Zinc in PDB 5iqk: RM3 Metallo-Beta-Lactamase

All present enzymatic activity of RM3 Metallo-Beta-Lactamase:
3.5.2.6;

The structure of RM3 Metallo-Beta-Lactamase, PDB code: 5iqk was solved by R.Salimraj, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.32 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.880, 74.450, 77.460, 90.00, 99.48, 90.00
R / Rfree (%)	20.3 / 22.9

The binding sites of Zinc atom in the RM3 Metallo-Beta-Lactamase (pdb code 5iqk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the RM3 Metallo-Beta-Lactamase, PDB code: 5iqk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:17.4 occ:1.00 O A:HOH613 1.9 20.8 1.0 NE2 A:HIS186 2.0 21.8 1.0 ND1 A:HIS110 2.1 16.7 1.0 NE2 A:HIS108 2.1 13.7 1.0 O A:HOH521 2.6 32.3 1.0 CD2 A:HIS186 2.9 16.9 1.0 CE1 A:HIS110 3.0 14.7 1.0 CD2 A:HIS108 3.0 15.7 1.0 CE1 A:HIS108 3.1 19.9 1.0 CG A:HIS110 3.1 14.3 1.0 CE1 A:HIS186 3.1 18.4 1.0 ZN A:ZN402 3.5 18.1 1.0 CB A:HIS110 3.5 15.9 1.0 O A:HOH624 3.8 16.0 1.0 NE2 A:HIS110 4.1 16.0 1.0 CG A:HIS186 4.1 16.7 1.0 ND1 A:HIS108 4.2 18.6 1.0 CG A:HIS108 4.2 18.6 1.0 CD2 A:HIS113 4.2 16.7 1.0 ND1 A:HIS186 4.2 18.9 1.0 CD2 A:HIS110 4.2 16.1 1.0 OD1 A:ASP112 4.2 17.8 1.0 NE2 A:HIS113 4.2 17.5 1.0 OE1 A:GLN149 4.5 17.9 1.0 CG2 A:THR187 4.6 16.3 1.0 OG A:SER211 4.6 23.1 1.0 OD2 A:ASP112 4.7 16.7 1.0 O A:HOH535 4.8 29.2 1.0 CB A:SER211 4.8 19.5 1.0 CA A:HIS110 4.9 13.3 1.0 CG A:ASP112 4.9 20.5 1.0 O A:HOH630 5.0 26.2 1.0 O A:HOH575 5.0 14.5 1.0

Zinc binding site 2 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:18.1 occ:1.00 OD2 A:ASP112 2.0 16.7 1.0 NE2 A:HIS113 2.0 17.5 1.0 NE2 A:HIS254 2.0 18.9 1.0 O A:HOH613 2.1 20.8 1.0 O A:HOH521 2.4 32.3 1.0 CD2 A:HIS113 2.9 16.7 1.0 CG A:ASP112 2.9 20.5 1.0 CD2 A:HIS254 3.0 18.6 1.0 CE1 A:HIS254 3.0 17.4 1.0 CE1 A:HIS113 3.1 22.4 1.0 OD1 A:ASP112 3.3 17.8 1.0 ZN A:ZN401 3.5 17.4 1.0 CG A:HIS113 4.0 19.9 1.0 NE2 A:HIS108 4.1 13.7 1.0 ND1 A:HIS113 4.1 20.9 1.0 CE1 A:HIS108 4.1 19.9 1.0 ND1 A:HIS254 4.1 23.0 1.0 O A:HOH535 4.1 29.2 1.0 CG A:HIS254 4.1 22.6 1.0 OG A:SER211 4.2 23.1 1.0 O A:HOH624 4.2 16.0 1.0 CB A:ASP112 4.3 19.6 1.0 O A:HOH630 4.3 26.2 1.0 CD2 A:LEU62 4.6 20.4 1.0 NE2 A:HIS186 4.8 21.8 1.0 CZ3 A:TRP41 4.9 17.7 1.0

Zinc binding site 3 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:21.3 occ:0.96 ND1 B:HIS151 2.1 18.5 1.0 O B:HOH621 2.1 23.5 1.0 SG A:CYS38 2.3 21.6 1.0 SG A:CYS35 2.3 20.6 1.0 CE1 B:HIS151 3.0 26.8 1.0 CB A:CYS35 3.2 24.5 1.0 CG B:HIS151 3.2 18.8 1.0 CB A:CYS38 3.3 17.1 1.0 CB B:HIS151 3.6 19.2 1.0 O A:HOH653 3.6 26.3 1.0 O B:HOH553 3.7 25.3 1.0 N A:CYS38 3.9 16.7 1.0 O B:HOH626 3.9 26.3 1.0 NE2 B:HIS151 4.1 24.0 1.0 CA A:CYS38 4.1 19.9 1.0 CD2 B:HIS151 4.3 20.6 1.0 NE B:ARG217 4.5 17.6 1.0 CA A:CYS35 4.6 25.9 1.0 O A:HOH513 4.7 28.8 1.0 O A:HOH654 4.9 27.6 1.0 CB A:VAL37 4.9 18.7 1.0 C A:VAL37 4.9 18.9 1.0

