Calcium in PDB 6op4: Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii

Enzymatic activity of Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii

All present enzymatic activity of Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii, PDB code: 6op4 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) 39.41 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.981, 129.326, 106.755, 90.00, 108.84, 90.00
R / Rfree (%) 17.6 / 22.3

Other elements in 6op4:

The structure of Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii 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, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii (pdb code 6op4). 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, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii, PDB code: 6op4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6op4

Go back to Calcium Binding Sites List in 6op4
Calcium binding site 1 out of 2 in the Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

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

b:39.0
occ:1.00
OD2 B:ASP357 2.2 28.0 1.0
O D:ARG108 2.2 20.8 1.0
OD2 B:ASP353 2.2 28.5 1.0
OE2 D:GLU109 2.4 27.9 1.0
O B:HOH708 2.4 34.9 1.0
O D:HOH771 2.4 30.7 1.0
CG B:ASP357 2.9 23.2 1.0
OD1 B:ASP357 2.9 26.8 1.0
CG B:ASP353 3.0 25.0 1.0
OD1 B:ASP353 3.2 26.6 1.0
C D:ARG108 3.4 21.3 1.0
CD D:GLU109 3.5 26.1 1.0
CG D:GLU109 3.9 24.8 1.0
O B:HOH713 4.0 38.7 1.0
CB D:ARG108 4.1 21.1 1.0
N D:GLU109 4.3 20.7 1.0
O D:PHE107 4.3 18.8 1.0
CA D:GLU109 4.3 21.0 1.0
CD1 C:PHE429 4.3 23.5 1.0
CA D:ARG108 4.4 21.2 1.0
CB B:ASP357 4.4 20.3 1.0
NZ C:LYS433 4.4 30.0 1.0
CB B:ASP353 4.5 23.1 1.0
O B:ASP353 4.5 22.6 1.0
OE1 D:GLU109 4.5 33.8 1.0
O D:HOH790 4.7 21.9 1.0
O D:HOH802 4.8 35.2 1.0
CB D:GLU109 4.8 21.9 1.0
CE1 C:PHE429 4.8 21.4 1.0
C B:ASP353 4.8 21.2 1.0
O D:HOH865 4.8 22.4 1.0
CE C:LYS433 4.8 28.1 1.0
CG C:PHE429 5.0 20.8 1.0

Calcium binding site 2 out of 2 in 6op4

Go back to Calcium Binding Sites List in 6op4
Calcium binding site 2 out of 2 in the Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Selenium-Incorporated, Carbon Monoxide-Inhibited, Reactivated Femo- Cofactor of Nitrogenase From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:37.5
occ:1.00
O B:ARG108 2.1 18.6 1.0
OD2 D:ASP357 2.2 27.3 1.0
OD2 D:ASP353 2.2 30.6 1.0
O B:HOH781 2.4 25.6 1.0
OE2 B:GLU109 2.4 28.3 1.0
O D:HOH739 2.4 32.0 1.0
CG D:ASP357 2.9 23.8 1.0
OD1 D:ASP357 3.0 26.7 1.0
CG D:ASP353 3.1 26.0 1.0
C B:ARG108 3.3 20.7 1.0
OD1 D:ASP353 3.3 28.6 1.0
CD B:GLU109 3.5 27.8 1.0
O D:HOH770 4.0 31.1 1.0
CB B:ARG108 4.0 20.3 1.0
CG B:GLU109 4.1 26.0 1.0
N B:GLU109 4.2 21.4 1.0
O B:PHE107 4.2 19.5 1.0
NZ A:LYS433 4.3 26.3 1.0
CA B:ARG108 4.3 20.0 1.0
CA B:GLU109 4.3 21.4 1.0
CD1 A:PHE429 4.4 24.2 1.0
CB D:ASP357 4.4 18.9 1.0
O D:ASP353 4.5 21.1 1.0
CB D:ASP353 4.5 23.4 1.0
OE1 B:GLU109 4.5 32.2 1.0
CE A:LYS433 4.6 23.7 1.0
CE1 A:PHE429 4.7 23.3 1.0
O B:HOH834 4.8 20.6 1.0
O B:HOH831 4.8 21.5 1.0
CB B:GLU109 4.8 24.0 1.0
O B:HOH744 4.8 30.6 1.0
C D:ASP353 4.8 20.0 1.0
CG A:PHE429 4.9 22.3 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 07:24:28 2020

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