Zinc in PDB 5zgt: Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit

Enzymatic activity of Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit

All present enzymatic activity of Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit, PDB code: 5zgt 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) 50.00 / 1.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.691, 73.475, 66.461, 90.00, 98.23, 90.00
R / Rfree (%) 11.4 / 13.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit (pdb code 5zgt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit, PDB code: 5zgt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5zgt

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Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit


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 (Hepes) with 2 Molecules Per Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:6.9
occ:1.00
O A:OH303 2.0 8.0 1.0
ND1 A:HIS122 2.0 7.7 1.0
NE2 A:HIS189 2.0 7.4 1.0
NE2 A:HIS120 2.1 7.1 1.0
CE1 A:HIS122 3.0 7.8 1.0
CD2 A:HIS189 3.0 7.0 1.0
CE1 A:HIS120 3.0 7.0 1.0
CE1 A:HIS189 3.0 7.4 1.0
CG A:HIS122 3.0 7.3 1.0
CD2 A:HIS120 3.1 6.7 1.0
CB A:HIS122 3.4 6.7 1.0
ZN A:ZN302 3.4 7.5 1.0
SG A:CYS208 3.9 7.0 1.0
OD1 A:ASP124 4.1 7.8 1.0
NE2 A:HIS122 4.1 8.2 1.0
CB A:CYS208 4.1 7.2 1.0
ND1 A:HIS120 4.1 6.8 1.0
ND1 A:HIS189 4.1 7.7 1.0
CD2 A:HIS122 4.1 7.7 1.0
CG A:HIS189 4.1 6.9 1.0
CG A:HIS120 4.2 6.6 1.0
CG2 A:THR190 4.4 7.7 1.0
OD2 A:ASP124 4.6 7.9 1.0
CG A:ASP124 4.8 6.7 1.0
CA A:HIS122 4.8 6.4 1.0
O A:HOH569 4.8 16.2 1.0

Zinc binding site 2 out of 4 in 5zgt

Go back to Zinc Binding Sites List in 5zgt
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit


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 (Hepes) with 2 Molecules Per Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:7.5
occ:1.00
OD2 A:ASP124 2.0 7.9 1.0
O A:OH303 2.0 8.0 1.0
NE2 A:HIS250 2.0 7.5 1.0
SG A:CYS208 2.3 7.0 1.0
CG A:ASP124 2.9 6.7 1.0
CE1 A:HIS250 3.0 7.5 1.0
CD2 A:HIS250 3.1 7.1 1.0
OD1 A:ASP124 3.2 7.8 1.0
CB A:CYS208 3.4 7.2 1.0
ZN A:ZN301 3.4 6.9 1.0
ND1 A:HIS250 4.1 7.6 1.0
CB A:SER249 4.1 6.6 1.0
CG A:HIS250 4.2 7.3 1.0
NE2 A:HIS189 4.2 7.4 1.0
CB A:ASP124 4.3 6.4 1.0
NE2 A:HIS120 4.4 7.1 1.0
CE1 A:HIS120 4.4 7.0 1.0
CE1 A:HIS189 4.4 7.4 1.0
OG A:SER249 4.5 6.9 1.0
CE A:LYS125 4.6 6.8 1.0
CD A:LYS125 4.6 6.8 1.0
CA A:CYS208 4.6 7.3 1.0
CG A:LYS125 4.7 6.6 1.0
OG A:SER75 4.9 7.0 1.0

Zinc binding site 3 out of 4 in 5zgt

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Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:7.4
occ:1.00
O B:OH303 2.0 8.8 1.0
NE2 B:HIS189 2.0 7.6 1.0
ND1 B:HIS122 2.0 7.8 1.0
NE2 B:HIS120 2.1 7.3 1.0
CE1 B:HIS122 3.0 8.1 1.0
CD2 B:HIS189 3.0 6.9 1.0
CE1 B:HIS189 3.0 7.9 1.0
CE1 B:HIS120 3.0 7.6 1.0
CG B:HIS122 3.0 7.3 1.0
CD2 B:HIS120 3.1 7.0 1.0
CB B:HIS122 3.4 7.0 1.0
ZN B:ZN302 3.4 8.1 1.0
SG B:CYS208 3.8 7.6 1.0
CB B:CYS208 4.0 7.6 1.0
NE2 B:HIS122 4.1 8.4 1.0
ND1 B:HIS189 4.1 7.9 1.0
ND1 B:HIS120 4.1 7.0 1.0
CG B:HIS189 4.1 6.9 1.0
OD1 B:ASP124 4.1 8.5 1.0
CD2 B:HIS122 4.1 7.9 1.0
CG B:HIS120 4.2 6.8 1.0
O B:HOH610 4.2 15.3 1.0
CG2 B:THR190 4.5 7.9 1.0
OD2 B:ASP124 4.6 8.1 1.0
CG B:ASP124 4.8 7.4 1.0
CA B:HIS122 4.8 7.0 1.0
O B:HOH565 4.8 16.6 1.0

Zinc binding site 4 out of 4 in 5zgt

Go back to Zinc Binding Sites List in 5zgt
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 at PH7.5 (Hepes) with 2 Molecules Per Asymmetric Unit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:8.1
occ:1.00
O B:OH303 2.0 8.8 1.0
OD2 B:ASP124 2.0 8.1 1.0
NE2 B:HIS250 2.0 8.1 1.0
SG B:CYS208 2.3 7.6 1.0
CG B:ASP124 2.9 7.4 1.0
CE1 B:HIS250 3.0 8.2 1.0
CD2 B:HIS250 3.0 8.3 1.0
OD1 B:ASP124 3.2 8.5 1.0
CB B:CYS208 3.4 7.6 1.0
ZN B:ZN301 3.4 7.4 1.0
ND1 B:HIS250 4.1 8.5 1.0
CB B:SER249 4.1 6.6 1.0
CG B:HIS250 4.2 8.5 1.0
NE2 B:HIS189 4.2 7.6 1.0
CB B:ASP124 4.3 7.2 1.0
NE2 B:HIS120 4.4 7.3 1.0
CE1 B:HIS120 4.4 7.6 1.0
OG B:SER249 4.5 6.9 1.0
CE1 B:HIS189 4.5 7.9 1.0
CA B:CYS208 4.6 7.4 1.0
O B:HOH697 4.7 29.4 1.0
CD B:LYS125 4.7 7.2 1.0
CE B:LYS125 4.7 7.4 1.0
CG B:LYS125 4.8 7.4 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 11:26:36 2020

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