Zinc in PDB 6rpn: Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.

The structure of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308., PDB code: 6rpn was solved by A.Parkova, A.Lucic, J.Brem, M.A.Mcdonough, G.W.Langley, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.34 / 1.41
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.081, 79.155, 67.746, 90.00, 130.03, 90.00
R / Rfree (%)	12.9 / 15.6

The structure of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. (pdb code 6rpn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308., PDB code: 6rpn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:11.1 occ:1.00 NE2 A:HIS153 2.0 12.0 1.0 CL A:CL306 2.2 14.3 1.0 CE1 A:HIS153 2.9 10.6 1.0 CD2 A:HIS153 3.1 9.9 1.0 ND1 A:HIS153 4.1 9.9 1.0 CG A:HIS153 4.2 10.5 1.0 CB A:ALA132 4.3 10.1 1.0 O A:HOH698 4.7 17.7 1.0 O A:HOH440 4.8 16.9 1.0

Zinc binding site 2 out of 6 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:9.6 occ:1.00 O01 A:KDZ301 1.9 7.7 0.5 NE2 A:HIS179 2.0 8.6 1.0 ND1 A:HIS116 2.0 7.9 1.0 NE2 A:HIS114 2.1 7.8 1.0 O03 A:KL8302 2.1 16.4 0.5 O01 A:KL8302 2.5 8.8 0.5 O03 A:KDZ301 2.8 11.4 0.5 B02 A:KDZ301 3.0 9.1 0.5 CD2 A:HIS179 3.0 7.4 1.0 CE1 A:HIS179 3.0 7.4 1.0 CE1 A:HIS116 3.0 8.6 1.0 CE1 A:HIS114 3.0 10.9 1.0 CG A:HIS116 3.0 7.2 1.0 B02 A:KL8302 3.0 27.1 0.5 CD2 A:HIS114 3.1 7.0 1.0 CB A:HIS116 3.3 7.5 1.0 O23 A:KDZ301 3.7 8.9 0.5 O23 A:KL8302 3.8 9.9 0.5 OD1 A:ASP118 4.1 8.9 1.0 ND1 A:HIS179 4.1 6.9 1.0 C04 A:KDZ301 4.1 8.4 0.5 NE2 A:HIS116 4.1 10.2 1.0 CG A:HIS179 4.1 6.7 1.0 ND1 A:HIS114 4.1 6.4 1.0 CD2 A:HIS116 4.1 8.9 1.0 CG A:HIS114 4.2 7.1 1.0 C04 A:KL8302 4.2 42.9 0.5 ZN A:ZN305 4.3 11.5 1.0 CB A:CYS198 4.4 5.7 1.0 SG A:CYS198 4.5 8.5 1.0 S05 A:KL8302 4.5 42.7 0.5 C06 A:KDZ301 4.6 10.9 0.5 O18 A:KDZ301 4.7 6.0 0.5 CA A:HIS116 4.7 6.4 1.0 O A:HOH533 4.8 18.4 0.5 O A:HOH533 4.8 10.7 0.5 OD2 A:ASP118 4.9 9.2 1.0 CG A:ASP118 4.9 8.9 1.0 O18 A:KL8302 4.9 21.3 0.5 C15 A:KDZ301 4.9 7.9 0.5 S05 A:KDZ301 5.0 9.0 0.5 N A:HIS116 5.0 6.2 1.0

