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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: Wed Dec 16 11:26:39 2020

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