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Molybdenum in PDB 5bvg: Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii

Enzymatic activity of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii

All present enzymatic activity of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii:
1.18.6.1;

Protein crystallography data

The structure of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii, PDB code: 5bvg was solved by T.Spatzal, K.A.Perez, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.38 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.582, 130.825, 107.128, 90.00, 108.85, 90.00
R / Rfree (%) 15.2 / 17.9

Other elements in 5bvg:

The structure of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii also contains other interesting chemical elements:

Iron (Fe) 32 atoms
Chlorine (Cl) 2 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii (pdb code 5bvg). 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 Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii, PDB code: 5bvg:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 5bvg

Go back to Molybdenum Binding Sites List in 5bvg
Molybdenum binding site 1 out of 2 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo502

b:8.9
occ:1.00
MO1 A:ICG502 0.0 8.9 1.0
O7 A:HCA501 2.2 9.6 1.0
O6 A:HCA501 2.2 9.1 1.0
S4B A:ICG502 2.3 9.0 1.0
S1B A:ICG502 2.3 9.6 1.0
S3B A:ICG502 2.4 9.4 1.0
ND1 A:HIS442 2.4 10.2 1.0
FE6 A:ICG502 2.7 9.2 1.0
FE7 A:ICG502 2.7 8.9 1.0
FE5 A:ICG502 2.7 9.4 1.0
C7 A:HCA501 3.0 9.6 1.0
C3 A:HCA501 3.2 9.4 1.0
CE1 A:HIS442 3.3 9.9 1.0
CG A:HIS442 3.4 10.1 1.0
CX A:ICG502 3.5 9.1 1.0
CB A:HIS442 3.7 9.9 1.0
C2 A:HCA501 4.1 9.5 1.0
O A:HOH709 4.1 7.7 1.0
O5 A:HCA501 4.2 9.9 1.0
C4 A:HCA501 4.3 9.6 1.0
C5 A:HCA501 4.3 9.4 1.0
O2 A:HCA501 4.4 10.9 1.0
NE2 A:HIS442 4.5 9.8 1.0
CD2 A:HIS442 4.6 10.0 1.0
CA A:HIS442 4.6 9.6 1.0
C1 A:HCA501 4.8 10.1 1.0
S5A A:ICG502 4.8 8.9 1.0
SE2B A:ICG502 4.8 11.6 1.0
S3A A:ICG502 4.9 9.2 1.0

Molybdenum binding site 2 out of 2 in 5bvg

Go back to Molybdenum Binding Sites List in 5bvg
Molybdenum binding site 2 out of 2 in the Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Selenium Incorporated Nitrogenase Mofe-Protein (AV1-SE2B) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo502

b:8.1
occ:1.00
MO1 C:ICG502 0.0 8.1 1.0
O5 C:HCA501 2.2 8.1 1.0
O7 C:HCA501 2.2 8.1 1.0
S4B C:ICG502 2.3 8.6 1.0
S1B C:ICG502 2.3 9.0 1.0
S3B C:ICG502 2.4 8.7 1.0
ND1 C:HIS442 2.4 8.6 1.0
FE6 C:ICG502 2.7 8.8 1.0
FE7 C:ICG502 2.7 8.1 1.0
FE5 C:ICG502 2.7 8.8 1.0
C7 C:HCA501 3.0 8.2 1.0
C3 C:HCA501 3.2 7.9 1.0
CE1 C:HIS442 3.3 8.8 1.0
CG C:HIS442 3.4 8.4 1.0
CX C:ICG502 3.5 8.5 1.0
CB C:HIS442 3.8 9.1 1.0
C2 C:HCA501 4.1 8.3 1.0
O C:HOH804 4.2 9.5 1.0
O6 C:HCA501 4.2 8.3 1.0
C5 C:HCA501 4.3 8.3 1.0
C4 C:HCA501 4.3 7.7 1.0
O1 C:HCA501 4.4 9.9 1.0
NE2 C:HIS442 4.5 8.8 1.0
CD2 C:HIS442 4.6 8.2 1.0
CA C:HIS442 4.6 9.1 1.0
C1 C:HCA501 4.8 9.2 1.0
S5A C:ICG502 4.8 8.4 1.0
SE2B C:ICG502 4.8 10.5 1.0
S3A C:ICG502 4.9 8.7 1.0

Reference:

T.Spatzal, K.A.Perez, J.B.Howard, D.C.Rees. Catalysis-Dependent Selenium Incorporation and Migration in the Nitrogenase Active Site Iron-Molybdenum Cofactor. Elife V. 4 11620 2015.
ISSN: ESSN 2050-084X
PubMed: 26673079
DOI: 10.7554/ELIFE.11620
Page generated: Tue Dec 15 05:19:32 2020

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