Calcium in PDB 2e39: Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution

All present enzymatic activity of Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution:
1.11.1.7;

The structure of Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution, PDB code: 2e39 was solved by K.Fukuyama, T.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.30
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.840, 73.840, 115.680, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 20.3

The structure of Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution (pdb code 2e39). 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 Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution, PDB code: 2e39:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution


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 Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:8.8 occ:1.00 O A:HOH1065 2.3 9.3 1.0 OD1 A:ASP57 2.3 9.2 1.0 OD1 A:ASP77 2.4 9.4 1.0 OG A:SER79 2.5 9.0 1.0 O A:HOH1066 2.5 9.3 1.0 O A:GLY75 2.5 9.2 1.0 O A:ASP57 2.5 8.2 1.0 HA A:ASP57 3.2 9.8 1.0 H A:ASP77 3.3 12.0 1.0 H A:SER79 3.3 11.2 1.0 CG A:ASP57 3.3 8.3 1.0 C A:ASP57 3.4 7.4 1.0 CG A:ASP77 3.4 10.6 1.0 CB A:SER79 3.6 9.9 1.0 HB3 A:SER79 3.6 11.9 1.0 C A:GLY75 3.7 8.3 1.0 CA A:ASP57 3.7 8.2 1.0 H A:ILE80 3.8 9.6 1.0 OD2 A:ASP77 4.0 11.2 1.0 N A:SER79 4.0 9.3 1.0 HB2 A:SER148 4.0 13.0 1.0 O A:HOH1010 4.1 11.3 1.0 N A:ASP77 4.1 10.0 1.0 OD2 A:ASP57 4.2 9.1 1.0 CB A:ASP57 4.2 8.0 1.0 H A:GLY78 4.2 10.7 1.0 H A:GLY75 4.2 12.3 1.0 HA3 A:GLY60 4.3 10.8 1.0 CA A:SER79 4.3 9.4 1.0 HB2 A:SER79 4.3 11.9 1.0 N A:GLY75 4.3 10.3 1.0 HA A:ALA76 4.4 11.1 1.0 H A:GLY60 4.4 9.8 1.0 CA A:GLY75 4.4 8.3 1.0 HA A:ALA58 4.5 9.7 1.0 N A:ILE80 4.5 8.0 1.0 HA2 A:GLY75 4.5 10.0 1.0 N A:ALA58 4.5 8.4 1.0 O A:GLY60 4.5 9.3 1.0 N A:GLY78 4.5 8.9 1.0 OE2 A:GLU87 4.6 9.2 1.0 HB A:ILE80 4.6 10.3 1.0 CB A:ASP77 4.6 10.5 1.0 N A:ALA76 4.7 9.1 1.0 OE1 A:GLU87 4.7 9.2 1.0 CA A:ASP77 4.8 10.5 1.0 H A:GLY74 4.8 13.4 1.0 O A:HIS56 4.8 9.8 1.0 HB2 A:ASP57 4.8 9.6 1.0 C A:SER79 4.8 8.4 1.0 HB3 A:ASP57 4.8 9.6 1.0 CA A:ALA76 4.9 9.3 1.0 C A:ASP77 4.9 9.2 1.0 CA A:GLY60 4.9 9.0 1.0 CA A:ALA58 5.0 8.1 1.0 CB A:SER148 5.0 10.8 1.0 C A:GLY78 5.0 9.7 1.0 C A:GLY74 5.0 10.0 1.0 C A:ALA76 5.0 9.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution


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 Cn-Bound Form of Arthromyces Ramosus Peroxidase at 1.3 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:7.8 occ:1.00 O A:THR204 2.4 8.1 1.0 O A:SER185 2.4 7.5 1.0 O A:VAL207 2.4 8.3 1.0 OD2 A:ASP202 2.5 8.2 1.0 OD1 A:ASP209 2.5 8.6 1.0 OG A:SER185 2.5 7.9 1.0 OG1 A:THR204 2.5 8.7 1.0 OD1 A:ASP202 2.7 8.2 1.0 CG A:ASP202 2.9 7.9 1.0 C A:THR204 3.3 7.8 1.0 HA A:SER185 3.4 7.9 1.0 C A:SER185 3.4 6.5 1.0 CG A:ASP209 3.4 7.6 1.0 H A:ASP209 3.5 9.3 1.0 CB A:THR204 3.6 8.7 1.0 CB A:SER185 3.6 8.0 1.0 HB2 A:GLN211 3.6 10.9 1.0 C A:VAL207 3.6 7.9 1.0 CA A:SER185 3.7 6.6 1.0 HB A:THR204 3.7 10.4 1.0 H A:THR204 3.7 9.5 1.0 H A:VAL207 3.8 10.7 1.0 OD2 A:ASP209 3.8 9.7 1.0 CA A:THR204 3.8 8.3 1.0 HA A:PRO205 3.9 9.9 1.0 HB A:VAL207 4.0 10.6 1.0 HB3 A:SER185 4.1 9.6 1.0 N A:ASP209 4.2 7.8 1.0 HA A:PHE208 4.2 9.2 1.0 N A:THR204 4.2 8.0 1.0 N A:PRO205 4.3 8.4 1.0 HB2 A:SER185 4.3 9.6 1.0 H A:PHE212 4.4 10.1 1.0 N A:VAL207 4.4 8.9 1.0 CB A:ASP202 4.4 8.4 1.0 O A:ASP209 4.5 8.9 1.0 CA A:VAL207 4.5 9.0 1.0 O A:HOH1134 4.5 9.8 1.0 H A:GLN211 4.5 10.1 1.0 CA A:PRO205 4.5 8.2 1.0 CB A:GLN211 4.6 9.1 1.0 N A:LEU186 4.6 6.7 1.0 HA A:LEU186 4.6 7.6 1.0 N A:PHE208 4.6 7.4 1.0 CB A:ASP209 4.7 8.2 1.0 CB A:VAL207 4.7 8.8 1.0 HB2 A:ASP202 4.8 10.0 1.0 CA A:ASP209 4.8 7.9 1.0 CA A:PHE208 4.8 7.6 1.0 HA A:THR204 4.8 10.0 1.0 HB3 A:ASP202 4.8 10.0 1.0 C A:ASP209 4.8 7.5 1.0 HG2 A:GLN211 4.8 12.8 1.0 CG2 A:THR204 4.9 10.2 1.0 HB2 A:PHE212 4.9 9.9 1.0 C A:PHE208 5.0 8.0 1.0

K.Fukuyama, T.Okada. Structures of Cyanide, Nitric Oxide and Hydroxylamine Complexes of Arthromyces Ramosusperoxidase at 100 K Refined to 1.3 A Resolution: Coordination Geometries of the Ligands to the Haem Iron Acta Crystallogr.,Sect.D V. 63 472 2007.
ISSN: ISSN 0907-4449
PubMed: 17372351
DOI: 10.1107/S0907444907003812