Zinc in PDB 6d1j: Crystal Structure of Ndm-1 Complexed with Compound 13

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 13:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 13, PDB code: 6d1j 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)	27.83 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.530, 60.150, 41.890, 90.00, 97.64, 90.00
R / Rfree (%)	13.1 / 15.8

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 13 (pdb code 6d1j). 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 13, PDB code: 6d1j:
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 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.3 occ:0.89 O10 A:7SX303 1.9 8.5 0.8 ND1 A:HIS122 2.0 8.2 1.0 NE2 A:HIS189 2.0 7.4 1.0 NE2 A:HIS120 2.0 7.3 1.0 O12 A:7SX303 2.9 8.7 0.8 P09 A:7SX303 3.0 9.3 0.8 CE1 A:HIS122 3.0 9.1 1.0 CE1 A:HIS120 3.0 7.6 1.0 CD2 A:HIS189 3.0 7.7 1.0 CD2 A:HIS120 3.0 7.1 1.0 CE1 A:HIS189 3.0 7.8 1.0 CG A:HIS122 3.0 7.8 1.0 CB A:HIS122 3.4 6.3 1.0 SG A:CYS208 3.9 9.4 1.0 O11 A:7SX303 3.9 13.0 0.8 OD1 A:ASP124 4.0 10.0 1.0 ND1 A:HIS120 4.1 7.7 1.0 NE2 A:HIS122 4.1 9.6 1.0 CG A:HIS120 4.1 6.7 1.0 ND1 A:HIS189 4.1 8.0 1.0 CD2 A:HIS122 4.1 8.7 1.0 CG A:HIS189 4.2 7.8 1.0 ZN A:ZN302 4.2 10.6 0.5 CB A:CYS208 4.2 9.8 1.0 C08 A:7SX303 4.4 10.9 0.8 CG2 A:THR190 4.5 8.7 1.0 OD2 A:ASP124 4.6 12.3 1.0 C05 A:7SX303 4.6 15.8 0.8 CG A:ASP124 4.7 10.3 1.0 CA A:HIS122 4.8 5.7 1.0 OXT A:ACT304 4.9 12.2 0.7 ND2 A:ASN220 5.0 12.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 13


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 13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.6 occ:0.51 O11 A:7SX303 1.8 13.0 0.8 NE2 A:HIS250 1.9 12.0 1.0 OXT A:ACT304 2.0 12.2 0.7 SG A:CYS208 2.2 9.4 1.0 CD2 A:HIS250 2.7 12.6 1.0 P09 A:7SX303 3.0 9.3 0.8 CE1 A:HIS250 3.0 11.1 1.0 OD2 A:ASP124 3.0 12.3 1.0 C A:ACT304 3.1 12.1 0.7 O10 A:7SX303 3.1 8.5 0.8 CB A:CYS208 3.2 9.8 1.0 CH3 A:ACT304 3.6 12.2 0.7 CG A:HIS250 3.9 12.2 1.0 O12 A:7SX303 4.0 8.7 0.8 ND1 A:HIS250 4.0 11.3 1.0 CB A:SER249 4.1 9.0 1.0 CG A:ASP124 4.2 10.3 1.0 O A:ACT304 4.2 14.2 0.7 C08 A:7SX303 4.2 10.9 0.8 CA A:CYS208 4.2 9.3 1.0 ZN A:ZN301 4.2 7.3 0.9 CE1 A:HIS189 4.2 7.8 1.0 NE2 A:HIS189 4.3 7.4 1.0 O A:HOH557 4.4 35.7 1.0 OG A:SER249 4.6 9.2 1.0 OD1 A:ASP124 4.6 10.0 1.0 O A:HOH544 4.7 48.5 1.0 NZ A:LYS211 4.8 17.5 1.0 C13 A:7SX303 4.9 15.0 0.8 C07 A:7SX303 5.0 13.2 0.8

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