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Molybdenum 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:

Magnesium (Mg) 2 atoms
Iron (Fe) 30 atoms
Calcium (Ca) 4 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum 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 Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Selenium Incorporated Femo-Cofactor of Nitrogenase From Azotobacter Vinelandii with Low Concentration of Selenium, PDB code: 6op3:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 6op3

Go back to Molybdenum Binding Sites List in 6op3
Molybdenum binding site 1 out of 2 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 Molybdenum with other atoms in the Mo 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
A:Mo502

b:7.2
occ:1.00
MO1 A:ICS502 0.0 7.2 1.0
O6 A:HCA501 2.2 6.8 1.0
O7 A:HCA501 2.2 7.3 1.0
S4B A:ICS502 2.3 7.9 1.0
S1B A:ICS502 2.3 7.7 1.0
S3B A:ICS502 2.4 7.2 1.0
ND1 A:HIS442 2.4 6.7 1.0
FE6 A:ICS502 2.7 7.5 1.0
FE7 A:ICS502 2.7 7.7 1.0
FE5 A:ICS502 2.7 7.7 1.0
C7 A:HCA501 3.0 7.9 1.0
C3 A:HCA501 3.1 7.9 1.0
CE1 A:HIS442 3.3 7.8 1.0
CG A:HIS442 3.4 7.2 1.0
CX A:ICS502 3.5 7.3 1.0
CB A:HIS442 3.7 7.7 1.0
C2 A:HCA501 4.1 8.4 1.0
O A:HOH856 4.2 9.1 1.0
O5 A:HCA501 4.2 8.0 1.0
C5 A:HCA501 4.2 8.8 1.0
O2 A:HCA501 4.2 12.6 1.0
C4 A:HCA501 4.2 8.6 1.0
NE2 A:HIS442 4.4 6.8 1.0
CD2 A:HIS442 4.5 7.1 1.0
CA A:HIS442 4.6 7.8 1.0
C1 A:HCA501 4.7 10.7 1.0
S5A A:ICS502 4.8 6.9 1.0
SE A:SE505 4.8 9.2 1.0
S3A A:ICS502 4.9 6.4 1.0

Molybdenum binding site 2 out of 2 in 6op3

Go back to Molybdenum Binding Sites List in 6op3
Molybdenum binding site 2 out of 2 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 Molybdenum with other atoms in the Mo 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:Mo502

b:7.2
occ:1.00
MO1 C:ICS502 0.0 7.2 1.0
O5 C:HCA501 2.2 7.0 1.0
O7 C:HCA501 2.2 8.3 1.0
S4B C:ICS502 2.3 7.7 1.0
S1B C:ICS502 2.4 7.2 1.0
S3B C:ICS502 2.4 7.6 1.0
ND1 C:HIS442 2.4 7.5 1.0
FE6 C:ICS502 2.7 7.5 1.0
FE7 C:ICS502 2.7 7.4 1.0
FE5 C:ICS502 2.7 7.5 1.0
C7 C:HCA501 3.0 8.4 1.0
C3 C:HCA501 3.2 8.2 1.0
CE1 C:HIS442 3.3 7.5 1.0
CG C:HIS442 3.4 8.0 1.0
CX C:ICS502 3.5 6.9 1.0
CB C:HIS442 3.7 7.7 1.0
C2 C:HCA501 4.1 8.4 1.0
O C:HOH878 4.2 8.0 1.0
C5 C:HCA501 4.2 8.2 1.0
O6 C:HCA501 4.2 7.7 1.0
O1 C:HCA501 4.3 12.3 1.0
C4 C:HCA501 4.3 8.5 1.0
NE2 C:HIS442 4.4 7.3 1.0
CD2 C:HIS442 4.5 8.0 1.0
CA C:HIS442 4.6 7.5 1.0
C1 C:HCA501 4.7 11.4 1.0
S5A C:ICS502 4.8 6.9 1.0
SE C:SE504 4.8 9.0 1.0
S3A C:ICS502 4.9 6.5 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 Dec 15 05:21:00 2020

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