Calcium in PDB 1c8i: Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase

All present enzymatic activity of Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase:
1.11.1.7;

The structure of Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase, PDB code: 1c8i was solved by H.Wariishi, D.Nonaka, T.Johjima, N.Nakamura, Y.Naruta, K.Kubo, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 2.00
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.400, 74.400, 117.500, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 22.3

The structure of Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Calcium atom in the Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase (pdb code 1c8i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase, PDB code: 1c8i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca346 b:19.1 occ:1.00 OD1 A:ASP57 2.3 21.4 1.0 O A:HOH424 2.4 17.2 1.0 OD1 A:ASP77 2.5 22.4 1.0 O A:ASP57 2.5 20.5 1.0 O A:GLY75 2.5 19.8 1.0 O A:HOH425 2.6 19.8 1.0 OG A:SER79 2.6 16.6 1.0 CG A:ASP57 3.4 21.5 1.0 C A:ASP57 3.4 19.4 1.0 CG A:ASP77 3.5 20.7 1.0 C A:GLY75 3.7 19.6 1.0 CB A:SER79 3.7 15.4 1.0 CA A:ASP57 3.8 18.7 1.0 OD2 A:ASP77 3.9 22.4 1.0 N A:SER79 3.9 18.6 1.0 O A:HOH363 4.1 19.5 1.0 N A:ASP77 4.1 18.0 1.0 CB A:ASP57 4.2 16.9 1.0 OD2 A:ASP57 4.2 20.7 1.0 CA A:SER79 4.4 18.4 1.0 N A:GLY75 4.4 20.4 1.0 N A:GLY78 4.5 15.9 1.0 CA A:GLY75 4.5 18.8 1.0 O A:GLY60 4.5 17.0 1.0 N A:ALA58 4.5 19.4 1.0 N A:ILE80 4.5 18.8 1.0 CB A:ASP77 4.7 17.7 1.0 OE2 A:GLU87 4.7 16.8 1.0 N A:ALA76 4.7 18.3 1.0 CA A:ASP77 4.8 18.5 1.0 OE1 A:GLU87 4.8 18.1 1.0 C A:SER79 4.9 19.8 1.0 C A:ASP77 4.9 18.1 1.0 CB A:SER148 4.9 21.2 1.0 CA A:ALA76 4.9 18.2 1.0 C A:GLY74 5.0 22.7 1.0 C A:GLY78 5.0 17.1 1.0

Calcium binding site 2 out of 2 in the Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Binding Mode of Hydroxylamine to Arthromyces Ramosus Peroxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca347 b:17.3 occ:1.00 O A:SER185 2.4 18.1 1.0 OD1 A:ASP209 2.4 15.5 1.0 O A:THR204 2.5 18.6 1.0 OG A:SER185 2.5 17.5 1.0 OD2 A:ASP202 2.5 16.4 1.0 O A:VAL207 2.5 18.0 1.0 OG1 A:THR204 2.6 17.3 1.0 OD1 A:ASP202 2.7 15.4 1.0 CG A:ASP202 2.9 19.0 1.0 C A:THR204 3.3 17.5 1.0 C A:SER185 3.4 15.7 1.0 CG A:ASP209 3.4 16.2 1.0 CB A:SER185 3.5 16.4 1.0 CB A:THR204 3.6 15.7 1.0 CA A:SER185 3.7 17.1 1.0 C A:VAL207 3.8 16.5 1.0 OD2 A:ASP209 3.8 15.9 1.0 CA A:THR204 3.9 15.9 1.0 N A:ASP209 4.1 17.1 1.0 N A:THR204 4.2 17.8 1.0 N A:PRO205 4.3 17.6 1.0 N A:VAL207 4.4 17.2 1.0 CB A:ASP202 4.4 15.0 1.0 O A:ASP209 4.5 17.3 1.0 CA A:VAL207 4.5 16.9 1.0 O A:HOH515 4.6 20.2 1.0 CA A:PRO205 4.6 19.3 1.0 N A:LEU186 4.6 15.6 1.0 CB A:ASP209 4.6 13.0 1.0 CB A:GLN211 4.7 14.1 1.0 CB A:VAL207 4.7 12.8 1.0 N A:PHE208 4.7 17.9 1.0 CA A:ASP209 4.8 15.0 1.0 CA A:PHE208 4.8 16.6 1.0 CD1 A:LEU186 4.8 18.9 1.0 C A:ASP209 4.9 17.5 1.0 CG2 A:THR204 4.9 12.8 1.0 C A:PRO205 4.9 20.3 1.0 C A:PHE208 4.9 17.7 1.0

H.Wariishi, D.Nonaka, T.Johjima, N.Nakamura, Y.Naruta, S.Kubo, K.Fukuyama. Direct Binding of Hydroxylamine to the Heme Iron of Arthromyces Ramosus Peroxidase. Substrate Analogue That Inhibits Compound I Formation in A Competetive Manner. J.Biol.Chem. V. 275 32919 2000.
ISSN: ISSN 0021-9258
PubMed: 10915789
DOI: 10.1074/JBC.M004223200