Manganese in PDB 1l3j: Crystal Structure of Oxalate Decarboxylase Formate Complex

The structure of Crystal Structure of Oxalate Decarboxylase Formate Complex, PDB code: 1l3j was solved by R.Anand, P.C.Dorrestein, C.Kinsland, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.72 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	154.800, 154.800, 122.160, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.3

The structure of Crystal Structure of Oxalate Decarboxylase Formate Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Oxalate Decarboxylase Formate Complex (pdb code 1l3j). 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 Oxalate Decarboxylase Formate Complex, PDB code: 1l3j:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Oxalate Decarboxylase Formate Complex


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 Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:6.1 occ:1.00 OE1 A:GLU101 2.0 7.1 1.0 O2 A:FMT550 2.1 13.5 1.0 NE2 A:HIS95 2.2 8.4 1.0 NE2 A:HIS140 2.2 6.6 1.0 NE2 A:HIS97 2.2 15.4 1.0 CE1 A:HIS97 2.7 15.6 1.0 CD A:GLU101 3.1 7.5 1.0 C A:FMT550 3.1 16.1 1.0 CE1 A:HIS95 3.1 9.0 1.0 CD2 A:HIS140 3.1 6.5 1.0 CD2 A:HIS95 3.2 7.4 1.0 CE1 A:HIS140 3.2 7.6 1.0 OE2 A:GLU101 3.4 9.9 1.0 CD2 A:HIS97 3.5 17.2 1.0 ND1 A:HIS97 3.9 18.9 1.0 O1 A:FMT550 4.2 18.7 1.0 ND1 A:HIS95 4.2 6.5 1.0 ND1 A:HIS140 4.3 6.4 1.0 CG A:HIS95 4.3 6.6 1.0 CG A:HIS140 4.3 6.5 1.0 CE1 A:PHE155 4.3 8.8 1.0 CG A:GLU101 4.4 7.7 1.0 CG A:HIS97 4.4 15.6 1.0 CZ A:PHE155 4.7 10.3 1.0 CB A:GLU101 4.7 7.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Oxalate Decarboxylase Formate Complex


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 Oxalate Decarboxylase Formate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:5.9 occ:1.00 OE1 A:GLU280 1.9 15.0 1.0 O A:HOH891 2.1 8.8 1.0 NE2 A:HIS275 2.1 7.1 1.0 NE2 A:HIS319 2.3 6.4 1.0 O A:HOH895 2.3 30.6 1.0 NE2 A:HIS273 2.3 8.9 1.0 CD A:GLU280 3.0 12.4 1.0 CE1 A:HIS275 3.1 8.0 1.0 CD2 A:HIS275 3.1 7.5 1.0 CE1 A:HIS319 3.2 7.2 1.0 CE1 A:HIS273 3.2 9.9 1.0 CD2 A:HIS273 3.3 8.0 1.0 CD2 A:HIS319 3.3 5.9 1.0 OE2 A:GLU280 3.4 12.6 1.0 OE2 A:GLU333 3.6 26.1 1.0 ND1 A:HIS275 4.2 7.2 1.0 CD A:GLU333 4.2 25.9 1.0 CG A:HIS275 4.2 7.7 1.0 ND1 A:HIS319 4.3 7.1 1.0 ND1 A:HIS273 4.3 9.8 1.0 CG A:GLU280 4.3 10.9 1.0 CG A:HIS273 4.4 8.5 1.0 CG A:HIS319 4.4 7.2 1.0 CZ A:PHE335 4.6 10.9 1.0 NH2 A:ARG270 4.6 13.4 1.0 OE1 A:GLU333 4.6 28.2 1.0 CB A:GLU280 4.7 9.0 1.0 CG A:GLU333 4.9 21.3 1.0 CE1 A:PHE335 5.0 10.6 1.0 NE A:ARG270 5.0 13.2 1.0

R.Anand, P.C.Dorrestein, C.Kinsland, T.P.Begley, S.E.Ealick. Structure of Oxalate Decarboxylase From Bacillus Subtilis at 1.75 A Resolution. Biochemistry V. 41 7659 2002.
ISSN: ISSN 0006-2960
PubMed: 12056897
DOI: 10.1021/BI0200965