Zinc in PDB 5zge: Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin

All present enzymatic activity of Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin, PDB code: 5zge 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 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.204, 79.071, 133.974, 90.00, 90.00, 90.00
R / Rfree (%)	12.8 / 14.5

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin (pdb code 5zge). 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 PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin, PDB code: 5zge:
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 PH5.5 (Bis-Tris) 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 PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.9 occ:1.00 O A:OH304 2.0 17.9 1.0 ND1 A:HIS122 2.0 16.8 1.0 NE2 A:HIS189 2.1 16.4 1.0 NE2 A:HIS120 2.1 17.0 1.0 OXT A:ZZ7301 2.3 18.6 1.0 CE1 A:HIS122 3.0 17.4 1.0 CD2 A:HIS189 3.0 16.3 1.0 CG A:HIS122 3.0 16.3 1.0 CE1 A:HIS189 3.1 16.6 1.0 CE1 A:HIS120 3.1 16.6 1.0 CD2 A:HIS120 3.1 16.2 1.0 C15 A:ZZ7301 3.2 18.2 1.0 CB A:HIS122 3.4 16.4 1.0 C14 A:ZZ7301 3.9 18.2 1.0 N3 A:ZZ7301 4.1 17.7 1.0 O4 A:ZZ7301 4.1 20.1 1.0 NE2 A:HIS122 4.1 18.2 1.0 CD2 A:HIS122 4.2 18.3 1.0 ND1 A:HIS189 4.2 16.2 1.0 CG A:HIS189 4.2 16.1 1.0 ND1 A:HIS120 4.2 16.5 1.0 OD1 A:ASP124 4.2 17.0 1.0 CG2 A:THR190 4.2 16.8 1.0 CG A:HIS120 4.3 16.0 1.0 SG A:CYS208 4.3 16.3 1.0 CB A:CYS208 4.5 16.9 1.0 C13 A:ZZ7301 4.6 17.9 1.0 ZN A:ZN303 4.6 16.8 1.0 O A:HOH549 4.8 25.6 1.0 CA A:HIS122 4.9 16.1 1.0 C12 A:ZZ7301 4.9 17.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) 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 PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:16.8 occ:1.00 NE2 A:HIS250 2.0 17.2 1.0 OD2 A:ASP124 2.1 16.6 1.0 O2 A:ZZ7301 2.1 17.1 1.0 N3 A:ZZ7301 2.2 17.7 1.0 SG A:CYS208 2.4 16.3 1.0 C2 A:ZZ7301 3.0 17.0 1.0 CE1 A:HIS250 3.0 16.6 1.0 O A:OH304 3.0 17.9 1.0 CD2 A:HIS250 3.0 16.9 1.0 C12 A:ZZ7301 3.0 17.1 1.0 C13 A:ZZ7301 3.3 17.9 1.0 CG A:ASP124 3.3 16.4 1.0 CB A:CYS208 3.4 16.9 1.0 C16 A:ZZ7301 3.6 18.8 1.0 OD1 A:ASP124 3.8 17.0 1.0 C6 A:ZZ7301 3.8 17.9 1.0 ND1 A:HIS250 4.1 17.5 1.0 CG A:HIS250 4.2 17.4 1.0 O1 A:ZZ7301 4.2 18.6 1.0 CB A:SER249 4.2 17.3 1.0 OXT A:ZZ7301 4.3 18.6 1.0 C14 A:ZZ7301 4.3 18.2 1.0 CB A:ASP124 4.5 17.0 1.0 S1 A:ZZ7301 4.5 18.9 1.0 CA A:CYS208 4.5 16.6 1.0 ZN A:ZN302 4.6 16.9 1.0 OG A:SER249 4.6 17.1 1.0 C15 A:ZZ7301 4.8 18.2 1.0 NE2 A:HIS189 4.9 16.4 1.0 CE1 A:HIS189 4.9 16.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) 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 PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.0 occ:1.00 O B:OH304 2.0 17.7 1.0 ND1 B:HIS122 2.0 16.8 1.0 NE2 B:HIS189 2.1 16.6 1.0 NE2 B:HIS120 2.1 17.1 1.0 OXT B:ZZ7302 2.3 18.4 1.0 CE1 B:HIS122 2.9 17.7 1.0 CG B:HIS122 3.0 16.5 1.0 CE1 B:HIS189 3.0 16.5 1.0 CD2 B:HIS189 3.0 16.3 1.0 CE1 B:HIS120 3.1 17.0 1.0 CD2 B:HIS120 3.2 15.9 1.0 C15 B:ZZ7302 3.3 17.8 1.0 CB B:HIS122 3.4 16.2 1.0 C14 B:ZZ7302 3.9 17.8 1.0 NE2 B:HIS122 4.1 18.1 1.0 N3 B:ZZ7302 4.1 17.9 1.0 CD2 B:HIS122 4.1 17.8 1.0 ND1 B:HIS189 4.2 16.8 1.0 O4 B:ZZ7302 4.2 21.2 1.0 CG B:HIS189 4.2 16.3 1.0 OD1 B:ASP124 4.2 17.3 1.0 ND1 B:HIS120 4.2 16.4 1.0 CG2 B:THR190 4.2 17.1 1.0 CG B:HIS120 4.3 15.7 1.0 SG B:CYS208 4.4 16.8 1.0 CB B:CYS208 4.5 16.7 1.0 C13 B:ZZ7302 4.6 18.1 1.0 ZN B:ZN303 4.6 17.1 1.0 O B:HOH511 4.8 22.8 1.0 CA B:HIS122 4.9 16.3 1.0 C12 B:ZZ7302 4.9 17.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Bis-Tris) 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 PH5.5 (Bis-Tris) in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:17.1 occ:1.00 NE2 B:HIS250 2.0 17.4 1.0 OD2 B:ASP124 2.1 17.4 1.0 O2 B:ZZ7302 2.1 18.2 1.0 N3 B:ZZ7302 2.2 17.9 1.0 SG B:CYS208 2.4 16.8 1.0 C2 B:ZZ7302 3.0 17.8 1.0 CE1 B:HIS250 3.0 17.6 1.0 CD2 B:HIS250 3.0 18.0 1.0 O B:OH304 3.0 17.7 1.0 C12 B:ZZ7302 3.0 17.6 1.0 C13 B:ZZ7302 3.3 18.1 1.0 CG B:ASP124 3.3 16.9 1.0 CB B:CYS208 3.4 16.7 1.0 C16 B:ZZ7302 3.6 20.1 1.0 OD1 B:ASP124 3.8 17.3 1.0 C6 B:ZZ7302 3.8 18.5 1.0 ND1 B:HIS250 4.1 18.0 1.0 CG B:HIS250 4.1 18.3 1.0 O1 B:ZZ7302 4.2 19.3 1.0 CB B:SER249 4.2 17.5 1.0 C14 B:ZZ7302 4.3 17.8 1.0 OXT B:ZZ7302 4.3 18.4 1.0 S1 B:ZZ7302 4.5 20.1 1.0 CA B:CYS208 4.5 17.2 1.0 CB B:ASP124 4.5 16.7 1.0 OG B:SER249 4.6 17.9 1.0 ZN B:ZN301 4.6 17.0 1.0 C15 B:ZZ7302 4.8 17.8 1.0 NE2 B:HIS189 4.9 16.6 1.0 CE1 B:HIS189 4.9 16.5 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