Manganese in PDB 3py5: Crystal Structure of A Beta-Lactamase-Like Protein From Brucella Melitensis Bound to Amp

The structure of Crystal Structure of A Beta-Lactamase-Like Protein From Brucella Melitensis Bound to Amp, PDB code: 3py5 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)	46.21 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.850, 75.200, 98.530, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 19.6

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

Potassium

(K)

1 atom

The binding sites of Manganese atom in the Crystal Structure of A Beta-Lactamase-Like Protein From Brucella Melitensis Bound to Amp (pdb code 3py5). 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 From Brucella Melitensis Bound to Amp, PDB code: 3py5:
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 From Brucella Melitensis Bound to Amp


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 From Brucella Melitensis Bound to Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:12.2 occ:1.00 O A:HOH321 2.1 11.3 1.0 NE2 A:HIS91 2.2 4.5 1.0 NE2 A:HIS241 2.2 6.5 1.0 O3P A:AMP303 2.2 14.9 1.0 OD2 A:ASP188 2.3 7.3 1.0 OD2 A:ASP90 2.3 8.5 1.0 CG A:ASP188 3.0 8.3 1.0 CD2 A:HIS91 3.1 7.9 1.0 OD1 A:ASP188 3.1 9.1 1.0 CE1 A:HIS241 3.1 7.6 1.0 CG A:ASP90 3.2 8.9 1.0 CD2 A:HIS241 3.2 9.0 1.0 CE1 A:HIS91 3.3 5.5 1.0 MN A:MN301 3.4 11.1 1.0 OD1 A:ASP90 3.4 8.5 1.0 P A:AMP303 3.4 16.9 1.0 O1P A:AMP303 3.8 10.2 1.0 O A:HOH345 4.1 6.3 1.0 O5' A:AMP303 4.1 16.1 1.0 NE2 A:HIS86 4.2 5.5 1.0 ND1 A:HIS241 4.3 9.3 1.0 CG A:HIS91 4.3 4.3 1.0 CE1 A:HIS86 4.3 8.5 1.0 CG A:HIS241 4.3 9.5 1.0 ND1 A:HIS91 4.3 6.5 1.0 CE1 A:HIS219 4.4 10.1 1.0 CB A:ASP188 4.5 9.4 1.0 CB A:ASP90 4.5 8.2 1.0 O2P A:AMP303 4.6 16.3 1.0 CB A:SER18 4.8 8.9 1.0 NE2 A:HIS219 5.0 11.2 1.0

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


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 From Brucella Melitensis Bound to Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:11.1 occ:1.00 O A:HOH321 2.0 11.3 1.0 O1P A:AMP303 2.2 10.2 1.0 ND1 A:HIS88 2.2 11.5 1.0 NE2 A:HIS86 2.3 5.5 1.0 NE2 A:HIS170 2.3 10.8 1.0 OD2 A:ASP188 2.5 7.3 1.0 CD2 A:HIS86 3.2 7.3 1.0 CE1 A:HIS88 3.2 12.2 1.0 P A:AMP303 3.2 16.9 1.0 CG A:HIS88 3.3 10.6 1.0 CE1 A:HIS170 3.3 13.1 1.0 CD2 A:HIS170 3.3 8.7 1.0 CE1 A:HIS86 3.3 8.5 1.0 MN A:MN300 3.4 12.2 1.0 CG A:ASP188 3.4 8.3 1.0 O3P A:AMP303 3.5 14.9 1.0 CB A:HIS88 3.6 9.3 1.0 O5' A:AMP303 3.9 16.1 1.0 CB A:ASP188 3.9 9.4 1.0 O A:HOH394 4.1 18.2 1.0 C5' A:AMP303 4.2 13.9 1.0 NE2 A:HIS91 4.2 4.5 1.0 NE2 A:HIS88 4.3 12.5 1.0 CD2 A:HIS91 4.3 7.9 1.0 CG A:HIS86 4.3 7.0 1.0 ND1 A:HIS86 4.4 8.5 1.0 ND1 A:HIS170 4.4 10.2 1.0 CD2 A:HIS88 4.4 12.0 1.0 CG A:HIS170 4.4 10.4 1.0 OD1 A:ASP188 4.4 9.1 1.0 OD1 A:ASP90 4.6 8.5 1.0 O2P A:AMP303 4.6 16.3 1.0 CE1 A:HIS219 4.7 10.1 1.0 NE2 A:HIS219 4.9 11.2 1.0 C4' A:AMP303 5.0 14.9 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