Zinc in PDB 7afx: Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139, PDB code: 7afx was solved by J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.14 / 1.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.251, 79.066, 67.951, 90, 130.37, 90
R / Rfree (%)	16.1 / 18.1

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 (pdb code 7afx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139, PDB code: 7afx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139


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 the Metallo-Beta-Lactamase VIM2 with 139 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.2 occ:1.00 O A:HOH444 1.9 10.6 1.0 NE2 A:HIS114 2.1 12.7 1.0 NE2 A:HIS179 2.1 12.9 1.0 ND1 A:HIS116 2.1 14.3 1.0 CE1 A:HIS114 2.9 12.1 1.0 HB2 A:HIS116 2.9 12.2 1.0 CE1 A:HIS116 3.0 12.6 1.0 CD2 A:HIS179 3.0 11.2 1.0 CE1 A:HIS179 3.0 12.2 1.0 HE1 A:HIS114 3.1 14.7 1.0 CG A:HIS116 3.1 13.2 1.0 CD2 A:HIS114 3.1 12.3 1.0 HE1 A:HIS116 3.2 15.2 1.0 HD2 A:HIS179 3.2 13.5 1.0 HE1 A:HIS179 3.3 14.8 1.0 HD2 A:HIS114 3.3 14.8 1.0 CB A:HIS116 3.4 10.6 1.0 ZN A:ZN302 3.5 11.6 1.0 H081 A:R9K304 3.5 14.4 1.0 HB3 A:HIS116 3.7 12.2 1.0 OD1 A:ASN210 3.8 23.8 0.6 HB2 A:CYS198 3.8 13.3 1.0 H011 A:R9K304 3.9 15.9 1.0 OD1 A:ASP118 3.9 10.7 1.0 HB3 A:CYS198 4.0 13.3 1.0 O20 A:R9K304 4.0 10.7 1.0 ND1 A:HIS114 4.1 12.3 1.0 NE2 A:HIS116 4.1 13.7 1.0 ND1 A:HIS179 4.1 12.2 1.0 CG A:HIS179 4.2 10.9 1.0 CB A:CYS198 4.2 11.0 1.0 CG A:HIS114 4.2 11.7 1.0 CD2 A:HIS116 4.2 13.2 1.0 SG A:CYS198 4.3 11.0 1.0 OD1 A:ASN210 4.4 20.6 0.4 N08 A:R9K304 4.4 11.9 1.0 H A:HIS116 4.5 12.0 1.0 OD2 A:ASP118 4.5 11.7 1.0 CG A:ASP118 4.7 11.7 1.0 HG2 A:ARG119 4.8 12.3 1.0 HE A:ARG119 4.8 16.3 1.0 HD1 A:HIS114 4.8 14.9 1.0 CA A:HIS116 4.8 10.5 1.0 HB3 A:SER180 4.8 15.3 1.0 C18 A:R9K304 4.9 11.5 1.0 C01 A:R9K304 4.9 13.2 1.0 HE2 A:HIS116 4.9 16.5 1.0 HD1 A:HIS179 4.9 14.7 1.0 CG A:ASN210 5.0 21.2 0.6 HG3 A:ARG119 5.0 12.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139


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 the Metallo-Beta-Lactamase VIM2 with 139 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.6 occ:1.00 O A:HOH444 2.1 10.6 1.0 NE2 A:HIS240 2.1 12.6 1.0 O20 A:R9K304 2.2 10.7 1.0 SG A:CYS198 2.3 11.0 1.0 OD2 A:ASP118 2.4 11.7 1.0 H081 A:R9K304 2.9 14.4 1.0 CD2 A:HIS240 3.0 11.3 1.0 HB3 A:CYS198 3.1 13.3 1.0 HH21 A:ARG119 3.1 19.0 1.0 C18 A:R9K304 3.1 11.5 1.0 HD2 A:HIS240 3.1 13.7 1.0 CE1 A:HIS240 3.2 11.4 1.0 CB A:CYS198 3.3 11.0 1.0 N08 A:R9K304 3.4 11.9 1.0 CG A:ASP118 3.4 11.7 1.0 HE1 A:HIS240 3.4 13.8 1.0 ZN A:ZN301 3.5 11.2 1.0 C09 A:R9K304 3.5 11.2 1.0 HE A:ARG119 3.5 16.3 1.0 HE1 A:HIS114 3.5 14.7 1.0 OD1 A:ASP118 3.7 10.7 1.0 HB2 A:CYS198 3.8 13.3 1.0 NH2 A:ARG119 3.9 15.8 1.0 NE2 A:HIS179 4.2 12.9 1.0 NE A:ARG119 4.2 13.5 1.0 CG A:HIS240 4.2 10.7 1.0 CE1 A:HIS114 4.2 12.1 1.0 O19 A:R9K304 4.2 11.8 1.0 ND1 A:HIS240 4.3 11.5 1.0 HE1 A:HIS179 4.3 14.8 1.0 O A:HOH487 4.3 11.7 1.0 H011 A:R9K304 4.4 15.9 1.0 CE1 A:HIS179 4.4 12.2 1.0 NE2 A:HIS114 4.4 12.7 1.0 HH22 A:ARG119 4.4 19.0 1.0 HA A:CYS198 4.4 13.4 1.0 C07 A:R9K304 4.5 12.2 1.0 CZ A:ARG119 4.5 15.9 1.0 CA A:CYS198 4.5 11.1 1.0 HA3 A:GLY239 4.5 13.4 1.0 CB A:ASP118 4.7 12.2 1.0 C10 A:R9K304 4.7 11.4 1.0 HB2 A:ASP118 4.7 14.8 1.0 H171 A:R9K304 4.8 15.5 1.0 HB3 A:ASP118 4.9 14.8 1.0 HG2 A:ARG119 4.9 12.3 1.0 OD1 A:ASN210 5.0 23.8 0.6

