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Molybdenum in PDB 5bvh: Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii

Enzymatic activity of Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii

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

Protein crystallography data

The structure of Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii, PDB code: 5bvh 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) 100.43 / 1.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.071, 130.833, 107.318, 90.00, 110.64, 90.00
R / Rfree (%) 14.4 / 16

Other elements in 5bvh:

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

Iron (Fe) 46 atoms
Chlorine (Cl) 2 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii (pdb code 5bvh). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 4 binding sites of Molybdenum where determined in the Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii, PDB code: 5bvh:
Jump to Molybdenum binding site number: 1; 2; 3; 4;

Molybdenum binding site 1 out of 4 in 5bvh

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Molybdenum binding site 1 out of 4 in the Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) 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 Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo502

b:8.1
occ:0.65
 MO1 A:ICS502 0.0 8.1 0.7
MO1 A:ICH503 0.0 8.1 0.3
O6 A:HCA501 2.2 8.5 1.0
O7 A:HCA501 2.3 8.7 1.0
S4B A:ICS502 2.3 8.5 0.7
S4B A:ICH503 2.3 8.5 0.3
S1B A:ICS502 2.3 8.3 0.7
S1B A:ICH503 2.3 8.3 0.3
ND1 A:HIS442 2.4 8.0 1.0
S3B A:ICS502 2.4 8.4 0.7
S3B A:ICH503 2.4 8.4 0.3
FE6 A:ICS502 2.6 8.9 0.7
FE6 A:ICH503 2.6 8.9 0.3
FE7 A:ICS502 2.7 8.6 0.7
FE7 A:ICH503 2.7 8.6 0.3
FE5 A:ICS502 2.7 8.7 0.7
FE5 A:ICH503 2.7 8.7 0.3
C7 A:HCA501 3.0 8.6 1.0
C3 A:HCA501 3.2 8.7 1.0
CE1 A:HIS442 3.3 8.0 1.0
CG A:HIS442 3.4 8.0 1.0
CX A:ICS502 3.5 8.4 0.7
CX A:ICH503 3.5 8.4 0.3
CB A:HIS442 3.7 8.1 1.0
C2 A:HCA501 4.1 9.0 1.0
O A:HOH820 4.2 9.4 1.0
O5 A:HCA501 4.2 8.6 1.0
C5 A:HCA501 4.2 8.3 1.0
C4 A:HCA501 4.3 8.4 1.0
O2 A:HCA501 4.4 10.3 1.0
NE2 A:HIS442 4.4 7.8 1.0
C A:CMO506 4.5 7.6 0.9
CD2 A:HIS442 4.5 7.9 1.0
CA A:HIS442 4.6 8.4 1.0
C1 A:HCA501 4.8 9.5 1.0
S5A A:ICS502 4.8 7.8 0.6
SE2B A:ICH503 4.8 4.2 0.1
SE5A A:ICH503 4.9 10.5 0.4
FE2 A:ICS502 4.9 8.5 0.7
FE2 A:ICH503 4.9 8.5 0.3
SE3A A:ICH503 5.0 9.5 0.3
S3A A:ICS502 5.0 7.6 0.7

Molybdenum binding site 2 out of 4 in 5bvh

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Molybdenum binding site 2 out of 4 in the Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) 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 Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo503

b:8.1
occ:0.35
 MO1 A:ICS502 0.0 8.1 0.7
MO1 A:ICH503 0.0 8.1 0.3
O6 A:HCA501 2.2 8.5 1.0
O7 A:HCA501 2.3 8.7 1.0
S4B A:ICS502 2.3 8.5 0.7
S4B A:ICH503 2.3 8.5 0.3
S1B A:ICS502 2.3 8.3 0.7
S1B A:ICH503 2.3 8.3 0.3
ND1 A:HIS442 2.4 8.0 1.0
S3B A:ICS502 2.4 8.4 0.7
S3B A:ICH503 2.4 8.4 0.3
FE6 A:ICS502 2.6 8.9 0.7
FE6 A:ICH503 2.6 8.9 0.3
FE7 A:ICS502 2.7 8.6 0.7
FE7 A:ICH503 2.7 8.6 0.3
FE5 A:ICS502 2.7 8.7 0.7
FE5 A:ICH503 2.7 8.7 0.3
C7 A:HCA501 3.0 8.6 1.0
C3 A:HCA501 3.2 8.7 1.0
CE1 A:HIS442 3.3 8.0 1.0
CG A:HIS442 3.4 8.0 1.0
CX A:ICS502 3.5 8.4 0.7
CX A:ICH503 3.5 8.4 0.3
CB A:HIS442 3.7 8.1 1.0
C2 A:HCA501 4.1 9.0 1.0
O A:HOH820 4.2 9.4 1.0
O5 A:HCA501 4.2 8.6 1.0
C5 A:HCA501 4.2 8.3 1.0
C4 A:HCA501 4.3 8.4 1.0
O2 A:HCA501 4.4 10.3 1.0
NE2 A:HIS442 4.4 7.8 1.0
C A:CMO506 4.5 7.6 0.9
CD2 A:HIS442 4.5 7.9 1.0
CA A:HIS442 4.6 8.4 1.0
C1 A:HCA501 4.8 9.5 1.0
S5A A:ICS502 4.8 7.8 0.6
SE2B A:ICH503 4.8 4.2 0.1
SE5A A:ICH503 4.9 10.5 0.4
FE2 A:ICS502 4.9 8.5 0.7
FE2 A:ICH503 4.9 8.5 0.3
SE3A A:ICH503 5.0 9.5 0.3
S3A A:ICS502 5.0 7.6 0.7

