Calcium in PDB 3m5q: 0.93 A Structure of Manganese-Bound Manganese Peroxidase

All present enzymatic activity of 0.93 A Structure of Manganese-Bound Manganese Peroxidase:
1.11.1.13;

The structure of 0.93 A Structure of Manganese-Bound Manganese Peroxidase, PDB code: 3m5q was solved by M.Sundaramoorthy, M.H.Gold, T.L.Poulos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 0.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.570, 45.300, 52.830, 90.00, 97.31, 90.00
R / Rfree (%)	n/a / 13.4

The structure of 0.93 A Structure of Manganese-Bound Manganese Peroxidase also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Iron	(Fe)	1 atom

The binding sites of Calcium atom in the 0.93 A Structure of Manganese-Bound Manganese Peroxidase (pdb code 3m5q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the 0.93 A Structure of Manganese-Bound Manganese Peroxidase, PDB code: 3m5q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the 0.93 A Structure of Manganese-Bound Manganese Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 0.93 A Structure of Manganese-Bound Manganese Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca371 b:5.9 occ:1.00 O A:SER174 2.4 6.5 1.0 O A:THR193 2.4 6.4 1.0 OD2 A:ASP191 2.4 6.4 1.0 OD1 A:ASP198 2.5 6.9 1.0 OG A:SER174 2.5 6.4 1.0 OG1 A:THR193 2.5 6.9 1.0 O A:THR196 2.5 7.0 1.0 OD1 A:ASP191 2.7 6.5 1.0 CG A:ASP191 2.9 5.8 1.0 C A:THR193 3.2 6.3 1.0 C A:SER174 3.3 5.8 1.0 CG A:ASP198 3.4 7.1 1.0 CB A:THR193 3.6 7.2 1.0 CB A:SER174 3.6 6.3 1.0 CA A:SER174 3.6 5.8 1.0 C A:THR196 3.7 6.5 1.0 OD2 A:ASP198 3.8 8.2 1.0 CA A:THR193 3.9 6.6 1.0 N A:ASP198 4.2 7.8 1.0 N A:PRO194 4.2 6.5 1.0 N A:THR193 4.3 6.6 1.0 CB A:ASP191 4.4 6.2 1.0 N A:THR196 4.4 6.9 1.0 CA A:THR196 4.5 7.3 1.0 CA A:PRO194 4.5 6.5 1.0 O A:ASP198 4.5 6.9 1.0 N A:VAL175 4.5 5.7 1.0 CB A:THR196 4.5 9.3 1.0 O A:HOH1024 4.6 9.0 1.0 CB A:GLN200 4.6 7.0 1.0 CB A:ASP198 4.7 7.3 1.0 N A:PHE197 4.7 6.8 1.0 CA A:ASP198 4.8 7.2 1.0 C A:ASP198 4.8 6.5 1.0 CG2 A:THR193 4.9 8.2 1.0 CG1 A:VAL175 4.9 7.5 1.0 CA A:PHE197 4.9 6.4 1.0 C A:PRO194 5.0 6.7 1.0

Calcium binding site 2 out of 2 in the 0.93 A Structure of Manganese-Bound Manganese Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 0.93 A Structure of Manganese-Bound Manganese Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca372 b:5.8 occ:1.00 OD2 A:ASP47 2.3 7.5 1.0 O A:HOH1127 2.3 6.6 1.0 O A:HOH1085 2.4 6.5 1.0 OD1 A:ASP64 2.4 6.2 1.0 O A:ASP47 2.4 6.4 1.0 O A:GLY62 2.5 6.2 1.0 OG A:SER66 2.5 6.2 1.0 C A:ASP47 3.3 5.8 1.0 CG A:ASP47 3.4 6.4 1.0 CG A:ASP64 3.5 6.5 1.0 CB A:SER66 3.6 6.1 1.0 C A:GLY62 3.7 6.0 1.0 CA A:ASP47 3.7 5.4 1.0 OD2 A:ASP64 4.0 7.3 1.0 N A:SER66 4.0 6.3 1.0 CB A:ASP47 4.1 6.0 1.0 O A:HOH1087 4.2 7.2 1.0 N A:ASP64 4.2 6.2 1.0 OD1 A:ASP47 4.3 7.8 1.0 N A:GLY62 4.4 6.5 1.0 CA A:SER66 4.4 6.1 1.0 CA A:GLY62 4.4 6.7 1.0 N A:ALA48 4.5 5.9 1.0 CB A:ALA50 4.6 7.5 1.0 OE2 A:GLU74 4.6 7.5 1.0 O A:ALA50 4.6 7.1 1.0 OE1 A:GLU74 4.6 7.8 1.0 CB A:ASP64 4.6 6.8 1.0 N A:GLY65 4.6 6.2 1.0 N A:ALA63 4.7 6.1 1.0 O A:HIS46 4.7 7.1 1.0 CA A:ASP64 4.8 6.4 1.0 N A:MET67 4.8 6.7 1.0 CA A:ALA63 4.9 6.4 1.0 C A:ASP64 4.9 6.3 1.0 CA A:ALA48 5.0 6.0 1.0 N A:ASP47 5.0 5.8 1.0

M.Sundaramoorthy, M.H.Gold, T.L.Poulos. Ultrahigh (0.93A) Resolution Structure of Manganese Peroxidase From Phanerochaete Chrysosporium: Implications For the Catalytic Mechanism. J.Inorg.Biochem. V. 104 683 2010.
ISSN: ISSN 0162-0134
PubMed: 20356630
DOI: 10.1016/J.JINORGBIO.2010.02.011