Zinc in PDB 6rmf: Crystal Structure of Ndm-1 with Vnrx-5133

All present enzymatic activity of Crystal Structure of Ndm-1 with Vnrx-5133:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 with Vnrx-5133, PDB code: 6rmf was solved by P.Hinchliffe, J.Spencer, J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.70 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.821, 73.837, 77.681, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.2

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 with Vnrx-5133 (pdb code 6rmf). 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 with Vnrx-5133, PDB code: 6rmf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 with Vnrx-5133


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 with Vnrx-5133 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.4 occ:1.00 O16 A:K9K306 2.0 7.3 0.4 O08 A:K9B307 2.0 16.5 0.6 NE2 A:HIS250 2.1 10.9 1.0 O20 A:K9K306 2.2 8.0 0.4 OD2 A:ASP124 2.2 11.7 1.0 SG A:CYS208 2.2 10.2 1.0 O13 A:K9B307 2.3 18.7 0.6 H141 A:K9K306 2.5 10.8 0.4 H061 A:K9B307 2.6 10.8 0.6 C09 A:K9B307 2.9 19.7 0.6 C17 A:K9K306 2.9 8.8 0.4 CD2 A:HIS250 3.0 10.2 1.0 CE1 A:HIS250 3.1 11.7 1.0 O14 A:K9K306 3.1 5.7 0.4 C19 A:K9K306 3.1 8.8 0.4 B13 A:K9K306 3.1 7.1 0.4 HB3 A:CYS208 3.1 14.2 1.0 C11 A:K9B307 3.2 17.2 0.6 O06 A:K9B307 3.2 15.0 0.6 HD2 A:HIS250 3.2 12.2 1.0 B05 A:K9B307 3.2 17.0 0.6 HE1 A:HIS250 3.3 13.9 1.0 CG A:ASP124 3.3 14.4 1.0 CB A:CYS208 3.3 11.8 1.0 C18 A:K9K306 3.4 9.1 0.4 C10 A:K9B307 3.4 18.7 0.6 HB3 A:SER249 3.7 12.7 1.0 OD1 A:ASP124 3.7 8.5 1.0 HB2 A:SER249 3.9 12.7 1.0 H181 A:K9B307 3.9 23.8 0.6 HG A:SER249 3.9 14.3 1.0 C17 A:K9B307 4.0 19.2 0.6 HB2 A:CYS208 4.0 14.2 1.0 C25 A:K9K306 4.0 8.1 0.4 H261 A:K9K306 4.1 25.1 0.4 H071 A:K9B307 4.1 20.5 0.6 O07 A:K9B307 4.1 19.9 0.6 O15 A:K9K306 4.1 7.3 0.4 CB A:SER249 4.2 10.6 1.0 ND1 A:HIS250 4.2 11.4 1.0 HA A:CYS208 4.2 9.1 1.0 CG A:HIS250 4.2 10.6 1.0 HE1 A:HIS120 4.2 12.2 1.0 HE1 A:HIS189 4.2 11.2 1.0 C18 A:K9B307 4.2 22.3 0.6 ZN A:ZN302 4.3 10.4 1.0 HE3 A:LYS125 4.3 17.4 1.0 O21 A:K9K306 4.3 9.9 0.4 C12 A:K9K306 4.3 8.1 0.4 C04 A:K9B307 4.3 17.8 0.6 C26 A:K9K306 4.4 8.5 0.4 O12 A:K9B307 4.4 22.6 0.6 CA A:CYS208 4.4 7.7 1.0 CE1 A:HIS189 4.5 9.3 1.0 NE2 A:HIS189 4.5 8.9 1.0 OG A:SER249 4.5 11.9 1.0 CB A:ASP124 4.6 7.8 1.0 H9 A:K9K306 4.6 23.3 0.4 C22 A:K9K306 4.7 9.5 0.4 HB2 A:ASP124 4.7 9.4 1.0 H10 A:K9B307 4.7 23.3 0.6 C14 A:K9B307 4.7 20.6 0.6 HB3 A:ASP124 4.8 9.4 1.0 HZ2 A:LYS211 4.8 21.8 1.0 HG2 A:LYS125 4.9 12.3 1.0 CE1 A:HIS120 4.9 10.1 1.0 HD1 A:HIS250 4.9 13.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 with Vnrx-5133


