Manganese in PDB 6ufi: W96Y Oxalate Decarboxylase (Bacillus Subtilis)

The structure of W96Y Oxalate Decarboxylase (Bacillus Subtilis), PDB code: 6ufi was solved by A.J.Pastore, M.J.Burg, U.T.Twahir, S.D.Bruner, A.Angerhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.45 / 1.72
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	155.270, 155.270, 124.088, 90.00, 90.00, 120.00
R / Rfree (%)	14.9 / 16.6

The structure of W96Y Oxalate Decarboxylase (Bacillus Subtilis) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Manganese atom in the W96Y Oxalate Decarboxylase (Bacillus Subtilis) (pdb code 6ufi). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the W96Y Oxalate Decarboxylase (Bacillus Subtilis), PDB code: 6ufi:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the W96Y Oxalate Decarboxylase (Bacillus Subtilis)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of W96Y Oxalate Decarboxylase (Bacillus Subtilis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:9.9 occ:1.00 OE1 A:GLU280 2.0 12.0 1.0 NE2 A:HIS275 2.1 8.8 1.0 O A:HOH516 2.2 12.3 1.0 NE2 A:HIS273 2.2 8.3 1.0 NE2 A:HIS319 2.3 10.2 1.0 OE1 A:GLU333 3.0 22.9 0.4 CD A:GLU280 3.0 11.2 1.0 CD2 A:HIS275 3.1 7.5 1.0 CE1 A:HIS273 3.1 8.8 1.0 CE1 A:HIS275 3.1 10.0 1.0 CE1 A:HIS319 3.2 9.3 1.0 CD2 A:HIS273 3.2 9.1 1.0 CD2 A:HIS319 3.2 9.1 1.0 OE2 A:GLU280 3.4 12.8 1.0 CD A:GLU333 3.6 19.2 0.4 OE2 A:GLU333 3.7 15.1 0.6 OE2 A:GLU333 3.8 16.8 0.4 CD A:GLU333 4.2 15.3 0.6 ND1 A:HIS273 4.2 9.2 1.0 ND1 A:HIS275 4.2 8.8 1.0 CG A:HIS275 4.2 9.4 1.0 CG A:HIS273 4.3 8.0 1.0 ND1 A:HIS319 4.3 8.6 1.0 CG A:GLU280 4.4 8.3 1.0 CG A:HIS319 4.4 7.4 1.0 CG A:GLU333 4.6 13.9 0.4 NH2 A:ARG270 4.6 14.9 1.0 CZ A:PHE335 4.7 11.2 1.0 OE1 A:GLU333 4.7 13.4 0.6 CG A:GLU333 4.7 14.6 0.6 CB A:GLU280 4.7 8.0 1.0 NE A:ARG270 4.9 14.9 1.0

Manganese binding site 2 out of 2 in the W96Y Oxalate Decarboxylase (Bacillus Subtilis)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of W96Y Oxalate Decarboxylase (Bacillus Subtilis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:10.7 occ:1.00 NE2 A:HIS97 2.0 15.8 1.0 OE1 A:GLU101 2.1 10.8 1.0 O A:HOH574 2.2 14.2 1.0 NE2 A:HIS95 2.2 10.4 1.0 NE2 A:HIS140 2.2 8.7 1.0 O A:HOH713 2.5 29.7 1.0 CE1 A:HIS97 2.7 22.3 1.0 CD2 A:HIS97 3.1 12.5 1.0 CD A:GLU101 3.1 8.7 1.0 CE1 A:HIS95 3.1 11.4 1.0 CD2 A:HIS140 3.2 10.2 1.0 CD2 A:HIS95 3.2 11.2 1.0 CE1 A:HIS140 3.2 11.8 1.0 OE2 A:GLU101 3.5 11.0 1.0 ND1 A:HIS97 3.9 19.1 1.0 CG A:HIS97 4.1 16.2 1.0 ND1 A:HIS95 4.3 10.8 1.0 CE1 A:PHE155 4.3 11.0 1.0 CG A:HIS95 4.3 8.6 1.0 ND1 A:HIS140 4.3 10.3 1.0 CG A:HIS140 4.4 8.8 1.0 CG A:GLU101 4.5 8.9 1.0 CZ A:PHE155 4.6 11.9 1.0 OG1 A:THR165 4.7 19.1 0.1 CB A:GLU101 4.7 9.7 1.0

A.J.Pastore, M.J.Burg, U.T.Twahir, S.D.Bruner, A.Angerhofer. The Electronic Structure of Quaternarily Pi-Stacked Residues Influences Decarboxylase Activity in Oxalate Decarboxylase of Bacillus Subtilis. To Be Published.