Zinc in PDB 5o7n: Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid

The structure of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid, PDB code: 5o7n was solved by D.Buettner, J.S.Kramer, D.Pogoryelov, E.Proschak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.51 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.989, 79.308, 67.645, 90.00, 130.45, 90.00
R / Rfree (%)	18.7 / 21.1

The binding sites of Zinc atom in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid (pdb code 5o7n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid, PDB code: 5o7n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:11.5 occ:0.95 ND1 A:HIS116 1.8 11.7 1.0 NE2 A:HIS179 2.0 8.3 1.0 NE2 A:HIS114 2.0 9.8 1.0 S01 A:9NK305 2.4 29.7 0.4 CE1 A:HIS116 2.7 17.8 1.0 CG A:HIS116 2.9 14.6 1.0 CE1 A:HIS179 2.9 13.9 1.0 CE1 A:HIS114 2.9 8.6 1.0 CD2 A:HIS179 3.0 11.5 1.0 CD2 A:HIS114 3.1 10.7 1.0 CB A:HIS116 3.3 13.8 1.0 NE2 A:HIS116 3.9 19.1 1.0 ZN A:ZN302 3.9 11.6 0.8 SG A:CYS198 3.9 21.6 0.2 CD2 A:HIS116 4.0 17.0 1.0 C04 A:9NK305 4.0 21.4 0.4 ND1 A:HIS179 4.0 12.0 1.0 ND1 A:HIS114 4.1 9.1 1.0 SG A:CYS198 4.1 14.9 0.8 OD1 A:ASP118 4.1 13.8 1.0 CG A:HIS179 4.1 10.2 1.0 CG A:HIS114 4.2 8.4 1.0 CB A:CYS198 4.2 8.6 0.8 C10 A:9NK305 4.2 27.0 0.4 C09 A:9NK305 4.2 27.0 0.4 CB A:CYS198 4.2 10.3 0.2 O03 A:9NK305 4.7 30.1 0.4 CA A:HIS116 4.8 11.2 1.0 OD2 A:ASP118 4.8 12.9 1.0 CG A:ASP118 4.9 13.7 1.0 O01 A:9NK305 5.0 28.1 0.4

Zinc binding site 2 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.6 occ:0.77 SG A:CYS198 1.9 21.6 0.2 OD2 A:ASP118 2.0 12.9 1.0 SG A:CYS198 2.1 14.9 0.8 NE2 A:HIS240 2.1 13.5 1.0 S01 A:9NK305 2.8 29.7 0.4 CE1 A:HIS240 3.0 18.2 1.0 CG A:ASP118 3.1 13.7 1.0 C04 A:9NK305 3.1 21.4 0.4 CD2 A:HIS240 3.1 14.1 1.0 CB A:CYS198 3.4 8.6 0.8 OD1 A:ASP118 3.5 13.8 1.0 NH2 A:ARG119 3.6 18.1 1.0 CB A:CYS198 3.7 10.3 0.2 ZN A:ZN301 3.9 11.5 0.9 NE A:ARG119 3.9 15.6 1.0 ND1 A:HIS240 4.1 14.6 1.0 CZ A:ARG119 4.2 20.7 1.0 CE1 A:HIS114 4.2 8.6 1.0 CG A:HIS240 4.2 14.5 1.0 C13 A:9NK305 4.2 22.8 0.4 C03 A:9NK305 4.3 23.6 0.4 CB A:ASP118 4.3 17.6 1.0 NE2 A:HIS114 4.5 9.8 1.0 O03 A:9NK305 4.5 30.1 0.4 C05 A:9NK305 4.6 27.2 0.4 CA A:CYS198 4.6 9.1 0.8 N01 A:9NK305 4.6 21.7 0.4 CA A:CYS198 4.7 9.4 0.2 O A:HOH482 4.7 18.6 1.0 NE2 A:HIS179 4.8 8.3 1.0 CE1 A:HIS179 5.0 13.9 1.0

