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Molybdenum 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:

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

Molybdenum Binding Sites:

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

Molybdenum binding site 1 out of 2 in 6op2

Go back to Molybdenum Binding Sites List in 6op2
Molybdenum 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 Molybdenum with other atoms in the Mo 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
A:Mo502

b:7.8
occ:1.00
MO1 A:ICS502 0.0 7.8 1.0
O7 A:HCA501 2.0 12.1 1.0
O6 A:HCA501 2.2 10.5 1.0
S4B A:ICS502 2.3 8.9 1.0
S1B A:ICS502 2.3 7.8 1.0
S3B A:ICS502 2.4 8.9 1.0
ND1 A:HIS442 2.5 9.1 1.0
FE7 A:ICS502 2.6 8.2 1.0
FE6 A:ICS502 2.6 8.9 1.0
FE5 A:ICS502 2.7 9.2 1.0
C7 A:HCA501 2.9 11.0 1.0
C3 A:HCA501 3.1 12.5 1.0
CE1 A:HIS442 3.2 9.4 1.0
CX A:ICS502 3.5 8.4 1.0
CG A:HIS442 3.6 8.7 1.0
CB A:HIS442 4.0 9.4 1.0
C2 A:HCA501 4.1 12.6 1.0
O5 A:HCA501 4.1 10.1 1.0
O A:HOH605 4.2 22.4 1.0
O A:HOH780 4.2 7.8 1.0
C4 A:HCA501 4.2 12.3 1.0
O2 A:HCA501 4.3 15.8 1.0
C5 A:HCA501 4.4 13.2 1.0
NE2 A:HIS442 4.4 9.8 1.0
CD2 A:HIS442 4.7 9.5 1.0
CA A:HIS442 4.7 8.8 1.0
C1 A:HCA501 4.7 13.3 1.0
S5A A:ICS502 4.7 6.7 1.0
SE A:SE505 4.9 11.8 1.0
S3A A:ICS502 4.9 8.0 1.0
FE2 A:ICS502 4.9 8.7 1.0

Molybdenum binding site 2 out of 2 in 6op2

Go back to Molybdenum Binding Sites List in 6op2
Molybdenum 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 Molybdenum with other atoms in the Mo 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
C:Mo502

b:8.3
occ:1.00
MO1 C:ICS502 0.0 8.3 1.0
O5 C:HCA501 2.2 9.0 1.0
S4B C:ICS502 2.3 9.6 1.0
O7 C:HCA501 2.3 13.3 1.0
S1B C:ICS502 2.4 8.5 1.0
S3B C:ICS502 2.4 9.3 1.0
FE6 C:ICS502 2.6 8.3 1.0
FE7 C:ICS502 2.6 8.4 1.0
CD2 C:HIS442 2.7 12.7 1.0
FE5 C:ICS502 2.7 9.0 1.0
C7 C:HCA501 3.0 11.1 1.0
C3 C:HCA501 3.2 11.7 1.0
CG C:HIS442 3.4 11.3 1.0
CX C:ICS502 3.5 8.7 1.0
CB C:HIS442 3.7 11.0 1.0
NE2 C:HIS442 3.9 11.9 1.0
O C:HOH730 4.0 45.8 1.0
O C:HOH811 4.1 31.9 1.0
O C:HOH759 4.1 1.6 1.0
C2 C:HCA501 4.1 11.9 1.0
C4 C:HCA501 4.2 12.0 1.0
O1 C:HCA501 4.2 13.2 1.0
C5 C:HCA501 4.2 11.6 1.0
O6 C:HCA501 4.2 11.5 1.0
CA C:HIS442 4.6 10.2 1.0
C1 C:HCA501 4.7 13.0 1.0
ND1 C:HIS442 4.7 13.1 1.0
S5A C:ICS502 4.8 7.0 1.0
SE C:SE505 4.9 14.0 1.0
CE1 C:HIS442 4.9 12.1 1.0
S3A C:ICS502 4.9 8.2 1.0
FE2 C:ICS502 4.9 8.9 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: Sun Oct 6 16:50:09 2024

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