Molybdenum binding site 3 out of 4 in 5bvh

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Molybdenum binding site 3 out of 4 in the Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo502

b:8.2
occ:0.65
 MO1 C:ICS502 0.0 8.2 0.7
MO1 C:ICH503 0.0 8.2 0.3
O7 C:HCA501 2.2 8.7 1.0
O5 C:HCA501 2.2 8.2 1.0
ND1 C:HIS442 2.3 7.7 1.0
S1B C:ICS502 2.3 8.7 0.7
S1B C:ICH503 2.3 8.7 0.3
S4B C:ICS502 2.4 8.6 0.7
S4B C:ICH503 2.4 8.6 0.3
S3B C:ICS502 2.4 8.7 0.7
S3B C:ICH503 2.4 8.7 0.3
FE6 C:ICS502 2.6 8.9 0.7
FE6 C:ICH503 2.6 8.9 0.3
FE7 C:ICS502 2.7 8.4 0.7
FE7 C:ICH503 2.7 8.4 0.3
FE5 C:ICS502 2.7 8.6 0.7
FE5 C:ICH503 2.7 8.6 0.3
C7 C:HCA501 3.0 8.5 1.0
C3 C:HCA501 3.2 8.7 1.0
CE1 C:HIS442 3.2 7.8 1.0
CG C:HIS442 3.4 7.9 1.0
CX C:ICS502 3.5 8.4 0.7
CX C:ICH503 3.5 8.4 0.3
CB C:HIS442 3.7 7.8 1.0
C2 C:HCA501 4.1 9.2 1.0
O C:HOH799 4.2 10.2 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 8.3 1.0
NE2 C:HIS442 4.4 7.9 1.0
O1 C:HCA501 4.4 11.2 1.0
CD2 C:HIS442 4.5 7.7 1.0
C C:CMO506 4.5 7.2 0.9
CA C:HIS442 4.6 8.0 1.0
C1 C:HCA501 4.8 9.9 1.0
SE2B C:ICH503 4.8 4.2 0.1
S5A C:ICS502 4.8 7.5 0.6
SE5A C:ICH503 4.8 10.2 0.4
FE2 C:ICS502 5.0 8.5 0.7
FE2 C:ICH503 5.0 8.5 0.3
SE3A C:ICH503 5.0 9.3 0.3
S3A C:ICS502 5.0 7.7 0.7

Molybdenum binding site 4 out of 4 in 5bvh

Go back to Molybdenum Binding Sites List in 5bvh
Molybdenum binding site 4 out of 4 in the Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Co-Bound Form of Selenium Incorporated Nitrogenase Mofe-Protein (AV1- Se-Co) From A. Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo503

b:8.2
occ:0.35
 MO1 C:ICS502 0.0 8.2 0.7
MO1 C:ICH503 0.0 8.2 0.3
O7 C:HCA501 2.2 8.7 1.0
O5 C:HCA501 2.2 8.2 1.0
ND1 C:HIS442 2.3 7.7 1.0
S1B C:ICS502 2.3 8.7 0.7
S1B C:ICH503 2.3 8.7 0.3
S4B C:ICS502 2.4 8.6 0.7
S4B C:ICH503 2.4 8.6 0.3
S3B C:ICS502 2.4 8.7 0.7
S3B C:ICH503 2.4 8.7 0.3
FE6 C:ICS502 2.6 8.9 0.7
FE6 C:ICH503 2.6 8.9 0.3
FE7 C:ICS502 2.7 8.4 0.7
FE7 C:ICH503 2.7 8.4 0.3
FE5 C:ICS502 2.7 8.6 0.7
FE5 C:ICH503 2.7 8.6 0.3
C7 C:HCA501 3.0 8.5 1.0
C3 C:HCA501 3.2 8.7 1.0
CE1 C:HIS442 3.2 7.8 1.0
CG C:HIS442 3.4 7.9 1.0
CX C:ICS502 3.5 8.4 0.7
CX C:ICH503 3.5 8.4 0.3
CB C:HIS442 3.7 7.8 1.0
C2 C:HCA501 4.1 9.2 1.0
O C:HOH799 4.2 10.2 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 8.3 1.0
NE2 C:HIS442 4.4 7.9 1.0
O1 C:HCA501 4.4 11.2 1.0
CD2 C:HIS442 4.5 7.7 1.0
C C:CMO506 4.5 7.2 0.9
CA C:HIS442 4.6 8.0 1.0
C1 C:HCA501 4.8 9.9 1.0
SE2B C:ICH503 4.8 4.2 0.1
S5A C:ICS502 4.8 7.5 0.6
SE5A C:ICH503 4.8 10.2 0.4
FE2 C:ICS502 5.0 8.5 0.7
FE2 C:ICH503 5.0 8.5 0.3
SE3A C:ICH503 5.0 9.3 0.3
S3A C:