Zinc in PDB 5zgx: Crystal Structure of Ndm-1 at PH7.5 (Succinate) with 1 Molecule Per Asymmetric Unit

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

The structure of Crystal Structure of Ndm-1 at PH7.5 (Succinate) with 1 Molecule Per Asymmetric Unit, PDB code: 5zgx 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)	33.88 / 0.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.451, 59.885, 41.972, 90.00, 97.94, 90.00
R / Rfree (%)	11.3 / 12.5

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

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 at PH7.5 (Succinate) with 1 Molecule 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 (Succinate) with 1 Molecule Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:6.1 occ:1.00 O A:OH309 2.0 7.2 1.0 NE2 A:HIS189 2.0 5.7 1.0 NE2 A:HIS120 2.1 5.3 1.0 ND1 A:HIS122 2.1 6.5 1.0 CE1 A:HIS120 3.0 5.4 1.0 CD2 A:HIS189 3.0 5.6 1.0 CE1 A:HIS122 3.0 7.0 1.0 CE1 A:HIS189 3.0 6.5 1.0 CD2 A:HIS120 3.1 5.0 1.0 CG A:HIS122 3.1 5.9 1.0 CB A:HIS122 3.4 5.4 1.0 ZN A:ZN302 3.6 7.3 1.0 O2 A:EDO307 3.7 16.0 1.0 O A:HOH420 3.8 12.2 1.0 SG A:CYS208 3.9 5.5 1.0 OD1 A:ASP124 4.0 6.8 1.0 ND1 A:HIS120 4.1 5.1 1.0 NE2 A:HIS122 4.1 7.4 1.0 ND1 A:HIS189 4.1 6.3 1.0 CG A:HIS189 4.2 5.6 1.0 CB A:CYS208 4.2 5.5 1.0 CG A:HIS120 4.2 4.8 1.0 CD2 A:HIS122 4.2 6.9 1.0 CG2 A:THR190 4.4 6.5 1.0 OD2 A:ASP124 4.6 7.2 1.0 CG A:ASP124 4.7 4.8 1.0 CA A:HIS122 4.8 4.8 1.0 C2 A:EDO307 4.8 16.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 at PH7.5 (Succinate) with 1 Molecule 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 (Succinate) with 1 Molecule Per Asymmetric Unit within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.3 occ:1.00 OD2 A:ASP124 2.0 7.2 1.0 NE2 A:HIS250 2.1 5.9 1.0 O A:OH309 2.1 7.2 1.0 O A:HOH420 2.2 12.2 1.0 SG A:CYS208 2.3 5.5 1.0 CE1 A:HIS250 3.0 6.0 1.0 CG A:ASP124 3.0 4.8 1.0 CD2 A:HIS250 3.1 6.3 1.0 OD1 A:ASP124 3.4 6.8 1.0 CB A:CYS208 3.4 5.5 1.0 ZN A:ZN301 3.6 6.1 1.0 O2 A:EDO307 4.1 16.0 1.0 O1 A:EDO307 4.1 20.2 1.0 ND1 A:HIS250 4.2 6.1 1.0 CG A:HIS250 4.2 6.3 1.0 NE2 A:HIS189 4.2 5.7 1.0 C2 A:EDO307 4.3 16.2 1.0 O A:HOH569 4.3 17.3 1.0 CB A:ASP124 4.3 4.6 1.0 CB A:SER249 4.4 5.1 1.0 CE1 A:HIS189 4.4 6.5 1.0 CA A:CYS208 4.6 5.6 1.0 OG A:SER249 4.6 5.3 1.0 NE2 A:HIS120 4.7 5.3 1.0 CE1 A:HIS120 4.7 5.4 1.0 C1 A:EDO307 4.8 17.2 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