Zinc binding site 3 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:8.5 occ:0.40 ND1 A:HIS251 2.0 7.8 1.0 O2 A:FMT306 2.2 17.7 0.4 O2 A:FMT307 2.3 23.4 0.4 O1 A:FMT307 2.3 21.2 0.4 O1 A:FMT306 2.5 24.2 0.4 C A:FMT307 2.6 6.9 0.4 C A:FMT306 2.7 0.0 0.4 CE1 A:HIS251 2.8 12.1 1.0 CG A:HIS251 3.2 11.4 1.0 CB A:HIS251 3.7 10.9 1.0 NE2 A:HIS251 4.0 11.1 1.0 CA A:HIS251 4.0 8.2 1.0 CD2 A:HIS251 4.2 10.0 1.0 O A:HIS251 4.4 11.0 1.0 C A:HIS251 4.7 10.2 1.0 ND2 A:ASN254 4.9 18.5 1.0 CG2 A:VAL255 4.9 11.1 1.0

Zinc binding site 4 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:7.4 occ:0.40 NE2 A:HIS153 1.9 9.9 1.0 O2 A:FMT308 2.0 18.4 0.4 O1 A:FMT309 2.3 17.8 0.4 O1 A:FMT308 2.5 19.6 0.4 C A:FMT308 2.6 0.0 0.4 O2 A:FMT309 2.7 26.3 0.4 C A:FMT309 2.8 6.7 0.4 CE1 A:HIS153 2.8 10.5 1.0 CD2 A:HIS153 3.0 10.7 1.0 ND1 A:HIS153 4.0 11.5 1.0 CG A:HIS153 4.1 9.0 1.0 CB A:ALA132 4.1 10.1 1.0 O A:HOH405 4.5 23.6 1.0 CG2 A:THR152 4.8 11.4 1.0 CA A:ALA132 4.9 7.5 1.0

Zinc binding site 5 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.4 occ:0.95 ND1 B:HIS116 1.8 11.8 1.0 NE2 B:HIS179 2.0 8.7 1.0 NE2 B:HIS114 2.0 9.7 1.0 S01 B:9NK305 2.3 13.7 0.8 CE1 B:HIS116 2.8 13.8 1.0 CG B:HIS116 2.9 14.1 1.0 CE1 B:HIS114 2.9 9.3 1.0 CE1 B:HIS179 3.0 12.4 1.0 CD2 B:HIS179 3.0 8.9 1.0 CD2 B:HIS114 3.1 10.4 1.0 C04 B:9NK305 3.3 26.8 0.8 CB B:HIS116 3.3 11.7 1.0 ZN B:ZN302 3.9 10.2 0.7 NE2 B:HIS116 3.9 16.9 1.0 SG B:CYS198 3.9 24.7 0.5 CD2 B:HIS116 4.0 16.6 1.0 ND1 B:HIS114 4.1 10.1 1.0 ND1 B:HIS179 4.1 13.8 1.0 OD1 B:ASP118 4.1 16.6 1.0 CG B:HIS179 4.1 8.8 1.0 CB B:CYS198 4.2 11.6 0.5 CG B:HIS114 4.2 9.1 1.0 CB B:CYS198 4.2 9.0 0.5 SG B:CYS198 4.5 7.0 0.5 O01 B:9NK305 4.5 26.1 0.8 C03 B:9NK305 4.7 30.3 0.8 CA B:HIS116 4.8 13.1 1.0 OD2 B:ASP118 4.8 15.9 1.0 C05 B:9NK305 4.8 29.3 0.8 CG B:ASP118 4.9 17.0 1.0

