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Calcium in PDB 6op3: Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium

Enzymatic activity of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium

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

Protein crystallography data

The structure of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium, PDB code: 6op3 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) 37.85 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.872, 131.023, 106.957, 90.00, 110.62, 90.00
R / Rfree (%) 12.7 / 15.2

Other elements in 6op3:

The structure of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low 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 with Low Concentration of Selenium (pdb code 6op3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium, PDB code: 6op3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6op3

Go back to Calcium Binding Sites List in 6op3
Calcium binding site 1 out of 4 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low 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 with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca607

b:19.2
occ:1.00
 O B:HOH764 2.0 15.2 1.0
O D:ARG108 2.1 7.3 1.0
OD2 B:ASP353 2.1 14.0 1.0
OD2 B:ASP357 2.1 13.0 1.0
OE2 D:GLU109 2.2 13.9 1.0
O D:HOH1018 2.3 11.1 1.0
CG B:ASP357 3.0 10.7 1.0
CG B:ASP353 3.1 11.9 1.0
OD1 B:ASP357 3.2 12.6 1.0
C D:ARG108 3.3 7.9 1.0
CD D:GLU109 3.3 12.8 1.0
OD1 B:ASP353 3.5 13.8 1.0
CG D:GLU109 3.9 10.4 1.0
CB D:ARG108 4.0 8.3 1.0
O B:HOH1104 4.2 18.9 1.0
N D:GLU109 4.2 8.2 1.0
CA D:ARG108 4.2 8.0 1.0
NZ C:LYS433 4.3 14.3 1.0
O D:PHE107 4.3 7.8 1.0
CA D:GLU109 4.3 8.5 1.0
OE1 D:GLU109 4.3 16.1 1.0
CD1 C:PHE429 4.4 11.5 1.0
CB B:ASP357 4.4 9.3 1.0
CB B:ASP353 4.5 10.7 1.0
O B:ASP353 4.6 9.2 1.0
O D:HOH1001 4.6 11.6 1.0
CB D:GLU109 4.8 9.7 1.0
C B:ASP353 4.9 9.4 1.0
CE C:LYS433 4.9 15.1 1.0
O D:HOH1079 4.9 13.4 1.0
CE1 C:PHE429 4.9 11.2 1.0
O D:HOH750 5.0 16.5 1.0

Calcium binding site 2 out of 4 in 6op3

Go back to Calcium Binding Sites List in 6op3
Calcium binding site 2 out of 4 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low 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 with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca506

b:36.1
occ:1.00
 O C:HOH757 3.2 20.5 1.0
O C:HOH927 3.3 33.1 1.0
O C:HOH992 3.3 23.4 1.0
CE C:LYS332 3.7 24.2 1.0
CD C:LYS332 3.7 19.4 1.0
CG2 C:ILE328 3.7 14.2 1.0
CG C:LYS332 3.9 16.2 1.0
CB C:LYS332 4.4 13.7 1.0
CZ2 C:TRP335 4.4 15.9 1.0
CD1 C:ILE306 4.4 13.8 1.0
O C:HOH916 4.5 31.4 1.0
O C:ILE328 4.8 12.5 1.0
NE1 C:TRP335 5.0 14.7 1.0

Calcium binding site 3 out of 4 in 6op3

Go back to Calcium Binding Sites List in 6op3
Calcium binding site 3 out of 4 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca607

b:35.3
occ:1.00
 CA D:CA608 2.1 19.6 1.0
OD1 D:ASP357 2.6 12.8 1.0
OD1 D:ASP353 2.7 13.9 1.0
OD2 D:ASP353 2.9 13.7 1.0
O B:ARG108 2.9 7.3 1.0
OE2 B:GLU109 3.1 14.8 1.0
CG D:ASP353 3.1 12.2 1.0
OD2 D:ASP357 3.2 13.1 1.0
CG D:ASP357 3.2 10.2 1.0
CD1 A:PHE429 3.4 10.1 1.0
O D:HOH773 3.6 37.8 1.0
CB A:PHE429 3.8 9.4 1.0
NZ A:LYS433 3.8 13.2 1.0
OE1 A:GLN432 3.9 18.7 1.0
CG A:PHE429 4.0 9.8 1.0
CE A:LYS433 4.0 13.7 1.0
C B:ARG108 4.1 7.4 1.0
CD B:GLU109 4.3 13.5 1.0
CE1 A:PHE429 4.3 10.5 1.0
O B:HOH1028 4.3 11.2 1.0
CA A:PHE429 4.4 9.1 1.0
O D:ASP353 4.5 9.4 1.0
OG1 D:THR356 4.5 10.8 1.0
O A:PHE429 4.5 12.9 1.0
CA B:GLU109 4.6 8.4 1.0
CB D:ASP353 4.6 9.3 1.0
CG A:LYS433 4.7 13.8 1.0
N B:GLU109 4.7 7.6 1.0
CB D:ASP357 4.7 9.3 1.0
CD A:LYS433 4.9 14.7 1.0
C A:PHE429 4.9 10.8 1.0
OE1 B:GLU109 5.0 16.5 1.0

Calcium binding site 4 out of 4 in 6op3

Go back to Calcium Binding Sites List in 6op3
Calcium binding site 4 out of 4 in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca608

b:19.6
occ:1.00
 O B:ARG108 2.1 7.3 1.0
CA D:CA607 2.1 35.3 1.0
OD2 D:ASP353 2.1 13.7 1.0
OD2 D:ASP357 2.1 13.1 1.0
OE2 B:GLU109 2.2 14.8 1.0
O B:HOH1028 2.2 11.2 1.0
CG D:ASP357 3.0 10.2 1.0
CG D:ASP353 3.1 12.2 1.0
OD1 D:ASP357 3.2 12.8 1.0
C B:ARG108 3.3 7.4 1.0
CD B:GLU109 3.4 13.5 1.0
OD1 D:ASP353 3.5 13.9 1.0
CG B:GLU109 4.0 10.7 1.0
CB B:ARG108 4.0 7.7 1.0
O D:HOH1075 4.1 19.1 1.0
N B:GLU109 4.2 7.6 1.0
CA B:ARG108 4.2 7.0 1.0
NZ A:LYS433 4.3 13.2 1.0
O B:PHE107 4.3 7.8 1.0
CA B:GLU109 4.3 8.4 1.0
CB D:ASP357 4.4 9.3 1.0
OE1 B:GLU109 4.4 16.5 1.0
CD1 A:PHE429 4.4 10.1 1.0
CB D:ASP353 4.5 9.3 1.0
O D:ASP353 4.6 9.4 1.0
O B:HOH949 4.7 10.7 1.0
CB B:GLU109 4.8 10.2 1.0
CE1 A:PHE429 4.9 10.5 1.0
O B:HOH1038 4.9 12.2 1.0
O B:HOH743 4.9 15.6 1.0
C D:ASP353 4.9 8.9 1.0
CE A:LYS433 4.9 13.7 1.0
CG A:PHE429 5.0 9.8 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: Tue Jul 16 12:33:34 2024

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