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 with Vnrx-5133 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.4 occ:1.00 O06 A:K9B307 1.9 15.0 0.6 H061 A:K9B307 1.9 10.8 0.6 H141 A:K9K306 1.9 10.8 0.4 O14 A:K9K306 1.9 5.7 0.4 NE2 A:HIS120 2.0 7.5 1.0 NE2 A:HIS189 2.0 8.9 1.0 ND1 A:HIS122 2.0 8.7 1.0 O07 A:K9B307 2.8 19.9 0.6 O15 A:K9K306 2.8 7.3 0.4 B05 A:K9B307 2.8 17.0 0.6 HB2 A:HIS122 2.8 9.4 1.0 B13 A:K9K306 2.9 7.1 0.4 CE1 A:HIS120 3.0 10.1 1.0 CD2 A:HIS120 3.0 6.8 1.0 CG A:HIS122 3.0 8.4 1.0 CD2 A:HIS189 3.0 7.8 1.0 CE1 A:HIS189 3.0 9.3 1.0 CE1 A:HIS122 3.0 11.9 1.0 HD2 A:HIS189 3.2 9.2 1.0 HD2 A:HIS120 3.2 8.1 1.0 HE1 A:HIS120 3.2 12.2 1.0 HE1 A:HIS189 3.2 11.2 1.0 HE1 A:HIS122 3.2 14.2 1.0 CB A:HIS122 3.3 7.8 1.0 H071 A:K9B307 3.4 20.5 0.6 HB3 A:HIS122 3.5 9.4 1.0 C10 A:K9K306 3.7 7.3 0.4 O16 A:K9K306 3.7 7.3 0.4 O08 A:K9B307 3.8 16.5 0.6 HG23 A:THR190 3.9 10.8 1.0 HG21 A:THR190 4.0 10.8 1.0 HB2 A:CYS208 4.0 14.2 1.0 ND1 A:HIS120 4.1 9.8 1.0 OD1 A:ASP124 4.1 8.5 1.0 SG A:CYS208 4.1 10.2 1.0 CG A:HIS120 4.1 6.8 1.0 ND1 A:HIS189 4.1 8.5 1.0 NE2 A:HIS122 4.1 14.8 1.0 CD2 A:HIS122 4.1 12.0 1.0 CG A:HIS189 4.1 7.6 1.0 C04 A:K9B307 4.2 17.8 0.6 C12 A:K9K306 4.2 8.1 0.4 H10 A:K9B307 4.2 23.3 0.6 H092 A:K9K306 4.2 19.6 0.4 H9 A:K9K306 4.2 23.3 0.4 ZN A:ZN301 4.3 11.4 1.0 HB3 A:CYS208 4.3 14.2 1.0 CG2 A:THR190 4.4 9.1 1.0 CB A:CYS208 4.4 11.8 1.0 N11 A:K9K306 4.4 9.0 0.4 C09 A:K9K306 4.5 11.6 0.4 CA A:HIS122 4.7 7.8 1.0 HG22 A:THR190 4.8 10.8 1.0 N03 A:K9B307 4.8 19.7 0.6 HD1 A:HIS120 4.8 11.7 1.0 O20 A:K9K306 4.9 8.0 0.4 O13 A:K9B307 4.9 18.7 0.6 OD2 A:ASP124 4.9 11.7 1.0 HD1 A:HIS189 4.9 10.1 1.0 HG2 A:LYS125 4.9 12.3 1.0 H031 A:K9B307 4.9 31.5 0.6 HE2 A:HIS122 4.9 17.7 1.0 CG A:ASP124 4.9 14.4 1.0 H081 A:K9K306 5.0 29.6 0.4 C17 A:K9K306 5.0 8.8 0.4 HD2 A:HIS122 5.0 14.4 1.0 C09 A:K9B307 5.0 19.7 0.6

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 with Vnrx-5133


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 with Vnrx-5133 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:10.0 occ:1.00 H141 B:K9K303 1.8 11.1 1.0 NE2 B:HIS120 2.0 8.6 1.0 O14 B:K9K303 2.0 11.6 1.0 NE2 B:HIS189 2.0 9.4 1.0 ND1 B:HIS122 2.1 10.2 1.0 HB2 B:HIS122 2.8 10.5 1.0 O15 B:K9K303 2.9 12.2 1.0 CD2 B:HIS189 2.9 8.5 1.0 CD2 B:HIS120 3.0 7.5 1.0 CE1 B:HIS120 3.0 9.0 1.0 CG B:HIS122 3.0 9.1 1.0 B13 B:K9K303 3.0 13.2 1.0 CE1 B:HIS189 3.1 10.3 1.0 CE1 B:HIS122 3.1 9.5 1.0 HD2 B:HIS189 3.1 10.2 1.0 HD2 B:HIS120 3.1 8.9 1.0 HE1 B:HIS120 3.2 10.8 1.0 CB B:HIS122 3.3 8.8 1.0 HE1 B:HIS122 3.3 11.3 1.0 HE1 B:HIS189 3.3 12.4 1.0 HB3 B:HIS122 3.5 10.5 1.0 O16 B:K9K303 3.8 10.3 1.0 HG23 B:THR190 3.8 13.0 1.0 C10 B:K9K303 3.9 14.5 1.0 HG21 B:THR190 3.9 13.0 1.0 HB2 B:CYS208 4.0 11.3 1.0 OD1 B:ASP124 4.0 9.8 1.0 ND1 B:HIS120 4.1 9.8 1.0 SG B:CYS208 4.1 9.0 1.0 CG B:HIS120 4.1 7.6 1.0 CG B:HIS189 4.1 8.4 1.0 ND1 B:HIS189 4.1 9.5 1.0 CD2 B:HIS122 4.2 10.2 1.0 NE2 B:HIS122 4.2 12.2 1.0 HB3 B:CYS208 4.2 11.3 1.0 ZN B:ZN302 4.3 11.2 1.0 C12 B:K9K303 4.3 13.3 1.0 H9 B:K9K303 4.3 11.1 1.0 CG2 B:THR190 4.4 10.8 1.0 CB B:CYS208 4.4 9.4 1.0 H092 B:K9K303 4.4 26.6 1.0 N11 B:K9K303 4.6 17.4 1.0 C09 B:K9K303 4.7 20.2 1.0 CA B:HIS122 4.7 8.8 1.0 HG22 B:THR190 4.7 13.0 1.0 OD2 B:ASP124 4.8 10.1 1.0 HD1 B:HIS120 4.8 11.8 1.0 CG B:ASP124 4.9 10.8 1.0 HG2 B:LYS125 4.9 16.9 1.0 O21 B:K9K303 4.9 10.5 1.0 H081 B:K9K303 4.9 29.7 1.0 HD1 B:HIS189 4.9 11.3 1.0 HG3 B:LYS125 4.9 16.9 1.0 HE2 B:HIS122 4.9 14.6 1.0 HD2 B:HIS122 5.0 12.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 with Vnrx-5133