Zinc binding site 3 out of 6 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:11.5 occ:1.00 O23 A:KL8302 1.9 9.9 0.5 NE2 A:HIS240 2.0 9.1 1.0 O23 A:KDZ301 2.1 8.9 0.5 O18 A:KDZ301 2.2 6.0 0.5 O18 A:KL8302 2.3 21.3 0.5 SG A:CYS198 2.3 8.5 1.0 OD2 A:ASP118 2.3 9.2 1.0 C15 A:KL8302 2.9 8.9 0.5 B02 A:KL8302 2.9 27.1 0.5 CD2 A:HIS240 3.0 8.8 1.0 CE1 A:HIS240 3.0 8.8 1.0 C15 A:KDZ301 3.0 7.9 0.5 O03 A:KL8302 3.1 16.4 0.5 O01 A:KDZ301 3.1 7.7 0.5 C17 A:KL8302 3.2 30.1 0.5 C17 A:KDZ301 3.2 6.7 0.5 B02 A:KDZ301 3.2 9.1 0.5 CG A:ASP118 3.4 8.9 1.0 C16 A:KL8302 3.4 11.7 0.5 CB A:CYS198 3.4 5.7 1.0 C16 A:KDZ301 3.5 7.4 0.5 OD1 A:ASP118 3.8 8.9 1.0 O01 A:KL8302 3.8 8.8 0.5 C14 A:KL8302 4.0 16.0 0.5 NH2 A:ARG119 4.0 10.7 1.0 C14 A:KDZ301 4.1 7.7 0.5 ND1 A:HIS240 4.1 7.6 1.0 CG A:HIS240 4.1 7.2 1.0 C04 A:KL8302 4.2 42.9 0.5 O03 A:KDZ301 4.2 11.4 0.5 C13 A:KL8302 4.2 25.1 0.5 O A:HOH409 4.2 8.5 1.0 ZN A:ZN304 4.3 9.6 1.0 O19 A:KDZ301 4.3 6.9 0.5 O19 A:KL8302 4.4 21.5 0.5 C04 A:KDZ301 4.4 8.4 0.5 CE1 A:HIS179 4.4 7.4 1.0 C13 A:KDZ301 4.4 8.1 0.5 CA A:CYS198 4.5 6.7 1.0 NE A:ARG119 4.5 8.1 1.0 NE2 A:HIS179 4.5 8.6 1.0 CB A:ASP118 4.6 7.9 1.0 C20 A:KL8302 4.7 21.2 0.5 CZ A:ARG119 4.7 6.9 1.0 C20 A:KDZ301 4.7 6.9 0.5 CE1 A:HIS114 4.8 10.9 1.0

Zinc binding site 4 out of 6 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:10.4 occ:1.00 O01 B:KDZ501 1.9 3.3 0.5 ND1 B:HIS116 2.0 8.6 1.0 NE2 B:HIS179 2.0 6.6 1.0 NE2 B:HIS114 2.1 6.9 1.0 O01 B:KL8502 2.2 27.8 0.5 O03 B:KL8502 2.5 8.5 0.5 CE1 B:HIS116 3.0 8.2 1.0 CG B:HIS116 3.0 8.6 1.0 CE1 B:HIS179 3.0 7.9 1.0 B02 B:KDZ501 3.0 11.8 0.5 CD2 B:HIS179 3.0 5.6 1.0 CE1 B:HIS114 3.0 5.8 1.0 O03 B:KDZ501 3.0 10.6 0.5 B02 B:KL8502 3.0 24.9 0.5 CD2 B:HIS114 3.1 6.6 1.0 CB B:HIS116 3.3 6.4 1.0 O23 B:KDZ501 3.6 34.0 0.5 O23 B:KL8502 3.7 4.2 0.5 OD1 B:ASP118 4.1 9.6 1.0 NE2 B:HIS116 4.1 10.4 1.0 ND1 B:HIS179 4.1 8.5 1.0 CD2 B:HIS116 4.1 10.3 1.0 ND1 B:HIS114 4.1 7.8 1.0 CG B:HIS179 4.1 7.1 1.0 C04 B:KDZ501 4.1 9.1 0.5 CG B:HIS114 4.2 8.1 1.0 C04 B:KL8502 4.2 45.2 0.5 ZN B:ZN505 4.2 11.5 1.0 CB B:CYS198 4.5 7.4 1.0 SG B:CYS198 4.5 8.4 1.0 C06 B:KDZ501 4.5 38.5 0.5 S05 B:KL8502 4.6 16.2 0.5 CA B:HIS116 4.7 7.5 1.0 O19 B:KDZ501 4.7 8.1 0.5 S05 B:KDZ501 4.8 22.6 0.5 OD2 B:ASP118 4.8 9.5 1.0 O B:HOH737 4.9 13.0 1.0 CG B:ASP118 4.9 9.2 1.0 O19 B:KL8502 4.9 11.2 0.5 C15 B:KDZ501 4.9 11.3 0.5 N B:HIS116 5.0 9.7 1.0

