Calcium in PDB 1yzp: Substrate-Free Manganese Peroxidase

All present enzymatic activity of Substrate-Free Manganese Peroxidase:
1.11.1.13;

The structure of Substrate-Free Manganese Peroxidase, PDB code: 1yzp 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 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.595, 45.356, 52.817, 90.00, 97.25, 90.00
R / Rfree (%)	15.3 / 20.3

The structure of Substrate-Free Manganese Peroxidase also contains other interesting chemical elements:

Iron

(Fe)

1 atom

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

Calcium binding site 1 out of 2 in the Substrate-Free Manganese Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Substrate-Free Manganese Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca371 b:15.6 occ:1.00 O A:THR193 2.4 15.0 1.0 O A:SER174 2.4 15.7 1.0 OD2 A:ASP191 2.4 13.8 1.0 OD1 A:ASP198 2.4 12.1 1.0 OG A:SER174 2.5 13.3 1.0 O A:THR196 2.5 12.2 1.0 OG1 A:THR193 2.5 14.2 1.0 OD1 A:ASP191 2.6 16.2 1.0 CG A:ASP191 2.9 14.5 1.0 C A:THR193 3.2 15.0 1.0 C A:SER174 3.3 21.5 1.0 CG A:ASP198 3.4 15.1 1.0 CB A:SER174 3.6 14.0 1.0 CB A:THR193 3.6 13.9 1.0 CA A:SER174 3.6 12.3 1.0 C A:THR196 3.7 12.8 1.0 OD2 A:ASP198 3.8 16.0 1.0 CA A:THR193 3.9 14.6 1.0 N A:ASP198 4.0 14.5 1.0 N A:PRO194 4.2 16.7 1.0 N A:THR193 4.2 12.7 1.0 CB A:ASP191 4.4 14.1 1.0 N A:THR196 4.4 14.9 1.0 CA A:PRO194 4.4 12.0 1.0 CA A:THR196 4.4 15.6 1.0 CB A:THR196 4.4 16.2 1.0 O A:ASP198 4.5 14.4 1.0 N A:VAL175 4.5 14.8 1.0 O A:HOH1024 4.6 12.1 1.0 CB A:GLN200 4.6 12.7 1.0 CB A:ASP198 4.7 16.3 1.0 N A:PHE197 4.7 12.7 1.0 CA A:ASP198 4.7 12.9 1.0 C A:ASP198 4.8 15.3 1.0 CG1 A:VAL175 4.8 13.6 1.0 CA A:PHE197 4.8 13.1 1.0 CG2 A:THR193 4.9 13.1 1.0 C A:PRO194 5.0 14.0 1.0 C A:PHE197 5.0 14.7 1.0

Calcium binding site 2 out of 2 in the Substrate-Free Manganese Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Substrate-Free Manganese Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca372 b:14.4 occ:1.00 OD2 A:ASP47 2.3 16.5 1.0 O A:HOH1128 2.4 14.4 1.0 O A:HOH1085 2.4 12.4 1.0 OG A:SER66 2.5 15.4 1.0 O A:ASP47 2.5 14.9 1.0 OD1 A:ASP64 2.5 12.4 1.0 O A:GLY62 2.5 13.0 1.0 C A:ASP47 3.3 19.9 1.0 CG A:ASP47 3.4 13.5 1.0 CG A:ASP64 3.5 19.9 1.0 CB A:SER66 3.6 14.6 1.0 CA A:ASP47 3.7 13.8 1.0 C A:GLY62 3.7 14.0 1.0 N A:SER66 4.0 14.0 1.0 OD2 A:ASP64 4.0 16.5 1.0 N A:ASP64 4.1 12.6 1.0 CB A:ASP47 4.2 13.1 1.0 O A:HOH1087 4.2 14.3 1.0 OD1 A:ASP47 4.3 15.0 1.0 CA A:SER66 4.4 14.2 1.0 N A:GLY62 4.4 13.8 1.0 CA A:GLY62 4.5 10.6 1.0 OE2 A:GLU74 4.5 14.1 1.0 CB A:ALA50 4.5 13.3 1.0 N A:ALA48 4.5 11.3 1.0 N A:GLY65 4.6 12.1 1.0 OE1 A:GLU74 4.6 13.3 1.0 O A:ALA50 4.6 14.4 1.0 O A:HIS46 4.7 15.8 1.0 CB A:ASP64 4.7 14.9 1.0 N A:ALA63 4.7 14.1 1.0 N A:MET67 4.7 12.9 1.0 CA A:ASP64 4.8 12.1 1.0 CA A:ALA63 4.8 11.7 1.0 C A:ASP64 4.9 15.2 1.0 CD A:GLU74 5.0 18.9 1.0 C A:SER66 5.0 13.3 1.0 CA A:ALA48 5.0 11.2 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