
CE1 A:HIS120 4.5 17.3 1.0
NE2 A:HIS120 4.5 13.9 1.0
OG A:SER249 4.6 16.6 1.0
C11 A:EEX303 4.6 21.9 1.0
NE2 A:HIS189 4.6 15.5 1.0
CA A:CYS208 4.6 16.6 1.0
CE A:LYS125 4.8 16.6 1.0
N1 A:EEX303 4.8 23.2 1.0
O A:HOH401 4.9 40.7 1.0
CD A:LYS125 4.9 18.5 1.0
CE1 A:HIS189 5.0 16.8 1.0

Zinc binding site 2 out of 2 in 6lj1

Go back to Zinc Binding Sites List in 6lj1
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS02127 Monomer


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 WSS02127 Monomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:16.0
occ:1.00
ND1 A:HIS122 2.1 16.3 1.0
NE2 A:HIS189 2.1 15.5 1.0
NE2 A:HIS120 2.1 13.9 1.0
S1 A:EEX303 2.3 16.1 1.0
CE1 A:HIS122 3.0 18.3 1.0
CE1 A:HIS120 3.0 17.3 1.0
CD2 A:HIS189 3.0 15.6 1.0
CE1 A:HIS189 3.0 16.8 1.0
CD2 A:HIS120 3.0 16.1 1.0
CG A:HIS122 3.1 15.3 1.0
C13 A:EEX303 3.2 18.2 1.0
CB A:HIS122 3.4 15.6 1.0
ZN A:ZN301 3.7 15.7 1.0
SG A:CYS208 4.0 15.5 0.8
CB A:CYS208 4.0 16.2 1.0
NE2 A:HIS122 4.1 19.1 1.0
ND1 A:HIS120 4.1 15.7 1.0
ND1 A:HIS189 4.2 17.6 1.0
CG A:HIS120 4.2 15.2 1.0
CD2 A:HIS122 4.2 18.7 1.0
CG A:HIS189 4.2 16.8 1.0
OD1 A:ASP124 4.2 17.9 1.0
O A:HOH496 4.4 45.5 1.0
CG2 A:THR190 4.5 17.9 1.0
C12 A:EEX303 4.7 20.5 1.0
OD2 A:ASP124 4.8 17.8 1.0
CA A:HIS122 4.9 15.9 1.0
CG A:ASP124 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: Wed Dec 16 12:15:23 2020

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