Magnesium in PDB 6kxo: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9, PDB code: 6kxo was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.49 / 1.49
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.501, 79.210, 67.660, 90.00, 130.13, 90.00
R / Rfree (%)	14.6 / 16.9

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 (pdb code 6kxo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9, PDB code: 6kxo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:17.0 occ:1.00 O A:HOH445 2.9 14.0 1.0 O A:HOH501 2.9 9.5 1.0 O A:HIS240 2.9 8.7 1.0 N A:GLU202 3.0 7.3 1.0 NH1 A:ARG205 3.1 16.5 1.0 CD A:ARG205 3.3 17.7 1.0 CA A:TYR201 3.5 7.4 1.0 C A:TYR201 3.7 7.2 1.0 CG A:GLU202 3.8 8.3 1.0 C A:HIS240 3.9 7.6 1.0 CB A:GLU202 3.9 8.0 1.0 CB A:HIS240 4.0 7.2 1.0 CB A:TYR201 4.0 8.2 1.0 CA A:GLU202 4.1 8.0 1.0 CZ A:ARG205 4.1 20.0 1.0 CB A:ARG205 4.2 13.5 1.0 NE A:ARG205 4.2 22.0 1.0 CA A:HIS240 4.2 7.1 1.0 CD1 A:TYR201 4.3 9.9 1.0 N A:HIS240 4.3 6.6 1.0 CG A:TYR201 4.3 10.3 1.0 O A:ILE200 4.3 5.8 1.0 CG A:ARG205 4.4 15.1 1.0 O A:HOH569 4.5 8.6 1.0 CB A:PRO238 4.6 6.8 1.0 N A:TYR201 4.6 6.9 1.0 OE2 A:GLU202 4.6 11.1 1.0 CD A:GLU202 4.7 9.2 1.0 O A:GLU202 4.8 7.7 1.0 CG A:HIS240 4.9 7.1 1.0 C A:ILE200 4.9 6.5 1.0 C A:GLU202 4.9 8.5 1.0 O A:TYR201 5.0 7.9 1.0 CD2 A:HIS240 5.0 6.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:21.4 occ:1.00 O A:PRO169 2.8 11.2 1.0 O A:HOH666 2.9 24.4 1.0 O A:HOH408 2.9 27.0 1.0 N A:SER190 3.1 13.4 1.0 OG A:SER190 3.2 17.9 1.0 CB A:SER190 3.3 15.4 1.0 CD A:PRO189 3.4 11.1 1.0 CG A:PRO189 3.5 14.4 1.0 N A:PRO189 3.6 10.6 1.0 CG1 A:VAL188 3.7 9.8 1.0 CA A:SER190 3.7 14.1 1.0 C A:PRO169 3.9 9.4 1.0 C A:PRO189 4.1 13.3 1.0 C A:VAL188 4.1 10.5 1.0 CA A:PRO189 4.2 12.5 1.0 CA A:PRO169 4.3 9.8 1.0 CB A:PRO169 4.3 10.0 1.0 CB A:PRO189 4.4 12.5 1.0 CA A:VAL188 4.4 8.7 1.0 NH2 A:ARG166 4.6 16.4 1.0 CB A:VAL188 4.7 9.4 1.0 O A:VAL188 4.8 10.8 1.0 O A:HOH564 4.8 23.3 1.0 C A:SER190 4.9 13.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:17.9 occ:1.00 O B:PRO169 2.8 9.2 1.0 O B:HOH702 2.8 17.5 1.0 O B:HOH418 2.9 19.9 1.0 N B:SER190 3.1 9.1 1.0 OG B:SER190 3.1 14.1 1.0 CB B:SER190 3.2 11.4 1.0 CD B:PRO189 3.4 9.4 1.0 N B:PRO189 3.6 8.5 1.0 CG B:PRO189 3.6 10.9 1.0 CG1 B:VAL188 3.7 8.1 1.0 CA B:SER190 3.7 10.2 1.0 C B:PRO169 3.8 7.9 1.0 C B:VAL188 4.1 8.3 1.0 C B:PRO189 4.1 9.7 1.0 CA B:PRO169 4.1 8.8 1.0 CB B:PRO169 4.2 9.6 1.0 O B:HOH679 4.2 28.8 1.0 CA B:PRO189 4.2 9.8 1.0 O B:HOH664 4.3 33.3 1.0 CB B:PRO189 4.4 11.4 1.0 CA B:VAL188 4.4 7.7 1.0 O B:HOH660 4.5 27.8 1.0 CB B:VAL188 4.7 8.4 1.0 O B:VAL188 4.8 8.5 1.0 O B:HOH604 4.8 9.6 1.0 C B:SER190 4.9 11.2 1.0 N B:VAL170 4.9 7.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:20.0 occ:1.00 O B:GLU43 2.6 13.4 1.0 N B:THR59 2.8 12.6 1.0 OG1 B:THR59 3.0 18.7 1.0 N B:GLY42 3.1 16.5 1.0 O B:THR59 3.1 10.8 1.0 OD1 B:ASN91 3.3 11.0 1.0 N B:GLU43 3.5 14.6 1.0 O B:PRO40 3.5 19.9 1.0 ND2 B:ASN91 3.6 10.0 1.0 CA B:VAL41 3.6 20.4 1.0 CG B:ASN91 3.6 10.7 1.0 CA B:THR59 3.7 12.3 1.0 CA B:ALA58 3.7 8.8 1.0 C B:GLU43 3.7 13.5 1.0 C B:ALA58 3.7 9.8 1.0 CB B:ALA58 3.8 9.3 1.0 C B:VAL41 3.8 20.9 1.0 C B:THR59 3.8 12.0 1.0 CB B:THR59 3.9 14.5 1.0 C B:GLY42 4.0 14.3 1.0 CA B:GLY42 4.0 15.7 1.0 CG2 B:ILE39 4.1 17.6 1.0 CA B:GLU43 4.2 14.5 1.0 C B:PRO40 4.3 22.0 1.0 N B:VAL41 4.3 20.9 1.0 CB B:VAL41 4.7 23.4 1.0 CG1 B:VAL41 4.7 24.1 1.0 CG2 B:THR59 4.8 14.4 1.0 CB B:ASN91 4.8 9.8 1.0 N B:VAL44 4.9 11.4 1.0 O B:GLY42 4.9 16.8 1.0 O B:ALA58 4.9 10.1 1.0 O B:VAL41 5.0 21.5 1.0

J.Wachino, J.Wachino. N/A N/A.