Calcium in PDB 1yyg: Manganese Peroxidase Complexed with Cd(II) Inhibitor

All present enzymatic activity of Manganese Peroxidase Complexed with Cd(II) Inhibitor:
1.11.1.13;

The structure of Manganese Peroxidase Complexed with Cd(II) Inhibitor, PDB code: 1yyg 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 (°)	160.352, 45.259, 52.714, 90.00, 97.21, 90.00
R / Rfree (%)	n/a / 22.5

The structure of Manganese Peroxidase Complexed with Cd(II) Inhibitor also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Manganese Peroxidase Complexed with Cd(II) Inhibitor (pdb code 1yyg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Manganese Peroxidase Complexed with Cd(II) Inhibitor, PDB code: 1yyg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Manganese Peroxidase Complexed with Cd(II) Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Manganese Peroxidase Complexed with Cd(II) Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca371 b:8.5 occ:1.00 O A:THR193 2.3 10.5 1.0 O A:SER174 2.4 10.9 1.0 OD1 A:ASP198 2.5 8.7 1.0 OG A:SER174 2.5 8.0 1.0 OG1 A:THR193 2.5 7.8 1.0 O A:THR196 2.5 6.2 1.0 OD2 A:ASP191 2.5 11.0 1.0 OD1 A:ASP191 2.6 12.0 1.0 CG A:ASP191 2.9 9.6 1.0 C A:THR193 3.2 7.4 1.0 C A:SER174 3.3 13.2 1.0 CG A:ASP198 3.4 10.6 1.0 CB A:THR193 3.5 15.4 1.0 CB A:SER174 3.6 10.8 1.0 CA A:SER174 3.6 9.2 1.0 C A:THR196 3.7 9.7 1.0 CA A:THR193 3.8 9.7 1.0 OD2 A:ASP198 3.8 10.9 1.0 N A:ASP198 4.1 8.9 1.0 N A:PRO194 4.1 13.4 1.0 N A:THR193 4.2 9.1 1.0 CA A:PRO194 4.4 9.0 1.0 N A:THR196 4.4 7.7 1.0 CA A:THR196 4.4 11.9 1.0 CB A:ASP191 4.4 8.0 1.0 O A:ASP198 4.5 9.7 1.0 CB A:THR196 4.5 10.5 1.0 N A:VAL175 4.5 9.5 1.0 O A:HOH1024 4.6 9.5 1.0 CB A:GLN200 4.7 9.4 1.0 CB A:ASP198 4.7 13.4 1.0 N A:PHE197 4.7 7.8 1.0 CA A:ASP198 4.7 10.6 1.0 C A:ASP198 4.8 11.4 1.0 CG2 A:THR193 4.8 11.3 1.0 CA A:PHE197 4.9 7.8 1.0 CG1 A:VAL175 4.9 13.5 1.0 C A:PRO194 5.0 11.0 1.0 C A:PHE197 5.0 11.5 1.0

Calcium binding site 2 out of 3 in the Manganese Peroxidase Complexed with Cd(II) Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Manganese Peroxidase Complexed with Cd(II) Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca372 b:7.8 occ:1.00 OD2 A:ASP47 2.3 9.5 1.0 O A:HOH1128 2.3 7.2 1.0 O A:HOH1085 2.4 8.7 1.0 O A:GLY62 2.5 9.9 1.0 O A:ASP47 2.5 9.1 1.0 OD1 A:ASP64 2.5 7.9 1.0 OG A:SER66 2.6 12.8 1.0 C A:ASP47 3.3 14.7 1.0 CG A:ASP47 3.4 11.5 1.0 CG A:ASP64 3.5 12.3 1.0 C A:GLY62 3.6 8.8 1.0 CB A:SER66 3.6 9.3 1.0 CA A:ASP47 3.6 10.3 1.0 N A:SER66 4.0 9.5 1.0 OD2 A:ASP64 4.0 10.6 1.0 N A:ASP64 4.0 7.7 1.0 CB A:ASP47 4.1 7.2 1.0 O A:HOH1087 4.2 9.7 1.0 N A:GLY62 4.3 12.0 1.0 OD1 A:ASP47 4.3 9.7 1.0 CA A:GLY62 4.3 7.6 1.0 CA A:SER66 4.4 9.0 1.0 CB A:ALA50 4.4 12.7 1.0 N A:ALA48 4.5 9.7 1.0 OE2 A:GLU74 4.5 11.0 1.0 OE1 A:GLU74 4.5 8.8 1.0 N A:GLY65 4.6 7.6 1.0 O A:ALA50 4.6 8.9 1.0 CB A:ASP64 4.6 9.6 1.0 N A:ALA63 4.6 6.5 1.0 O A:HIS46 4.7 11.3 1.0 N A:MET67 4.8 7.8 1.0 CA A:ASP64 4.8 12.3 1.0 CA A:ALA63 4.8 9.1 1.0 C A:ASP64 4.9 13.8 1.0 CD A:GLU74 5.0 11.8 1.0 CA A:ALA48 5.0 8.1 1.0 C A:ALA63 5.0 8.1 1.0 N A:ASP47 5.0 10.5 1.0

Calcium binding site 3 out of 3 in the Manganese Peroxidase Complexed with Cd(II) Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Manganese Peroxidase Complexed with Cd(II) Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca381 b:16.3 occ:1.00 OE1 A:GLU39 2.0 53.9 0.5 O1D A:HEM396 2.2 19.2 1.0 OE2 A:GLU39 2.3 15.0 0.5 OE1 A:GLU35 2.3 17.6 1.0 OD2 A:ASP179 2.4 22.4 1.0 O A:HOH1040 2.4 12.8 1.0 O A:HOH1109 2.4 13.2 1.0 CGD A:HEM396 3.1 26.7 1.0 CD A:GLU39 3.1 20.6 0.5 CD A:GLU39 3.2 30.0 0.5 CD A:GLU35 3.2 19.0 1.0 CG A:ASP179 3.3 21.4 1.0 OE2 A:GLU35 3.4 18.6 1.0 O2D A:HEM396 3.5 19.5 1.0 OD1 A:ASP179 3.6 18.2 1.0 CG A:GLU39 3.7 16.0 0.5 O A:HOH1595 3.9 23.4 0.5 CG A:GLU39 3.9 23.1 0.5 O A:HOH1195 4.0 14.9 1.0 OE1 A:GLU39 4.0 26.2 0.5 OE2 A:GLU39 4.2 8.1 0.5 CBD A:HEM396 4.3 17.1 1.0 O A:HOH1229 4.3 25.1 1.0 O A:ARG177 4.3 12.3 1.0 O A:HOH1356 4.4 30.2 1.0 CB A:ASP179 4.5 17.3 1.0 O2A A:HEM396 4.6 16.9 1.0 O A:HOH1500 4.6 22.7 1.0 CG A:GLU35 4.6 12.9 1.0 O A:HOH1057 4.7 29.4 1.0 O A:HOH1400 4.9 29.0 1.0 C A:ARG177 5.0 11.8 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