Calcium in PDB 1yyd: High Resolution Crystal Structure of Manganese Peroxidase

All present enzymatic activity of High Resolution Crystal Structure of Manganese Peroxidase:
1.11.1.13;

The structure of High Resolution Crystal Structure of Manganese Peroxidase, PDB code: 1yyd was solved by M.Sundaramoorthy, H.L.Youngs, 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 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.967, 45.423, 52.930, 90.00, 96.89, 90.00
R / Rfree (%)	18 / 22.7

The structure of High Resolution Crystal Structure of Manganese Peroxidase also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the High Resolution Crystal Structure of Manganese Peroxidase (pdb code 1yyd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the High Resolution Crystal Structure of Manganese Peroxidase, PDB code: 1yyd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the High Resolution Crystal Structure of Manganese Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Crystal Structure of Manganese Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca371 b:6.1 occ:1.00 O A:SER174 2.4 7.7 1.0 O A:THR193 2.4 7.6 1.0 OD2 A:ASP191 2.5 7.0 1.0 OD1 A:ASP198 2.5 6.6 1.0 OG A:SER174 2.5 7.3 1.0 O A:THR196 2.6 6.0 1.0 OG1 A:THR193 2.6 7.4 1.0 OD1 A:ASP191 2.7 7.6 1.0 CG A:ASP191 3.0 7.9 1.0 C A:THR193 3.3 6.1 1.0 C A:SER174 3.3 8.1 1.0 CG A:ASP198 3.4 9.1 1.0 CB A:SER174 3.6 7.2 1.0 CB A:THR193 3.6 5.7 1.0 CA A:SER174 3.6 5.7 1.0 C A:THR196 3.8 5.8 1.0 OD2 A:ASP198 3.9 8.8 1.0 CA A:THR193 3.9 6.0 1.0 N A:ASP198 4.1 8.5 1.0 N A:PRO194 4.3 7.6 1.0 N A:THR193 4.3 5.9 1.0 O A:ASP198 4.5 7.8 1.0 N A:THR196 4.5 7.7 1.0 CB A:ASP191 4.5 8.4 1.0 CA A:PRO194 4.5 6.7 1.0 CA A:THR196 4.5 7.3 1.0 CB A:THR196 4.6 10.5 1.0 N A:VAL175 4.6 5.6 1.0 O A:HOH1024 4.6 7.9 1.0 CB A:ASP198 4.7 8.2 1.0 CB A:GLN200 4.7 6.3 1.0 N A:PHE197 4.8 6.1 1.0 CA A:ASP198 4.8 6.2 1.0 C A:ASP198 4.8 6.4 1.0 CG1 A:VAL175 4.9 6.0 1.0 CA A:PHE197 4.9 5.5 1.0 CG2 A:THR193 4.9 7.3 1.0

Calcium binding site 2 out of 2 in the High Resolution Crystal Structure of Manganese Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Crystal Structure of Manganese Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca372 b:6.0 occ:1.00 OD2 A:ASP47 2.3 8.9 1.0 O A:HOH1128 2.4 5.0 1.0 OD1 A:ASP64 2.4 7.3 1.0 O A:HOH1085 2.4 5.4 1.0 O A:GLY62 2.4 6.0 1.0 O A:ASP47 2.5 8.3 1.0 OG A:SER66 2.5 7.4 1.0 C A:ASP47 3.4 9.4 1.0 CG A:ASP47 3.4 5.9 1.0 CG A:ASP64 3.5 11.9 1.0 C A:GLY62 3.6 4.5 1.0 CB A:SER66 3.6 5.5 1.0 CA A:ASP47 3.7 6.2 1.0 OD2 A:ASP64 4.0 8.2 1.0 N A:SER66 4.0 7.5 1.0 N A:ASP64 4.1 6.1 1.0 CB A:ASP47 4.1 3.2 1.0 O A:HOH1087 4.2 9.0 1.0 N A:GLY62 4.3 6.3 1.0 OD1 A:ASP47 4.4 7.8 1.0 CA A:GLY62 4.4 6.4 1.0 CA A:SER66 4.4 5.5 1.0 OE2 A:GLU74 4.5 7.1 1.0 N A:ALA48 4.6 5.2 1.0 N A:GLY65 4.6 7.5 1.0 CB A:ALA50 4.6 9.0 1.0 CB A:ASP64 4.6 8.2 1.0 O A:ALA50 4.6 7.4 1.0 OE1 A:GLU74 4.6 7.2 1.0 N A:ALA63 4.7 4.8 1.0 O A:HIS46 4.7 7.6 1.0 N A:MET67 4.8 7.1 1.0 CA A:ASP64 4.8 6.6 1.0 CA A:ALA63 4.9 6.2 1.0 C A:ASP64 4.9 7.9 1.0 C A:ALA63 5.0 7.0 1.0

M.Sundaramoorthy, H.L.Youngs, M.H.Gold, T.L.Poulos. High-Resolution Crystal Structure of Manganese Peroxidase: Substrate and Inhibitor Complexes. Biochemistry V. 44 6463 2005.
ISSN: ISSN 0006-2960
PubMed: 15850380
DOI: 10.1021/BI047318E