Zinc binding site 3 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139


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 the Metallo-Beta-Lactamase VIM2 with 139 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.1 occ:1.00 O1 A:FMT306 1.8 13.6 1.0 O2 A:FMT305 1.9 17.0 1.0 ND1 A:HIS251 2.1 15.9 1.0 C A:FMT306 2.6 15.7 1.0 O2 A:FMT306 2.7 15.0 1.0 C A:FMT305 2.8 19.1 1.0 CE1 A:HIS251 3.0 14.8 1.0 HA A:HIS251 3.1 13.3 1.0 CG A:HIS251 3.1 12.0 1.0 HB2 A:HIS251 3.1 13.7 1.0 O1 A:FMT305 3.1 19.2 1.0 HE1 A:HIS251 3.2 17.8 1.0 CB A:HIS251 3.5 11.9 1.0 H A:FMT306 3.6 18.9 1.0 HD22 A:ASN254 3.7 20.7 1.0 HD22 A:LEU203 3.8 16.5 1.0 CA A:HIS251 3.8 11.5 1.0 H A:FMT305 3.8 23.0 1.0 NE2 A:HIS251 4.1 12.5 1.0 CD2 A:HIS251 4.2 12.8 1.0 HD23 A:LEU203 4.3 16.5 1.0 HB3 A:HIS251 4.4 13.7 1.0 CD2 A:LEU203 4.5 13.7 1.0 HB2 A:ASN254 4.5 15.9 1.0 ND2 A:ASN254 4.5 17.2 1.0 O A:HIS251 4.6 12.1 1.0 HA A:LEU203 4.6 14.4 1.0 C A:HIS251 4.6 12.6 1.0 HG23 A:VAL255 4.8 17.3 1.0 N A:HIS251 4.8 11.7 1.0 HD21 A:ASN254 4.9 20.7 1.0 HD21 A:LEU203 4.9 16.5 1.0 HE2 A:HIS251 4.9 14.5 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139


