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Sodium in PDB 4gog: Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex

Protein crystallography data

The structure of Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex, PDB code: 4gog was solved by C.A.Smith, S.B.Vakulenko, J.Munoz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.31 / 1.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.950, 81.220, 72.120, 90.00, 102.29, 90.00
R / Rfree (%) 14.9 / 16.8

Other elements in 4gog:

The structure of Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex also contains other interesting chemical elements:

Iodine (I) 19 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 4gog

Go back to Sodium Binding Sites List in 4gog
Sodium binding site 1 out of 2 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:8.1
occ:1.00
OD1 A:ASP94 1.9 15.5 1.0
CG A:ASP94 2.7 17.8 1.0
CB A:ASP94 3.0 17.0 1.0
N A:ASP94 3.2 13.5 1.0
I A:IOD508 3.6 24.0 0.2
N A:PRO93 3.7 10.4 1.0
CA A:ASP94 3.7 15.8 1.0
C A:GLY92 3.8 9.8 1.0
CA A:GLY92 3.8 10.1 1.0
CD A:PRO93 3.8 11.8 1.0
OD2 A:ASP94 3.8 20.7 1.0
CG A:PRO93 4.2 14.7 1.0
C A:PRO93 4.3 13.1 1.0
O A:GLY92 4.4 10.1 1.0
N A:GLY92 4.5 10.2 1.0
CA A:PRO93 4.5 12.2 1.0
CB A:PRO93 4.9 14.4 1.0
C A:ASP94 4.9 15.7 1.0

Sodium binding site 2 out of 2 in 4gog

Go back to Sodium Binding Sites List in 4gog
Sodium binding site 2 out of 2 in the Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Ges-1 Imipenem Acyl-Enzyme Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na513

b:17.4
occ:1.00
OD1 B:ASP94 3.0 16.9 0.9
N B:GLY92 3.5 9.2 1.0
OD1 B:ASP94 3.5 13.2 0.1
OD2 B:ASP94 3.5 13.1 0.1
NH1 B:ARG135 3.6 15.6 0.2
O B:HOH750 3.6 28.6 1.0
O B:HOH773 3.8 35.0 1.0
CG B:ASP94 3.8 12.6 0.1
CA B:TYR91 3.9 8.3 1.0
NH2 B:ARG135 3.9 15.8 0.2
CE B:MET95 4.0 12.8 1.0
CG B:ASP94 4.0 16.1 0.9
CB B:TYR91 4.0 8.4 1.0
C B:TYR91 4.2 8.4 1.0
CZ B:ARG135 4.2 15.6 0.2
NH1 B:ARG135 4.3 14.3 0.8
O B:GLY92 4.3 8.7 1.0
OD2 B:ASP94 4.3 17.4 0.9
CA B:GLY92 4.4 9.7 1.0
CB B:MET95 4.5 10.5 1.0
CB B:MET95 4.5 10.1 0.0
N B:MET95 4.5 9.5 1.0
C B:GLY92 4.6 9.1 1.0
O B:HOH665 4.7 16.6 1.0
CA B:MET95 4.9 9.9 0.0
CA B:MET95 4.9 10.0 1.0
SD B:MET95 5.0 10.5 0.0

Reference:

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
Page generated: Tue Dec 15 06:41:58 2020

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