Zinc binding site 4 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:20.7 occ:0.97 O A:HOH628 2.1 20.8 1.0 ND1 A:HIS151 2.2 21.9 1.0 SG B:CYS35 2.3 20.6 1.0 SG B:CYS38 2.3 21.9 1.0 CE1 A:HIS151 3.1 27.3 1.0 CB B:CYS35 3.2 23.6 1.0 CG A:HIS151 3.3 22.0 1.0 CB B:CYS38 3.3 21.4 1.0 O A:HOH567 3.6 22.3 1.0 CB A:HIS151 3.7 21.4 1.0 N B:CYS38 3.8 18.9 1.0 O A:HOH637 3.9 23.2 1.0 CA B:CYS38 4.2 21.4 1.0 NE2 A:HIS151 4.3 23.1 1.0 CD2 A:HIS151 4.4 23.9 1.0 NE A:ARG217 4.5 16.6 1.0 O B:HOH502 4.5 23.2 1.0 CA B:CYS35 4.6 23.7 1.0 CB B:VAL37 4.8 18.4 1.0 C B:VAL37 4.9 20.4 1.0

Zinc binding site 5 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:20.0 occ:0.78 SG B:CYS203 2.3 23.3 1.0 SG B:CYS198 2.3 23.9 1.0 CB B:CYS198 3.0 21.2 1.0 N B:CYS203 3.4 18.6 1.0 CB B:CYS203 3.4 22.8 1.0 CA B:CYS203 3.7 21.9 1.0 C B:ARG202 3.8 21.6 1.0 CA B:CYS198 4.1 22.6 1.0 O B:HOH597 4.2 33.9 1.0 O B:ARG202 4.3 22.1 1.0 CA B:ARG202 4.5 23.7 1.0 O B:HOH636 4.6 31.4 1.0 O B:GLY200 4.7 25.7 1.0 N B:ARG202 4.9 25.5 1.0

Zinc binding site 6 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:19.6 occ:1.00 O B:HOH619 1.8 21.6 1.0 ND1 B:HIS110 2.0 19.1 1.0 NE2 B:HIS186 2.0 19.9 1.0 NE2 B:HIS108 2.2 16.7 1.0 O B:HOH569 2.7 33.2 1.0 CE1 B:HIS110 2.9 14.8 1.0 CD2 B:HIS186 2.9 16.2 1.0 CD2 B:HIS108 3.1 16.9 1.0 CG B:HIS110 3.1 17.5 1.0 CE1 B:HIS186 3.1 18.6 1.0 CE1 B:HIS108 3.2 21.1 1.0 CB B:HIS110 3.5 17.8 1.0 ZN B:ZN403 3.5 18.5 1.0 O B:HOH616 3.7 14.1 1.0 NE2 B:HIS110 4.1 17.1 1.0 CG B:HIS186 4.1 18.5 1.0 ND1 B:HIS186 4.1 19.5 1.0 CD2 B:HIS110 4.1 15.8 1.0 CD2 B:HIS113 4.2 17.5 1.0 CG B:HIS108 4.2 19.0 1.0 ND1 B:HIS108 4.2 18.4 1.0 OD1 B:ASP112 4.2 18.4 1.0 NE2 B:HIS113 4.3 18.9 1.0 OE1 B:GLN149 4.4 20.5 1.0 OG B:SER211 4.6 21.6 1.0 O B:HOH552 4.7 29.1 1.0 CB B:SER211 4.8 21.1 1.0 CG2 B:THR187 4.8 18.8 1.0 OD2 B:ASP112 4.8 15.4 1.0 CA B:HIS110 4.9 17.9 1.0 CG B:ASP112 5.0 16.7 1.0

Zinc binding site 7 out of 7 in the RM3 Metallo-Beta-Lactamase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of RM3 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.5 occ:1.00 OD2 B:ASP112 2.0 15.4 1.0 NE2 B:HIS254 2.0 18.4 1.0 O B:HOH619 2.0 21.6 1.0 NE2 B:HIS113 2.0 18.9 1.0 O B:HOH569 2.2 33.2 1.0 CD2 B:HIS113 2.9 17.5 1.0 CG B:ASP112 2.9 16.7 1.0 CE1 B:HIS254 3.0 20.8 1.0 CD2 B:HIS254 3.0 20.2 1.0 CE1 B:HIS113 3.1 18.7 1.0 OD1 B:ASP112 3.2 18.4 1.0 ZN B:ZN402 3.5 19.6 1.0 O B:HOH552 4.0 29.1 1.0 CG B:HIS113 4.0 19.8 1.0 NE2 B:HIS108 4.1 16.7 1.0 ND1 B:HIS254 4.1 19.2 1.0 ND1 B:HIS113 4.1 21.2 1.0 CG B:HIS254 4.1 20.4 1.0 CE1 B:HIS108 4.2 21.1 1.0 OG B:SER211 4.2 21.6 1.0 O B:HOH616 4.2 14.1 1.0 CB B:ASP112 4.3 16.6 1.0 CD2 B:LEU62 4.6 18.0 1.0 O B:HOH618 4.7 23.8 1.0 CZ3 B:TRP41 4.7 23.5 1.0 NE2 B:HIS186 4.8 19.9 1.0 CH2 B:TRP41 4.9 21.5 1.0

R.Salimraj, L.Zhang, P.Hinchliffe, E.M.Wellington, J.Brem, C.J.Schofield, W.H.Gaze, J.Spencer. Structural and Biochemical Characterization of RM3, A Subclass B3 Metallo-Beta-Lactamase Identified From A Functional Metagenomic Study. Antimicrob.Agents Chemother. V. 60 5828 2016.
ISSN: ESSN 1098-6596
PubMed: 27431213
DOI: 10.1128/AAC.00750-16