Zinc in PDB 6d1g: Crystal Structure of Ndm-1 Complexed with Compound 9

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 9:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 9, PDB code: 6d1g was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.31 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.500, 60.150, 41.850, 90.00, 98.10, 90.00
R / Rfree (%)	13.4 / 16.4

The structure of Crystal Structure of Ndm-1 Complexed with Compound 9 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 9 (pdb code 6d1g). 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 Complexed with Compound 9, PDB code: 6d1g:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 9


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 Complexed with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.8 occ:0.92 O12 A:YKG303 1.9 7.5 0.7 ND1 A:HIS122 2.0 8.8 1.0 NE2 A:HIS189 2.0 8.1 1.0 NE2 A:HIS120 2.1 7.4 1.0 O10 A:YKG303 2.9 8.2 0.7 P09 A:YKG303 2.9 8.3 0.7 CE1 A:HIS122 3.0 10.0 1.0 CD2 A:HIS189 3.0 8.1 1.0 CG A:HIS122 3.0 9.0 1.0 CE1 A:HIS120 3.0 7.5 1.0 CE1 A:HIS189 3.0 8.5 1.0 CD2 A:HIS120 3.0 7.2 1.0 CB A:HIS122 3.3 7.6 1.0 O11 A:YKG303 3.9 10.9 0.7 SG A:CYS208 4.0 8.4 1.0 OD1 A:ASP124 4.1 9.2 1.0 NE2 A:HIS122 4.1 10.9 1.0 ND1 A:HIS120 4.1 7.7 1.0 ND1 A:HIS189 4.1 8.6 1.0 CD2 A:HIS122 4.1 10.2 1.0 CG A:HIS189 4.2 8.3 1.0 CG A:HIS120 4.2 7.0 1.0 CB A:CYS208 4.3 9.2 1.0 ZN A:ZN302 4.3 9.0 0.7 C08 A:YKG303 4.3 9.6 0.7 CG2 A:THR190 4.4 9.3 1.0 OD2 A:ASP124 4.6 11.2 1.0 CG A:ASP124 4.8 9.2 1.0 CA A:HIS122 4.8 6.7 1.0 ND2 A:ASN220 4.9 12.8 1.0 OXT A:ACT304 4.9 11.0 0.9 BR05 A:YKG303 4.9 18.2 0.7

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 9


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 Complexed with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.0 occ:0.65 O11 A:YKG303 1.8 10.9 0.7 NE2 A:HIS250 1.9 10.8 1.0 OXT A:ACT304 1.9 11.0 0.9 SG A:CYS208 2.3 8.4 1.0 CD2 A:HIS250 2.8 11.5 1.0 OD2 A:ASP124 2.9 11.2 1.0 C A:ACT304 2.9 12.1 0.9 CE1 A:HIS250 3.0 10.0 1.0 P09 A:YKG303 3.0 8.3 0.7 CB A:CYS208 3.2 9.2 1.0 CH3 A:ACT304 3.3 13.3 0.9 O12 A:YKG303 3.3 7.5 0.7 O10 A:YKG303 3.9 8.2 0.7 CG A:HIS250 4.0 11.0 1.0 ND1 A:HIS250 4.0 10.5 1.0 O A:ACT304 4.1 13.4 0.9 CG A:ASP124 4.1 9.2 1.0 CB A:SER249 4.1 8.3 1.0 CE1 A:HIS189 4.2 8.5 1.0 CA A:CYS208 4.3 8.8 1.0 ZN A:ZN301 4.3 7.8 0.9 NE2 A:HIS189 4.3 8.1 1.0 C08 A:YKG303 4.4 9.6 0.7 O A:HOH564 4.4 30.8 1.0 OD1 A:ASP124 4.6 9.2 1.0 OG A:SER249 4.6 8.1 1.0 C13 A:YKG303 4.7 12.2 0.7 NZ A:LYS211 4.7 17.2 1.0 ND1 A:HIS189 5.0 8.6 1.0 C07 A:YKG303 5.0 10.7 0.7 O A:HOH586 5.0 31.7 1.0

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728