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Calcium in PDB 6iqy: High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared

Enzymatic activity of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared

All present enzymatic activity of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared:
1.3.3.5;

Protein crystallography data

The structure of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared, PDB code: 6iqy was solved by N.Shibata, M.Akter, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.86 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.298, 152.253, 69.908, 90.00, 91.66, 90.00
R / Rfree (%) 19.1 / 22.5

Other elements in 6iqy:

The structure of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared also contains other interesting chemical elements:

Copper (Cu) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared (pdb code 6iqy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared, PDB code: 6iqy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6iqy

Go back to Calcium Binding Sites List in 6iqy
Calcium binding site 1 out of 2 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca613

b:19.0
occ:0.58
 O A:HOH1006 2.4 22.2 1.0
O A:HOH1402 2.4 40.0 1.0
O A:HOH1061 2.4 26.0 1.0
O A:HOH1106 2.5 29.3 1.0
O A:HOH851 2.6 33.3 1.0
O A:HOH1358 3.3 40.0 1.0
O A:HOH1190 4.4 33.6 1.0
O A:HOH820 4.5 20.4 1.0
O A:ALA496 4.7 13.9 1.0
NE2 A:GLN495 4.8 9.8 1.0
OE1 A:GLU492 4.8 26.3 1.0
O A:HOH949 4.9 29.4 1.0

Calcium binding site 2 out of 2 in 6iqy

Go back to Calcium Binding Sites List in 6iqy
Calcium binding site 2 out of 2 in the High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of High Resolution Structure of Bilirubin Oxidase From Myrothecium Verrucaria - M467Q Mutant, Anaerobically Prepared within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca614

b:16.9
occ:0.55
 O B:HOH938 2.4 19.3 1.0
O B:HOH1444 2.4 34.9 1.0
O B:HOH701 2.5 27.1 1.0
O B:HOH1207 2.5 33.3 1.0
O B:HOH1401 2.5 41.8 1.0
O B:HOH1074 2.5 28.5 1.0
OE2 B:GLU492 4.2 42.4 1.0
O B:HOH834 4.5 21.2 1.0
O B:ALA496 4.6 12.0 1.0
O B:HOH1206 4.6 27.3 1.0
NE2 B:GLN495 4.7 12.1 1.0
O B:HOH953 4.8 26.1 1.0
CB B:GLN495 5.0 12.8 1.0

Reference:

M.Akter, T.Tokiwa, M.Shoji, K.Nishikawa, Y.Shigeta, T.Sakurai, Y.Higuchi, K.Kataoka, N.Shibata. Redox Potential-Dependent Formation of An Unusual His-Trp Bond in Bilirubin Oxidase. Chemistry V. 24 18052 2018.
ISSN: ISSN 1521-3765
PubMed: 30156345
DOI: 10.1002/CHEM.201803798
Page generated: Tue Jul 16 09:33:06 2024

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