Magnesium 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
Iron (Fe) 30 atoms
Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii at High Concentration of Selenium, PDB code: 6op2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6op2

Go back to Magnesium Binding Sites List in 6op2
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg605

b:36.6
occ:1.00
O B:HOH883 2.3 21.7 1.0
O D:HOH1018 2.8 18.2 1.0
O B:HOH928 3.0 15.5 1.0
O B:HOH982 3.5 32.1 1.0
O D:HOH876 3.8 22.9 1.0
CE B:LYS365 3.9 16.5 1.0
O B:HOH1026 4.1 17.3 1.0
NZ B:LYS365 4.2 16.8 1.0
CD1 B:LEU505 4.2 11.6 1.0
CB B:LEU505 4.3 10.5 1.0
CZ3 B:TRP361 4.4 11.9 1.0
CD2 B:LEU505 4.4 11.2 1.0
CG2 B:ILE501 4.5 12.9 1.0
CG B:LEU505 4.5 10.9 1.0
CE3 B:TRP361 4.6 12.0 1.0

Magnesium binding site 2 out of 2 in 6op2

Go back to Magnesium Binding Sites List in 6op2
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg606

b:54.0
occ:1.00
O D:HOH731 2.6 18.3 1.0
CE D:LYS9 3.5 17.0 1.0
CG D:PRO13 3.7 13.4 1.0
CD D:LYS9 3.9 14.5 1.0
CB D:PRO13 4.0 13.3 1.0
O D:HOH1019 4.1 26.1 1.0
OD1 D:ASP17 4.3 18.4 1.0
O D:PRO13 4.6 11.8 1.0
CG D:LYS9 4.8 14.2 1.0
NZ D:LYS9 4.8 18.0 1.0
C D:PRO13 5.0 12.6 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: Mon Dec 14 23:44:09 2020

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