Zinc binding site 6 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:10.2 occ:0.70 SG B:CYS198 1.8 24.7 0.5 OD2 B:ASP118 2.0 15.9 1.0 NE2 B:HIS240 2.1 12.3 1.0 SG B:CYS198 2.3 7.0 0.5 S01 B:9NK305 2.3 13.7 0.8 CG B:ASP118 3.0 17.0 1.0 CE1 B:HIS240 3.0 15.4 1.0 CD2 B:HIS240 3.2 12.9 1.0 CB B:CYS198 3.4 9.0 0.5 C04 B:9NK305 3.4 26.8 0.8 OD1 B:ASP118 3.4 16.6 1.0 CB B:CYS198 3.5 11.6 0.5 NH2 B:ARG119 3.7 18.0 1.0 NE B:ARG119 3.8 15.6 1.0 ZN B:ZN301 3.9 11.4 0.9 C03 B:9NK305 3.9 30.3 0.8 CZ B:ARG119 4.1 18.3 1.0 ND1 B:HIS240 4.2 13.0 1.0 CE1 B:HIS114 4.2 9.3 1.0 CG B:HIS240 4.3 12.1 1.0 CB B:ASP118 4.3 16.7 1.0 O02 B:9NK305 4.3 29.8 0.8 C05 B:9NK305 4.4 29.3 0.8 C13 B:9NK305 4.4 27.4 0.8 NE2 B:HIS114 4.5 9.7 1.0 CA B:CYS198 4.6 9.6 0.5 CA B:CYS198 4.6 9.6 0.5 N01 B:9NK305 4.6 26.4 0.8 O B:HOH428 4.7 18.9 1.0 NE2 B:HIS179 4.8 8.7 1.0 CD B:ARG119 4.9 13.5 1.0 N B:CYS198 5.0 10.3 0.5

Zinc binding site 7 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:9.4 occ:0.40 NE2 B:HIS153 1.9 9.4 1.0 O1 B:FMT306 2.0 29.5 0.4 O1 B:FMT307 2.1 25.9 0.4 O2 B:FMT306 2.1 13.3 0.4 O2 B:FMT307 2.2 28.6 0.4 C B:FMT306 2.4 0.0 0.4 C B:FMT307 2.4 1.5 0.4 CE1 B:HIS153 2.7 11.2 1.0 CD2 B:HIS153 3.1 11.1 1.0 ND1 B:HIS153 3.9 15.1 1.0 CB B:ALA132 4.0 11.0 1.0 CG B:HIS153 4.1 14.2 1.0 O B:HOH427 4.6 20.6 1.0 CA B:ALA132 4.9 7.3 1.0

Zinc binding site 8 out of 8 in the Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Beta-Lactamase Vim-2 in Complex with (2R)-1-(2-Benzyl-3- Mercaptopropanoyl)Piperidine-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:8.0 occ:0.40 ND1 B:HIS251 2.0 5.8 1.0 O1 B:FMT309 2.0 19.8 0.4 O2 B:FMT309 2.1 18.2 0.4 O1 B:FMT308 2.2 28.4 0.4 C B:FMT309 2.4 0.0 0.4 O2 B:FMT308 2.6 13.1 0.4 C B:FMT308 2.7 3.3 0.4 CE1 B:HIS251 2.8 8.6 1.0 CG B:HIS251 3.2 10.0 1.0 CB B:HIS251 3.7 7.7 1.0 NE2 B:HIS251 4.0 11.2 1.0 CA B:HIS251 4.1 6.9 1.0 CD2 B:HIS251 4.2 11.4 1.0 O B:HIS251 4.5 10.4 1.0 C B:HIS251 4.7 9.6 1.0 CD2 B:LEU203 4.8 12.7 1.0 O B:LEU203 4.9 12.8 1.0 CG2 B:THR206 4.9 15.0 1.0 CG2 B:VAL255 4.9 9.9 1.0

D.Buttner, J.S.Kramer, F.M.Klingler, S.K.Wittmann, M.R.Hartmann, C.G.Kurz, D.Kohnhauser, L.Weizel, A.Bruggerhoff, D.Frank, D.Steinhilber, T.A.Wichelhaus, D.Pogoryelov, E.Proschak. Challenges in the Development of A Thiol-Based Broad-Spectrum Inhibitor For Metallo-Beta-Lactamases. Acs Infect Dis. V. 4 360 2018.
ISSN: ESSN 2373-8227
PubMed: 29172434
DOI: 10.1021/ACSINFECDIS.7B00129