Sodium in PDB 4h8r: Imipenem Complex of Ges-5 Carbapenemase

The structure of Imipenem Complex of Ges-5 Carbapenemase, PDB code: 4h8r was solved by C.A.Smith, S.B.Vakulenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.82 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.940, 81.240, 71.930, 90.00, 102.04, 90.00
R / Rfree (%)	14.8 / 17

The structure of Imipenem Complex of Ges-5 Carbapenemase also contains other interesting chemical elements:

Iodine

(I)

17 atoms

The binding sites of Sodium atom in the Imipenem Complex of Ges-5 Carbapenemase (pdb code 4h8r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Imipenem Complex of Ges-5 Carbapenemase, PDB code: 4h8r:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:8.5 occ:1.00 OD2 A:ASP94 2.0 26.3 1.0 CG A:ASP94 2.8 29.6 1.0 CB A:ASP94 3.0 24.9 1.0 N A:ASP94 3.2 16.6 1.0 I A:IOD507 3.7 23.1 0.2 N A:PRO93 3.7 12.2 1.0 CA A:ASP94 3.7 20.0 1.0 C A:GLY92 3.8 11.2 1.0 CA A:GLY92 3.8 11.2 1.0 CD A:PRO93 3.8 12.6 1.0 OD1 A:ASP94 3.9 32.0 1.0 CG A:PRO93 4.2 14.7 1.0 C A:PRO93 4.3 14.8 1.0 O A:GLY92 4.4 11.6 1.0 N A:GLY92 4.5 11.1 1.0 CA A:PRO93 4.5 13.7 1.0 O A:HOH607 4.6 16.0 1.0 CB A:PRO93 4.9 15.0 1.0 C A:ASP94 4.9 18.3 1.0

Sodium binding site 2 out of 4 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na510 b:42.7 occ:0.94 OE2 B:GLU163 3.6 25.4 1.0 N B:LYS160 3.6 12.3 1.0 CA B:ARG159 3.9 11.7 1.0 CG B:LYS160 3.9 17.8 1.0 CB B:ARG159 4.0 12.8 1.0 CG B:ARG159 4.1 13.1 1.0 C B:ARG159 4.3 11.6 1.0 CG B:GLU163 4.4 21.7 1.0 CD B:GLU163 4.4 23.5 1.0 CB B:LYS160 4.6 16.1 1.0 CD B:LYS160 4.6 20.5 1.0 CA B:LYS160 4.7 13.4 1.0 CE B:LYS160 4.7 22.5 1.0 O B:ASP158 4.8 12.8 1.0

Sodium binding site 3 out of 4 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na512 b:23.3 occ:0.69 O B:HOH830 3.7 27.5 1.0 CB B:GLN210 4.1 9.0 1.0 CG2 B:THR211 4.1 11.2 1.0 CZ2 B:TRP99 4.2 23.2 1.0 CD2 B:LEU124 4.2 14.1 1.0 O B:GLN210 4.2 11.7 1.0 O B:HOH813 4.2 35.9 1.0 OE1 B:GLN210 4.3 14.9 1.0 I B:IOD504 4.4 17.4 0.3 C B:GLN210 4.5 8.8 1.0 CH2 B:TRP99 4.7 24.1 1.0 CA B:LEU124 4.9 8.8 1.0 CA B:GLN210 5.0 8.9 1.0 O B:LEU124 5.0 10.3 1.0

Sodium binding site 4 out of 4 in the Imipenem Complex of Ges-5 Carbapenemase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Imipenem Complex of Ges-5 Carbapenemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na513 b:23.1 occ:1.00 OG1 B:THR113 3.3 10.0 1.0 O A:HOH710 3.4 26.0 1.0 CB B:THR113 4.0 9.8 1.0 O B:GLY85 4.0 12.4 1.0 CG2 B:THR113 4.0 10.8 1.0 O B:HOH751 4.1 25.2 1.0 CA B:ASP86 4.2 14.0 1.0 CB B:LEU115 4.2 13.4 1.0 O B:HOH720 4.4 32.2 0.5 CB B:ASP86 4.4 18.1 1.0 C B:GLY85 4.5 12.5 1.0 CD1 B:LEU115 4.6 18.3 1.0 N B:ASP86 4.7 12.4 1.0 CG B:GLU116 4.7 11.6 1.0 N B:GLU116 4.9 10.1 1.0 CG B:LEU115 5.0 17.0 1.0

C.A.Smith, H.Frase, M.Toth, M.Kumarasiri, K.Wiafe, J.Munoz, S.Mobashery, S.B.Vakulenko. Structural Basis For Progression Toward the Carbapenemase Activity in the Ges Family of Beta-Lactamases. J.Am.Chem.Soc. V. 134 19512 2012.
ISSN: ISSN 0002-7863
PubMed: 23148776
DOI: 10.1021/JA308197J