Zinc in PDB 5zgr: Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin

All present enzymatic activity of Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin, PDB code: 5zgr 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 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.142, 79.215, 134.141, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 14.8

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin (pdb code 5zgr). 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 PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin, PDB code: 5zgr:
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 PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin


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 PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.9 occ:1.00 ND1 A:HIS122 2.0 11.8 1.0 O A:HOH412 2.0 10.8 1.0 NE2 A:HIS189 2.0 10.9 1.0 NE2 A:HIS120 2.1 10.6 1.0 O4 A:ZZ7303 2.3 12.0 1.0 CE1 A:HIS122 2.9 11.7 1.0 CE1 A:HIS189 3.0 10.4 1.0 CD2 A:HIS189 3.0 10.0 1.0 CG A:HIS122 3.0 11.1 1.0 CE1 A:HIS120 3.1 9.4 1.0 CD2 A:HIS120 3.2 10.3 1.0 C15 A:ZZ7303 3.2 12.3 1.0 CB A:HIS122 3.4 11.0 1.0 C14 A:ZZ7303 3.8 11.5 1.0 N3 A:ZZ7303 4.0 11.3 1.0 NE2 A:HIS122 4.1 11.8 1.0 OXT A:ZZ7303 4.1 13.8 1.0 ND1 A:HIS189 4.1 10.8 1.0 CD2 A:HIS122 4.1 11.5 1.0 CG A:HIS189 4.2 10.6 1.0 ND1 A:HIS120 4.2 10.4 1.0 OD1 A:ASP124 4.3 11.0 1.0 CG2 A:THR190 4.3 11.1 1.0 CG A:HIS120 4.3 10.3 1.0 SG A:CYS208 4.4 11.2 1.0 CB A:CYS208 4.5 11.2 1.0 C13 A:ZZ7303 4.5 11.6 1.0 ZN A:ZN302 4.6 11.3 1.0 O A:HOH555 4.7 17.8 1.0 C12 A:ZZ7303 4.9 11.5 1.0 CA A:HIS122 4.9 10.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin


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 PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.3 occ:1.00 NE2 A:HIS250 2.0 12.6 1.0 OD2 A:ASP124 2.1 12.2 1.0 O1 A:ZZ7303 2.1 11.8 1.0 N3 A:ZZ7303 2.1 11.3 1.0 SG A:CYS208 2.4 11.2 1.0 C2 A:ZZ7303 3.0 11.7 1.0 CD2 A:HIS250 3.0 12.4 1.0 CE1 A:HIS250 3.0 12.4 1.0 O A:HOH412 3.0 10.8 1.0 C12 A:ZZ7303 3.0 11.5 1.0 CG A:ASP124 3.3 11.4 1.0 C13 A:ZZ7303 3.3 11.6 1.0 CB A:CYS208 3.4 11.2 1.0 C16 A:ZZ7303 3.6 13.3 1.0 OD1 A:ASP124 3.8 11.0 1.0 C6 A:ZZ7303 3.9 12.5 1.0 ND1 A:HIS250 4.1 12.2 1.0 CG A:HIS250 4.2 12.4 1.0 O2 A:ZZ7303 4.2 14.4 1.0 CB A:SER249 4.2 11.5 1.0 C14 A:ZZ7303 4.3 11.5 1.0 O4 A:ZZ7303 4.3 12.0 1.0 S1 A:ZZ7303 4.5 13.4 1.0 CA A:CYS208 4.5 11.5 1.0 CB A:ASP124 4.5 11.5 1.0 OG A:SER249 4.6 11.4 1.0 ZN A:ZN301 4.6 10.9 1.0 C15 A:ZZ7303 4.8 12.3 1.0 NE2 A:HIS189 4.8 10.9 1.0 CE1 A:HIS189 4.9 10.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin


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 PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.1 occ:1.00 O B:HOH410 2.0 10.5 1.0 ND1 B:HIS122 2.0 11.8 1.0 NE2 B:HIS189 2.0 11.7 1.0 NE2 B:HIS120 2.1 11.5 1.0 O4 B:ZZ7303 2.3 11.7 1.0 CE1 B:HIS122 3.0 10.8 1.0 CD2 B:HIS189 3.0 10.7 1.0 CE1 B:HIS189 3.0 11.6 1.0 CG B:HIS122 3.0 11.4 1.0 CE1 B:HIS120 3.1 10.7 1.0 CD2 B:HIS120 3.1 10.5 1.0 C15 B:ZZ7303 3.2 12.4 1.0 CB B:HIS122 3.4 11.4 1.0 C14 B:ZZ7303 3.9 11.9 1.0 N3 B:ZZ7303 4.0 11.5 1.0 OXT B:ZZ7303 4.0 13.3 1.0 NE2 B:HIS122 4.1 12.2 1.0 ND1 B:HIS189 4.1 11.2 1.0 CD2 B:HIS122 4.1 12.0 1.0 CG B:HIS189 4.2 10.8 1.0 ND1 B:HIS120 4.2 10.3 1.0 CG2 B:THR190 4.2 10.9 1.0 OD1 B:ASP124 4.3 11.8 1.0 CG B:HIS120 4.3 10.1 1.0 SG B:CYS208 4.4 11.2 1.0 CB B:CYS208 4.5 11.3 1.0 C13 B:ZZ7303 4.6 11.8 1.0 ZN B:ZN302 4.6 11.3 1.0 O B:HOH408 4.8 20.4 1.0 CA B:HIS122 4.9 11.1 1.0 C12 B:ZZ7303 4.9 11.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin


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 PH7.3 (Hepes) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:11.3 occ:1.00 NE2 B:HIS250 2.0 12.8 1.0 OD2 B:ASP124 2.1 12.5 1.0 O1 B:ZZ7303 2.1 11.8 1.0 N3 B:ZZ7303 2.1 11.5 1.0 SG B:CYS208 2.4 11.2 1.0 C2 B:ZZ7303 2.9 12.0 1.0 CD2 B:HIS250 3.0 12.3 1.0 CE1 B:HIS250 3.0 13.1 1.0 O B:HOH410 3.0 10.5 1.0 C12 B:ZZ7303 3.0 11.7 1.0 C13 B:ZZ7303 3.3 11.8 1.0 CG B:ASP124 3.3 11.7 1.0 CB B:CYS208 3.4 11.3 1.0 C16 B:ZZ7303 3.6 12.9 1.0 OD1 B:ASP124 3.8 11.8 1.0 C6 B:ZZ7303 3.9 12.3 1.0 ND1 B:HIS250 4.1 12.7 1.0 CG B:HIS250 4.2 12.5 1.0 O2 B:ZZ7303 4.2 13.4 1.0 CB B:SER249 4.2 11.1 1.0 C14 B:ZZ7303 4.3 11.9 1.0 O4 B:ZZ7303 4.3 11.7 1.0 S1 B:ZZ7303 4.5 13.1 1.0 CB B:ASP124 4.5 11.5 1.0 CA B:CYS208 4.5 11.1 1.0 ZN B:ZN301 4.6 11.1 1.0 OG B:SER249 4.6 10.8 1.0 C15 B:ZZ7303 4.8 12.4 1.0 NE2 B:HIS189 4.9 11.7 1.0 CE1 B:HIS189 4.9 11.6 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