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Calcium in PDB 1arp: Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases

Enzymatic activity of Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases

All present enzymatic activity of Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases:
1.11.1.7;

Protein crystallography data

The structure of Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases, PDB code: 1arp was solved by N.Kunishima, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.570, 74.570, 117.470, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / n/a

Other elements in 1arp:

The structure of Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases also contains other interesting chemical elements:

Iron (Fe) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases (pdb code 1arp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases, PDB code: 1arp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1arp

Go back to Calcium Binding Sites List in 1arp
Calcium binding site 1 out of 2 in the Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca346

b:12.8
occ:1.00
 OG A:SER79 2.4 10.2 1.0
O A:HOH425 2.5 16.4 1.0
OD1 A:ASP57 2.5 11.2 1.0
O A:HOH424 2.5 12.3 1.0
OD1 A:ASP77 2.5 11.7 1.0
O A:GLY75 2.6 11.2 1.0
O A:ASP57 2.6 12.1 1.0
CB A:SER79 3.5 11.2 1.0
C A:ASP57 3.5 12.3 1.0
CG A:ASP57 3.5 10.9 1.0
CG A:ASP77 3.7 12.8 1.0
C A:GLY75 3.8 10.3 1.0
CA A:ASP57 3.8 11.6 1.0
N A:SER79 4.0 13.0 1.0
O A:HOH363 4.1 14.8 1.0
CA A:SER79 4.2 12.8 1.0
OD2 A:ASP77 4.2 14.7 1.0
CB A:ASP57 4.3 9.6 1.0
N A:ASP77 4.3 11.9 1.0
OD2 A:ASP57 4.4 11.1 1.0
O A:GLY60 4.5 13.5 1.0
N A:ILE80 4.6 11.9 1.0
N A:GLY75 4.6 10.7 1.0
CA A:GLY75 4.6 10.4 1.0
OE2 A:GLU87 4.6 10.8 1.0
N A:GLY78 4.7 10.6 1.0
N A:ALA58 4.7 11.1 1.0
C A:SER79 4.8 13.6 1.0
N A:ALA76 4.8 11.2 1.0
OE1 A:GLU87 4.8 11.2 1.0
CB A:SER148 4.8 12.8 1.0
CB A:ASP77 4.9 10.9 1.0
O A:HIS56 4.9 10.4 1.0
CA A:ALA76 4.9 11.2 1.0
CA A:ASP77 5.0 11.8 1.0

Calcium binding site 2 out of 2 in 1arp

Go back to Calcium Binding Sites List in 1arp
Calcium binding site 2 out of 2 in the Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 Angstroms Resolution: Structural Comparisons with the Lignin and Cytochrome C Peroxidases within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca347

b:14.0
occ:1.00
 OD2 A:ASP202 2.5 8.8 1.0
O A:THR204 2.5 11.7 1.0
O A:VAL207 2.5 9.8 1.0
O A:SER185 2.5 11.8 1.0
OD1 A:ASP209 2.6 10.3 1.0
OD1 A:ASP202 2.6 10.0 1.0
OG A:SER185 2.7 10.3 1.0
OG1 A:THR204 2.7 10.8 1.0
CG A:ASP202 2.9 10.4 1.0
C A:THR204 3.3 12.7 1.0
C A:SER185 3.5 10.4 1.0
CG A:ASP209 3.6 9.3 1.0
CB A:THR204 3.6 12.1 1.0
C A:VAL207 3.7 9.8 1.0
CB A:SER185 3.7 10.3 1.0
CA A:SER185 3.7 9.8 1.0
CA A:THR204 3.9 12.1 1.0
OD2 A:ASP209 4.0 12.0 1.0
N A:ASP209 4.2 9.5 1.0
N A:THR204 4.2 12.2 1.0
O A:ASP209 4.3 11.1 1.0
N A:PRO205 4.3 11.8 1.0
N A:VAL207 4.4 11.7 1.0
CB A:ASP202 4.4 9.1 1.0
CA A:VAL207 4.5 9.8 1.0
O A:HOH515 4.5 13.2 1.0
CA A:PRO205 4.6 12.3 1.0
N A:PHE208 4.7 9.7 1.0
N A:LEU186 4.7 9.4 1.0
CD1 A:LEU186 4.7 11.6 1.0
CB A:VAL207 4.7 9.6 1.0
CB A:ASP209 4.7 9.3 1.0
CA A:PHE208 4.8 10.0 1.0
CB A:GLN211 4.8 7.6 1.0
CA A:ASP209 4.9 8.8 1.0
C A:ASP209 4.9 10.1 1.0
CG2 A:THR204 5.0 12.2 1.0

Reference:

N.Kunishima, K.Fukuyama, H.Matsubara, H.Hatanaka, Y.Shibano, T.Amachi. Crystal Structure of the Fungal Peroxidase From Arthromyces Ramosus at 1.9 A Resolution. Structural Comparisons with the Lignin and Cytochrome C Peroxidases. J.Mol.Biol. V. 235 331 1994.
ISSN: ISSN 0022-2836
PubMed: 8289254
DOI: 10.1016/S0022-2836(05)80037-3
Page generated: Thu Jul 11 06:02:18 2024

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