Manganese 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
Sodium	(Na)	2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of A Beta-Lactamase-Like Protein Bound to Gmp From Brucella Melitensis, PDB code: 3md7:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn300 b:6.8 occ:0.75 O A:HOH330 2.1 12.8 1.0 NE2 A:HIS241 2.2 9.7 1.0 NE2 A:HIS91 2.3 6.8 1.0 OD2 A:ASP188 2.3 8.4 1.0 OD2 A:ASP90 2.3 7.2 1.0 O1P A:5GP303 2.4 12.5 0.5 CG A:ASP188 3.0 7.6 1.0 OD1 A:ASP188 3.0 8.4 1.0 CD2 A:HIS91 3.1 7.2 1.0 CD2 A:HIS241 3.1 8.5 1.0 CG A:ASP90 3.2 7.2 1.0 CE1 A:HIS241 3.2 9.4 1.0 CE1 A:HIS91 3.3 7.0 1.0 MN A:MN301 3.4 7.9 1.0 OD1 A:ASP90 3.5 7.9 1.0 P A:5GP303 3.6 12.2 0.5 O3P A:5GP303 3.9 9.7 0.5 O A:HOH374 4.1 7.5 1.0 O A:HOH340 4.2 16.1 0.5 CE1 A:HIS86 4.2 6.5 1.0 NE2 A:HIS86 4.3 7.5 1.0 O5' A:5GP303 4.3 10.0 0.5 CG A:HIS241 4.3 7.8 1.0 ND1 A:HIS241 4.3 9.5 1.0 CG A:HIS91 4.3 6.4 1.0 ND1 A:HIS91 4.4 7.0 1.0 CE1 A:HIS219 4.4 10.0 1.0 CB A:ASP188 4.5 7.2 1.0 CB A:ASP90 4.5 7.6 1.0 O2P A:5GP303 4.7 11.8 0.5 CB A:SER18 4.8 9.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:7.9 occ:1.00 O A:HOH330 2.1 12.8 1.0 O3P A:5GP303 2.2 9.7 0.5 NE2 A:HIS170 2.2 8.4 1.0 ND1 A:HIS88 2.2 9.2 1.0 NE2 A:HIS86 2.2 7.5 1.0 OD2 A:ASP188 2.3 8.4 1.0 O A:HOH340 2.3 16.1 0.5 CE1 A:HIS170 3.1 8.2 1.0 CE1 A:HIS88 3.2 9.6 1.0 CD2 A:HIS86 3.2 6.4 1.0 CE1 A:HIS86 3.2 6.5 1.0 CD2 A:HIS170 3.3 8.5 1.0 CG A:HIS88 3.3 8.5 1.0 P A:5GP303 3.3 12.2 0.5 CG A:ASP188 3.3 7.6 1.0 MN A:MN300 3.4 6.8 0.8 CB A:HIS88 3.6 6.9 1.0 O1P A:5GP303 3.6 12.5 0.5 CB A:ASP188 3.9 7.2 1.0 O5' A:5GP303 4.1 10.0 0.5 C5' A:5GP303 4.2 8.1 0.5 ND1 A:HIS170 4.3 8.9 1.0 NE2 A:HIS88 4.3 12.9 1.0 NE2 A:HIS91 4.3 6.8 1.0 CG A:HIS86 4.4 6.4 1.0 OD1 A:ASP188 4.4 8.4 1.0 CG A:HIS170 4.4 8.8 1.0 CD2 A:HIS88 4.4 10.8 1.0 ND1 A:HIS86 4.4 7.0 1.0 CD2 A:HIS91 4.5 7.2 1.0 OD1 A:ASP90 4.6 7.9 1.0 O2P A:5GP303 4.6 11.8 0.5 CE1 A:HIS219 4.7 10.0 1.0 NE2 A:HIS219 4.9 10.5 1.0

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