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Calcium in PDB 3m8m: 1.05 A Structure of Manganese-Free Manganese Peroxidase

Enzymatic activity of 1.05 A Structure of Manganese-Free Manganese Peroxidase

All present enzymatic activity of 1.05 A Structure of Manganese-Free Manganese Peroxidase:
1.11.1.13;

Protein crystallography data

The structure of 1.05 A Structure of Manganese-Free Manganese Peroxidase, PDB code: 3m8m 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 / 1.05
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 (%) 11.6 / 13.9

Other elements in 3m8m:

The structure of 1.05 A Structure of Manganese-Free Manganese Peroxidase also contains other interesting chemical elements:

Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.05 A Structure of Manganese-Free Manganese Peroxidase (pdb code 3m8m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the 1.05 A Structure of Manganese-Free Manganese Peroxidase, PDB code: 3m8m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3m8m

Go back to Calcium Binding Sites List in 3m8m
Calcium binding site 1 out of 2 in the 1.05 A Structure of Manganese-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 1.05 A Structure of Manganese-Free 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 6.2 1.0
OD2 A:ASP191 2.4 6.3 1.0
OD1 A:ASP198 2.5 6.4 1.0
OG A:SER174 2.5 6.6 1.0
O A:THR196 2.5 6.6 1.0
OG1 A:THR193 2.5 6.8 1.0
OD1 A:ASP191 2.6 6.3 1.0
CG A:ASP191 2.9 5.9 1.0
C A:THR193 3.2 6.5 1.0
C A:SER174 3.3 5.8 1.0
CG A:ASP198 3.4 6.5 1.0
CB A:THR193 3.6 6.9 1.0
CB A:SER174 3.6 6.2 1.0
CA A:SER174 3.6 5.8 1.0
C A:THR196 3.7 6.1 1.0
OD2 A:ASP198 3.8 7.7 1.0
CA A:THR193 3.9 6.5 1.0
N A:ASP198 4.2 7.2 1.0
N A:PRO194 4.2 6.1 1.0
N A:THR193 4.2 6.5 1.0
CB A:ASP191 4.4 6.4 1.0
N A:THR196 4.4 6.6 1.0
CA A:THR196 4.4 6.9 1.0
CB A:THR196 4.4 7.9 1.0
CA A:PRO194 4.5 6.4 1.0
O A:ASP198 4.5 6.5 1.0
N A:VAL175 4.5 5.9 1.0
O A:HOH1024 4.6 7.6 1.0
CB A:GLN200 4.6 6.8 1.0
CB A:ASP198 4.7 6.7 1.0
N A:PHE197 4.7 6.2 1.0
CA A:ASP198 4.7 6.8 1.0
C A:ASP198 4.8 6.1 1.0
CG1 A:VAL175 4.8 6.9 1.0
CG2 A:THR193 4.9 7.0 1.0
CA A:PHE197 4.9 6.4 1.0
C A:PRO194 5.0 6.2 1.0

Calcium binding site 2 out of 2 in 3m8m

Go back to Calcium Binding Sites List in 3m8m
Calcium binding site 2 out of 2 in the 1.05 A Structure of Manganese-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 1.05 A Structure of Manganese-Free Manganese Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca372

b:5.6
occ:1.00
OD2 A:ASP47 2.3 7.2 1.0
O A:HOH1127 2.3 6.4 1.0
O A:HOH1085 2.4 6.2 1.0
OD1 A:ASP64 2.4 6.1 1.0
O A:GLY62 2.4 6.2 1.0
O A:ASP47 2.4 6.1 1.0
OG A:SER66 2.5 6.2 1.0
C A:ASP47 3.4 5.8 1.0
CG A:ASP47 3.4 6.2 1.0
CG A:ASP64 3.4 6.5 1.0
CB A:SER66 3.6 6.2 1.0
C A:GLY62 3.6 5.6 1.0
CA A:ASP47 3.7 5.9 1.0
OD2 A:ASP64 4.0 6.6 1.0
N A:SER66 4.0 6.2 1.0
CB A:ASP47 4.1 5.5 1.0
N A:ASP64 4.2 6.1 1.0
O A:HOH1087 4.2 6.7 1.0
OD1 A:ASP47 4.3 7.3 1.0
N A:GLY62 4.3 6.4 1.0
CA A:SER66 4.4 6.0 1.0
CA A:GLY62 4.4 6.4 1.0
N A:ALA48 4.5 5.7 1.0
OE2 A:GLU74 4.5 6.9 1.0
CB A:ALA50 4.6 6.9 1.0
CB A:ASP64 4.6 6.6 1.0
O A:ALA50 4.6 6.9 1.0
OE1 A:GLU74 4.6 6.9 1.0
N A:GLY65 4.6 6.1 1.0
N A:ALA63 4.6 5.9 1.0
O A:HIS46 4.7 6.7 1.0
N A:MET67 4.8 6.5 1.0
CA A:ASP64 4.8 6.2 1.0
CA A:ALA63 4.8 6.0 1.0
C A:ASP64 4.9 6.1 1.0
CA A:ALA48 5.0 6.0 1.0
CD A:GLU74 5.0 6.6 1.0
N A:ASP47 5.0 5.7 1.0

Reference:

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
Page generated: Sat Jul 13 13:31:16 2024

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