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 the Metallo-Beta-Lactamase VIM2 with 139 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.6 occ:1.00 O B:HOH457 2.0 10.6 1.0 NE2 B:HIS240 2.2 14.8 1.0 O19 B:R9K304 2.2 12.9 1.0 SG B:CYS198 2.3 10.3 1.0 OD2 B:ASP118 2.3 11.6 1.0 H081 B:R9K304 2.9 17.4 1.0 CD2 B:HIS240 3.1 13.4 1.0 HB3 B:CYS198 3.1 13.6 1.0 C18 B:R9K304 3.2 13.8 1.0 HH21 B:ARG119 3.2 18.8 1.0 CE1 B:HIS240 3.2 13.7 1.0 HD2 B:HIS240 3.2 16.2 1.0 CB B:CYS198 3.3 11.3 1.0 N08 B:R9K304 3.3 14.4 1.0 CG B:ASP118 3.3 11.4 1.0 HE1 B:HIS240 3.4 16.6 1.0 ZN B:ZN302 3.5 12.1 1.0 C09 B:R9K304 3.5 14.4 1.0 HE B:ARG119 3.6 15.5 1.0 HE1 B:HIS114 3.6 13.3 1.0 OD1 B:ASP118 3.7 10.8 1.0 HB2 B:CYS198 3.8 13.6 1.0 NH2 B:ARG119 3.9 15.5 1.0 NE2 B:HIS179 4.2 12.6 1.0 NE B:ARG119 4.2 12.8 1.0 CG B:HIS240 4.2 12.8 1.0 O20 B:R9K304 4.3 13.8 1.0 H011 B:R9K304 4.3 19.9 1.0 O B:HOH473 4.3 11.7 1.0 ND1 B:HIS240 4.3 13.5 1.0 CE1 B:HIS114 4.3 11.0 1.0 HE1 B:HIS179 4.3 13.3 1.0 CE1 B:HIS179 4.4 11.0 1.0 C07 B:R9K304 4.4 15.7 1.0 HA B:CYS198 4.4 14.1 1.0 NE2 B:HIS114 4.4 12.5 1.0 HH22 B:ARG119 4.4 18.8 1.0 CZ B:ARG119 4.5 15.5 1.0 CA B:CYS198 4.5 11.7 1.0 HA3 B:GLY239 4.6 12.3 1.0 CB B:ASP118 4.6 11.9 1.0 C10 B:R9K304 4.7 15.1 1.0 HB2 B:ASP118 4.7 14.4 1.0 H171 B:R9K304 4.8 16.3 1.0 HB3 B:ASP118 4.9 14.4 1.0 OD1 B:ASN210 5.0 22.9 0.5 HG2 B:ARG119 5.0 13.9 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.1 occ:1.00 O B:HOH457 1.9 10.6 1.0 NE2 B:HIS179 2.0 12.6 1.0 ND1 B:HIS116 2.1 15.9 1.0 NE2 B:HIS114 2.1 12.5 1.0 HB2 B:HIS116 2.9 11.1 1.0 CD2 B:HIS179 3.0 10.1 1.0 CE1 B:HIS114 3.0 11.0 1.0 CE1 B:HIS116 3.0 15.5 1.0 CE1 B:HIS179 3.1 11.0 1.0 CG B:HIS116 3.1 15.1 1.0 HE1 B:HIS114 3.1 13.3 1.0 HD2 B:HIS179 3.1 12.2 1.0 CD2 B:HIS114 3.1 11.3 1.0 HE1 B:HIS116 3.2 18.6 1.0 HE1 B:HIS179 3.3 13.3 1.0 HD2 B:HIS114 3.4 13.7 1.0 CB B:HIS116 3.4 9.7 1.0 ZN B:ZN301 3.5 11.6 1.0 H081 B:R9K304 3.5 17.4 1.0 HB3 B:HIS116 3.7 11.1 1.0 OD1 B:ASN210 3.7 22.9 0.5 HB2 B:CYS198 3.8 13.6 1.0 HB3 B:CYS198 3.9 13.6 1.0 H011 B:R9K304 3.9 19.9 1.0 OD1 B:ASP118 4.0 10.8 1.0 O19 B:R9K304 4.0 12.9 1.0 ND1 B:HIS114 4.1 10.7 1.0 CG B:HIS179 4.1 10.3 1.0 NE2 B:HIS116 4.1 16.1 1.0 ND1 B:HIS179 4.1 11.0 1.0 CB B:CYS198 4.1 11.3 1.0 CD2 B:HIS116 4.2 15.6 1.0 SG B:CYS198 4.2 10.3 1.0 CG B:HIS114 4.2 9.5 1.0 OD1 B:ASN210 4.4 23.1 0.5 N08 B:R9K304 4.4 14.4 1.0 OD2 B:ASP118 4.5 11.6 1.0 H B:HIS116 4.5 10.4 1.0 CG B:ASP118 4.7 11.4 1.0 HG2 B:ARG119 4.7 13.9 1.0 CA B:HIS116 4.8 10.3 1.0 HE B:ARG119 4.8 15.5 1.0 HB3 B:SER180 4.9 15.7 1.0 HD1 B:HIS114 4.9 13.0 1.0 C18 B:R9K304 4.9 13.8 1.0 C01 B:R9K304 4.9 16.5 1.0 HE2 B:HIS116 4.9 19.4 1.0 HD1 B:HIS179 4.9 13.3 1.0 CG B:ASN210 4.9 22.8 0.5 HG3 B:ARG119 4.9 13.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:13.0 occ:1.00 O1 B:FMT305 1.8 15.6 1.0 O2 B:FMT306 1.9 14.5 1.0 ND1 B:HIS251 2.0 15.6 1.0 C B:FMT306 2.6 15.9 1.0 O1 B:FMT306 2.7 16.3 1.0 C B:FMT305 2.8 17.7 1.0 CE1 B:HIS251 3.0 13.7 1.0 CG B:HIS251 3.1 13.6 1.0 HA B:HIS251 3.1 13.5 1.0 HE1 B:HIS251 3.1 16.5 1.0 HB2 B:HIS251 3.1 13.8 1.0 O2 B:FMT305 3.1 17.2 1.0 CB B:HIS251 3.5 11.9 1.0 HD22 B:ASN254 3.6 21.7 1.0 H B:FMT306 3.6 19.1 1.0 H B:FMT305 3.7 21.4 1.0 CA B:HIS251 3.8 11.7 1.0 HD22 B:LEU203 3.9 17.3 1.0 NE2 B:HIS251 4.1 12.1 1.0 CD2 B:HIS251 4.2 11.7 1.0 HB3 B:HIS251 4.4 13.8 1.0 HB2 B:ASN254 4.4 17.3 1.0 ND2 B:ASN254 4.4 18.0 1.0 HD23 B:LEU203 4.5 17.3 1.0 O B:HIS251 4.5 11.5 1.0 C B:HIS251 4.6 11.6 1.0 CD2 B:LEU203 4.6 14.3 1.0 HA B:LEU203 4.8 15.7 1.0 HG23 B:VAL255 4.8 16.4 1.0 HD21 B:ASN254 4.8 21.7 1.0 N B:HIS251 4.8 12.4 1.0 HE2 B:HIS251 4.9 14.0 1.0 HG22 B:THR206 4.9 34.0 1.0

J.Brem, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM2 with 139 To Be Published.