Zinc binding site 5 out of 6 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:12.8 occ:1.00 NE2 B:HIS153 2.0 9.4 1.0 CE1 B:HIS153 2.9 11.1 1.0 CD2 B:HIS153 3.1 9.3 1.0 ND1 B:HIS153 4.1 11.9 1.0 CG B:HIS153 4.2 9.0 1.0 CB B:ALA132 4.2 9.3 1.0 O B:HOH618 4.5 24.0 1.0 CG2 B:THR152 4.9 10.5 1.0 CA B:ALA132 5.0 8.7 1.0

Zinc binding site 6 out of 6 in the Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Metallo Beta Lactamase Vim-2 with Cyclic Boronate APC308. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:11.5 occ:1.00 O23 B:KL8502 2.0 4.2 0.5 NE2 B:HIS240 2.1 8.3 1.0 O23 B:KDZ501 2.1 34.0 0.5 O19 B:KL8502 2.2 11.2 0.5 OD2 B:ASP118 2.3 9.5 1.0 SG B:CYS198 2.3 8.4 1.0 O19 B:KDZ501 2.3 8.1 0.5 C15 B:KL8502 2.9 10.6 0.5 CD2 B:HIS240 3.0 8.1 1.0 B02 B:KL8502 3.0 24.9 0.5 C15 B:KDZ501 3.0 11.3 0.5 O01 B:KDZ501 3.1 3.3 0.5 CE1 B:HIS240 3.1 9.4 1.0 B02 B:KDZ501 3.1 11.8 0.5 C17 B:KL8502 3.1 9.2 0.5 O01 B:KL8502 3.1 27.8 0.5 C17 B:KDZ501 3.3 8.4 0.5 C16 B:KL8502 3.4 5.1 0.5 CB B:CYS198 3.4 7.4 1.0 CG B:ASP118 3.4 9.2 1.0 C16 B:KDZ501 3.5 20.3 0.5 OD1 B:ASP118 3.8 9.6 1.0 NH2 B:ARG119 3.9 10.3 1.0 O03 B:KL8502 4.0 8.5 0.5 C14 B:KL8502 4.0 17.8 0.5 C14 B:KDZ501 4.1 10.8 0.5 CG B:HIS240 4.2 8.1 1.0 C04 B:KDZ501 4.2 9.1 0.5 ND1 B:HIS240 4.2 8.7 1.0 ZN B:ZN503 4.2 10.4 1.0 O B:HOH620 4.3 9.9 1.0 C04 B:KL8502 4.3 45.2 0.5 O18 B:KL8502 4.3 13.5 0.5 C13 B:KL8502 4.3 20.6 0.5 C13 B:KDZ501 4.4 19.5 0.5 O03 B:KDZ501 4.4 10.6 0.5 CE1 B:HIS179 4.4 7.9 1.0 O18 B:KDZ501 4.4 9.6 0.5 NE2 B:HIS179 4.5 6.6 1.0 NE B:ARG119 4.5 8.2 1.0 CA B:CYS198 4.5 6.0 1.0 CB B:ASP118 4.6 8.2 1.0 C20 B:KL8502 4.6 9.2 0.5 CZ B:ARG119 4.7 9.3 1.0 CE1 B:HIS114 4.7 5.8 1.0 C20 B:KDZ501 4.8 28.9 0.5

A.Parkova, A.Lucic, A.Krajnc, J.Brem, K.Calvopina, G.W.Langley, M.A.Mcdonough, P.Trapencieris, C.J.Schofield. Broad Spectrum Beta-Lactamase Inhibition By A Thioether Substituted Bicyclic Boronate. Acs Infect Dis. 2020.
ISSN: ESSN 2373-8227
PubMed: 31841636
DOI: 10.1021/ACSINFECDIS.9B00330