Atomistry » Zinc » PDB 5zg3-5znf » 5zgw
Atomistry »
  Zinc »
    PDB 5zg3-5znf »
      5zgw »

Zinc in PDB 5zgw: Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5)

Enzymatic activity of Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5)

All present enzymatic activity of Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5), PDB code: 5zgw was solved by H.Zhang, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.32 / 0.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.456, 59.905, 41.740, 90.00, 98.14, 90.00
R / Rfree (%) 12.9 / 14

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5) (pdb code 5zgw). 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 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5), PDB code: 5zgw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5zgw

Go back to Zinc Binding Sites List in 5zgw
Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5)


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 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:7.2
occ:1.00
 O A:OH303 2.0 8.6 0.9
NE2 A:HIS189 2.1 7.3 1.0
NE2 A:HIS120 2.1 6.6 1.0
ND1 A:HIS122 2.1 7.5 1.0
CD2 A:HIS189 3.0 7.0 1.0
CE1 A:HIS120 3.0 6.7 1.0
CD2 A:HIS120 3.0 6.3 1.0
CE1 A:HIS122 3.0 8.2 1.0
CG A:HIS122 3.1 6.9 1.0
CE1 A:HIS189 3.1 8.5 1.0
CB A:HIS122 3.4 6.2 1.0
ZN A:ZN302 3.5 10.0 0.9
O A:HOH404 3.8 15.6 1.0
SG A:CYS208 3.9 7.8 1.0
OD1 A:ASP124 4.0 8.1 1.0
ND1 A:HIS120 4.1 6.3 1.0
CG A:HIS189 4.2 7.0 1.0
CB A:CYS208 4.2 7.0 1.0
NE2 A:HIS122 4.2 8.4 1.0
ND1 A:HIS189 4.2 8.1 1.0
CG A:HIS120 4.2 6.0 1.0
CD2 A:HIS122 4.2 7.8 1.0
CG2 A:THR190 4.4 7.8 1.0
OD2 A:ASP124 4.6 9.4 1.0
CG A:ASP124 4.7 6.4 1.0
CA A:HIS122 4.8 5.7 1.0

Zinc binding site 2 out of 2 in 5zgw

Go back to Zinc Binding Sites List in 5zgw
Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5)


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 at PH7.5 with 1 Molecule Per Asymmetric Unit (Crystallized at Succinate PH5.5 and Soaked at Succinate PH7.5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:10.0
occ:0.90
 OD2 A:ASP124 2.0 9.4 1.0
O A:OH303 2.0 8.6 0.9
NE2 A:HIS250 2.1 7.6 1.0
SG A:CYS208 2.3 7.8 1.0
O A:HOH404 2.4 15.6 1.0
CG A:ASP124 3.0 6.4 1.0
CE1 A:HIS250 3.0 7.6 1.0
CD2 A:HIS250 3.1 7.7 1.0
OD1 A:ASP124 3.3 8.1 1.0
CB A:CYS208 3.4 7.0 1.0
ZN A:ZN301 3.5 7.2 1.0
ND1 A:HIS250 4.2 8.1 1.0
CG A:HIS250 4.2 7.7 1.0
NE2 A:HIS189 4.2 7.3 1.0
CB A:SER249 4.3 6.6 1.0
CB A:ASP124 4.3 5.9 1.0
O A:HOH564 4.4 16.8 1.0
CE1 A:HIS189 4.4 8.5 1.0
O A:HOH643 4.5 37.3 1.0
NE2 A:HIS120 4.6 6.6 1.0
OG A:SER249 4.6 6.9 1.0
CE1 A:HIS120 4.6 6.7 1.0
CA A:CYS208 4.6 6.8 1.0
CE A:LYS125 4.9 6.3 1.0
CD A:LYS125 5.0 6.5 1.0

Reference:

H.Zhang, G.Ma, Y.Zhu, L.Zeng, A.Ahmad, C.Wang, B.Pang, H.Fang, L.Zhao, Q.Hao. Active-Site Conformational Fluctuations Promote the Enzymatic Activity of Ndm-1. Antimicrob. Agents V. 62 2018CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 30150473
DOI: 10.1128/AAC.01579-18
Page generated: Mon Oct 28 16:49:58 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy