Calcium in PDB 6op2: Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium

Enzymatic activity of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium

All present enzymatic activity of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium:
1.18.6.1;

Protein crystallography data

The structure of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium, PDB code: 6op2 was solved by R.J.Arias, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.81 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.761, 130.380, 106.896, 90.00, 110.54, 90.00
R / Rfree (%) 17.7 / 21.5

Other elements in 6op2:

The structure of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium also contains other interesting chemical elements:

Molybdenum (Mo) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 30 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium (pdb code 6op2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium, PDB code: 6op2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6op2

Go back to Calcium Binding Sites List in 6op2
Calcium binding site 1 out of 2 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:36.7
occ:1.00
 O D:ARG108 2.2 12.4 1.0
OD2 B:ASP357 2.2 15.2 1.0
OD2 B:ASP353 2.2 18.3 1.0
O D:HOH873 2.2 11.1 1.0
O B:HOH743 2.3 13.0 1.0
OE2 D:GLU109 2.4 21.8 1.0
CG B:ASP357 2.9 13.4 1.0
OD1 B:ASP357 3.0 14.1 1.0
CG B:ASP353 3.1 15.8 1.0
C D:ARG108 3.4 12.2 1.0
OD1 B:ASP353 3.5 18.1 1.0
CD D:GLU109 3.5 19.1 1.0
CB D:ARG108 4.0 12.0 1.0
CG D:GLU109 4.0 17.6 1.0
O B:HOH921 4.2 23.8 1.0
O D:PHE107 4.2 9.4 1.0
CA D:ARG108 4.3 11.8 1.0
N D:GLU109 4.3 13.5 1.0
CD1 C:PHE429 4.3 13.9 1.0
CA D:GLU109 4.4 14.2 1.0
CB B:ASP357 4.4 11.4 1.0
NZ C:LYS433 4.5 12.7 1.0
OE1 D:GLU109 4.5 21.8 1.0
O D:HOH926 4.5 17.5 1.0
CB B:ASP353 4.5 14.9 1.0
O B:ASP353 4.5 10.9 1.0
CE1 C:PHE429 4.8 13.2 1.0
O D:HOH861 4.8 20.7 1.0
CB D:GLU109 4.8 15.5 1.0
C B:ASP353 4.8 12.6 1.0
O D:HOH862 4.8 15.5 1.0
CG C:PHE429 4.9 12.8 1.0

Calcium binding site 2 out of 2 in 6op2

Go back to Calcium Binding Sites List in 6op2
Calcium binding site 2 out of 2 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:32.5
occ:1.00
 O B:ARG108 2.0 10.2 1.0
OD2 D:ASP357 2.2 13.7 1.0
O D:HOH760 2.3 20.9 1.0
OD2 D:ASP353 2.3 20.4 1.0
O B:HOH816 2.4 18.0 1.0
OE2 B:GLU109 2.6 21.3 1.0
CG D:ASP357 3.0 11.7 1.0
OD1 D:ASP357 3.1 12.8 1.0
CG D:ASP353 3.2 16.0 1.0
C B:ARG108 3.2 10.0 1.0
OD1 D:ASP353 3.3 18.7 1.0
CD B:GLU109 3.5 16.2 1.0
CB B:ARG108 3.9 10.1 1.0
CG B:GLU109 4.1 14.6 1.0
O D:HOH723 4.1 23.0 1.0
N B:GLU109 4.2 10.8 1.0
CA B:ARG108 4.2 9.7 1.0
CD1 A:PHE429 4.2 13.7 1.0
CA B:GLU109 4.3 11.3 1.0
O B:PHE107 4.3 8.9 1.0
NZ A:LYS433 4.4 15.8 1.0
CB D:ASP357 4.5 10.7 1.0
OE1 B:GLU109 4.5 19.5 1.0
CB D:ASP353 4.6 14.2 1.0
O D:ASP353 4.6 10.6 1.0
O B:HOH950 4.7 16.1 1.0
CE1 A:PHE429 4.7 12.9 1.0
O B:HOH889 4.7 18.5 1.0
CB B:GLU109 4.8 12.7 1.0
CE A:LYS433 4.8 15.6 1.0
CG A:PHE429 4.9 12.8 1.0
C D:ASP353 4.9 11.7 1.0
O B:HOH775 5.0 17.8 1.0

Reference:

J.T.Henthorn, R.J.Arias, S.Koroidov, T.Kroll, D.Sokaras, U.Bergmann, D.C.Rees, S.Debeer. Localized Electronic Structure of Nitrogenase Femoco Revealed By Selenium K-Edge High Resolution X-Ray Absorption Spectroscopy. J.Am.Chem.Soc. V. 141 13676 2019.
ISSN: ESSN 1520-5126
PubMed: 31356071
DOI: 10.1021/JACS.9B06988
Page generated: Sat Dec 12 07:24:24 2020

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