Zinc in PDB 5zh1: Crystal Structure of Ndm-1 at PH7.5 (Imidazole) with 2 Molecules Per Asymmetric Unit

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

The structure of Crystal Structure of Ndm-1 at PH7.5 (Imidazole) with 2 Molecules Per Asymmetric Unit, PDB code: 5zh1 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)	32.75 / 1.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.540, 73.619, 66.055, 90.00, 97.88, 90.00
R / Rfree (%)	12.7 / 14.7

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH7.5 (Imidazole) with 2 Molecules Per Asymmetric Unit (pdb code 5zh1). 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 (Imidazole) with 2 Molecules Per Asymmetric Unit, PDB code: 5zh1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Imidazole) 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 (Imidazole) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.3 occ:1.00 O A:OH303 1.9 19.5 1.0 ND1 A:HIS122 2.1 17.5 1.0 NE2 A:HIS120 2.1 17.0 1.0 NE2 A:HIS189 2.1 17.6 1.0 CE1 A:HIS122 3.0 18.0 1.0 CD2 A:HIS189 3.0 17.1 1.0 CG A:HIS122 3.0 17.6 1.0 CE1 A:HIS120 3.1 17.0 1.0 CD2 A:HIS120 3.1 16.3 1.0 CE1 A:HIS189 3.1 18.0 1.0 CB A:HIS122 3.4 17.1 1.0 ZN A:ZN302 3.4 18.6 1.0 SG A:CYS208 3.9 18.1 1.0 O A:HOH477 4.0 27.2 1.0 OD1 A:ASP124 4.0 19.4 1.0 CB A:CYS208 4.1 18.4 1.0 NE2 A:HIS122 4.1 18.8 1.0 ND1 A:HIS120 4.2 17.3 1.0 CD2 A:HIS122 4.2 18.1 1.0 CG A:HIS120 4.2 16.8 1.0 ND1 A:HIS189 4.2 17.9 1.0 CG A:HIS189 4.2 17.4 1.0 O A:HOH611 4.4 39.9 1.0 CG2 A:THR190 4.4 18.1 1.0 OD2 A:ASP124 4.6 18.9 1.0 CG A:ASP124 4.7 16.7 1.0 CA A:HIS122 4.8 16.5 1.0 O A:HOH546 4.9 29.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Imidazole) 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 (Imidazole) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.6 occ:1.00 O A:OH303 2.0 19.5 1.0 OD2 A:ASP124 2.0 18.9 1.0 NE2 A:HIS250 2.1 18.8 1.0 SG A:CYS208 2.3 18.1 1.0 CG A:ASP124 2.9 16.7 1.0 CE1 A:HIS250 3.0 17.9 1.0 CD2 A:HIS250 3.1 17.8 1.0 OD1 A:ASP124 3.2 19.4 1.0 ZN A:ZN301 3.4 17.3 1.0 CB A:CYS208 3.4 18.4 1.0 O A:HOH611 3.8 39.9 1.0 ND1 A:HIS250 4.1 18.1 1.0 CB A:SER249 4.2 16.9 1.0 CG A:HIS250 4.2 17.5 1.0 CB A:ASP124 4.3 16.8 1.0 NE2 A:HIS189 4.3 17.6 1.0 NE2 A:HIS120 4.3 17.0 1.0 CE1 A:HIS120 4.4 17.0 1.0 OG A:SER249 4.5 17.6 1.0 CE1 A:HIS189 4.5 18.0 1.0 CE A:LYS125 4.6 18.0 1.0 CD A:LYS125 4.6 17.9 1.0 CA A:CYS208 4.7 18.3 1.0 CG A:LYS125 4.7 17.4 1.0 OG A:SER75 4.8 17.8 1.0 O A:HOH625 4.8 38.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Imidazole) 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 (Imidazole) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.7 occ:1.00 O B:OH303 1.9 20.6 1.0 ND1 B:HIS122 2.1 17.5 1.0 NE2 B:HIS120 2.1 16.8 1.0 NE2 B:HIS189 2.1 17.3 1.0 CE1 B:HIS122 3.0 18.4 1.0 CG B:HIS122 3.0 17.8 1.0 CE1 B:HIS120 3.0 17.4 1.0 CD2 B:HIS189 3.1 16.9 1.0 CD2 B:HIS120 3.1 16.9 1.0 CE1 B:HIS189 3.1 18.3 1.0 CB B:HIS122 3.3 17.2 1.0 ZN B:ZN302 3.4 20.9 1.0 SG B:CYS208 3.9 19.5 1.0 OD1 B:ASP124 4.1 20.4 1.0 CB B:CYS208 4.1 18.4 1.0 O B:HOH547 4.1 25.3 1.0 NE2 B:HIS122 4.1 19.0 1.0 ND1 B:HIS120 4.2 17.1 1.0 CD2 B:HIS122 4.2 18.4 1.0 ND1 B:HIS189 4.2 18.0 1.0 CG B:HIS120 4.2 16.8 1.0 O B:HOH601 4.2 46.1 1.0 CG B:HIS189 4.2 16.9 1.0 CG2 B:THR190 4.5 17.8 1.0 O B:HOH540 4.5 48.3 1.0 OD2 B:ASP124 4.6 20.2 1.0 CG B:ASP124 4.8 18.0 1.0 CA B:HIS122 4.8 16.6 1.0 O B:HOH562 4.9 25.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH7.5 (Imidazole) 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 (Imidazole) with 2 Molecules Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.9 occ:1.00 O B:OH303 1.9 20.6 1.0 OD2 B:ASP124 2.0 20.2 1.0 NE2 B:HIS250 2.1 20.4 1.0 SG B:CYS208 2.3 19.5 1.0 CG B:ASP124 2.9 18.0 1.0 CE1 B:HIS250 3.0 19.8 1.0 CD2 B:HIS250 3.1 20.5 1.0 OD1 B:ASP124 3.2 20.4 1.0 CB B:CYS208 3.4 18.4 1.0 ZN B:ZN301 3.4 17.7 1.0 O B:HOH540 3.7 48.3 1.0 O B:HOH601 3.7 46.1 1.0 ND1 B:HIS250 4.1 20.4 1.0 CB B:SER249 4.1 17.8 1.0 CG B:HIS250 4.2 20.1 1.0 CB B:ASP124 4.3 17.7 1.0 NE2 B:HIS189 4.3 17.3 1.0 NE2 B:HIS120 4.3 16.8 1.0 CE1 B:HIS120 4.4 17.4 1.0 OG B:SER249 4.5 18.7 1.0 CE1 B:HIS189 4.6 18.3 1.0 CA B:CYS208 4.6 19.2 1.0 CE B:LYS125 4.7 17.9 1.0 CD B:LYS125 4.7 18.4 1.0 O B:HOH634 4.7 56.8 1.0 CG B:LYS125 4.7 17.9 1.0 OG B:SER75 4.9 19.6 1.0 O B:HOH510 5.0 40.5 1.0

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