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 with Vnrx-5133 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:11.2 occ:1.00 NE2 B:HIS250 2.0 10.8 1.0 O16 B:K9K303 2.1 10.3 1.0 O21 B:K9K303 2.2 10.5 1.0 SG B:CYS208 2.3 9.0 1.0 OD2 B:ASP124 2.3 10.1 1.0 C17 B:K9K303 3.0 13.1 1.0 CD2 B:HIS250 3.0 10.2 1.0 O14 B:K9K303 3.0 11.6 1.0 CE1 B:HIS250 3.0 11.8 1.0 HB3 B:CYS208 3.1 11.3 1.0 B13 B:K9K303 3.1 13.2 1.0 HD2 B:HIS250 3.1 12.1 1.0 C19 B:K9K303 3.1 11.3 1.0 HE1 B:HIS250 3.3 14.0 1.0 CB B:CYS208 3.3 9.4 1.0 C18 B:K9K303 3.4 12.2 1.0 CG B:ASP124 3.4 10.8 1.0 HB3 B:SER249 3.7 14.6 1.0 HB2 B:SER249 3.8 14.6 1.0 OD1 B:ASP124 3.8 9.8 1.0 H141 B:K9K303 3.9 11.1 1.0 HG B:SER249 4.0 15.6 1.0 HB2 B:CYS208 4.0 11.3 1.0 H261 B:K9K303 4.0 18.4 1.0 C25 B:K9K303 4.0 13.8 1.0 HA B:CYS208 4.1 8.5 1.0 CG B:HIS250 4.1 10.8 1.0 ND1 B:HIS250 4.1 11.8 1.0 O15 B:K9K303 4.2 12.2 1.0 CB B:SER249 4.2 12.1 1.0 HE1 B:HIS189 4.2 12.4 1.0 HE1 B:HIS120 4.2 10.8 1.0 ZN B:ZN301 4.3 10.0 1.0 C12 B:K9K303 4.3 13.3 1.0 O20 B:K9K303 4.3 15.8 1.0 C26 B:K9K303 4.3 15.4 1.0 HE3 B:LYS125 4.3 20.7 1.0 CA B:CYS208 4.3 7.1 1.0 CE1 B:HIS189 4.4 10.3 1.0 NE2 B:HIS189 4.4 9.4 1.0 OG B:SER249 4.5 13.0 1.0 H9 B:K9K303 4.6 11.1 1.0 CB B:ASP124 4.6 9.3 1.0 C22 B:K9K303 4.6 13.6 1.0 HB2 B:ASP124 4.7 11.1 1.0 HB3 B:ASP124 4.8 11.1 1.0 HZ2 B:LYS211 4.8 19.0 1.0 HZ3 B:LYS211 4.9 19.0 1.0 HD1 B:HIS250 4.9 14.1 1.0 HZ1 B:LYS211 4.9 19.0 1.0 CE1 B:HIS120 4.9 9.0 1.0 HG2 B:LYS125 5.0 16.9 1.0

A.Krajnc, J.Brem, P.Hinchliffe, K.Calvopina, T.D.Panduwawala, P.A.Lang, J.J.A.G.Kamps, J.M.Tyrrell, E.Widlake, B.G.Saward, T.R.Walsh, J.Spencer, C.J.Schofield. Bicyclic Boronate Vnrx-5133 Inhibits Metallo- and Serine-Beta-Lactamases. J.Med.Chem. V. 62 8544 2019.
ISSN: ISSN 0022-2623
PubMed: 31454231
DOI: 10.1021/ACS.JMEDCHEM.9B00911