Sodium in PDB 3md7: Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis

The structure of Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis, PDB code: 3md7 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.85 / 1.27
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.890, 75.250, 98.360, 90.00, 90.00, 90.00
R / Rfree (%)	10.7 / 13.4

The structure of Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis also contains other interesting chemical elements:

Potassium	(K)	1 atom
Manganese	(Mn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis (pdb code 3md7). 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 A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis, PDB code: 3md7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis


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 A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:18.2 occ:1.00 O A:HOH396 2.4 26.1 1.0 O A:HIS216 2.4 11.8 1.0 O A:HOH416 2.5 35.0 1.0 O A:HOH496 2.5 17.3 1.0 O A:HOH375 2.7 13.3 1.0 C A:HIS216 3.5 11.3 1.0 O A:HIS219 4.0 12.7 1.0 N A:HIS216 4.1 10.6 1.0 CA A:PRO217 4.1 13.0 1.0 OE1 A:GLU224 4.1 16.5 1.0 C A:PRO217 4.2 11.6 1.0 N A:PRO217 4.2 11.8 1.0 O A:PRO217 4.3 13.8 1.0 OE2 A:GLU224 4.4 24.5 1.0 CA A:HIS216 4.5 11.2 1.0 CB A:SER190 4.6 10.4 1.0 CD A:GLU224 4.7 17.0 1.0 C A:HIS219 4.8 8.7 1.0 N A:SER218 4.8 10.4 1.0 O A:SER190 5.0 11.9 1.0 N A:HIS219 5.0 9.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis


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 A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:15.8 occ:1.00 O A:HOH521 2.4 21.9 1.0 O A:ASN56 2.4 9.7 1.0 O A:HOH458 2.5 19.6 1.0 O A:HOH402 2.5 17.4 1.0 OD1 A:ASN56 2.6 15.0 1.0 SD A:MET78 2.9 20.6 0.5 C A:ASN56 3.5 7.9 1.0 CG A:ASN56 3.6 9.6 1.0 CG A:MET78 3.8 14.2 0.5 CE A:MET78 3.8 21.6 0.5 CG A:MET78 3.8 16.0 0.5 O A:HOH522 3.8 24.0 1.0 N A:ASN56 3.9 8.5 1.0 CA A:ASN56 4.0 8.3 1.0 CB A:ALA157 4.1 10.6 1.0 SD A:MET78 4.1 19.7 0.5 CB A:ASN56 4.4 8.6 1.0 ND2 A:ASN56 4.6 10.6 1.0 N A:THR57 4.6 6.8 1.0 O A:HOH325 4.7 28.3 1.0 O A:HOH322 4.7 43.8 1.0 OD2 A:ASP80 4.7 9.3 1.0 CG2 A:VAL58 4.8 8.1 1.0 CE A:MET78 4.8 20.6 0.5 CB A:MET78 4.9 13.1 0.5 CB A:MET78 5.0 12.2 0.5

J.Abendroth, B.Sankaran, T.E.Edwards, A.S.Gardberg, S.Dieterich, J.Bhandari, A.J.Napuli, W.C.Van Voorhis, B.L.Staker, P.J.Myler, L.J.Stewart. Braba.11339.A: Anomalous Diffraction and Ligand Binding Guide Towards the Elucidation of the Function of A `Putative Beta-Lactamase-Like Protein From Brucella Melitensis. Acta Crystallogr.,Sect.F V. 67 1106 2011.
ISSN: ESSN 1744-3091
PubMed: 21904058
DOI: 10.1107/S1744309111010220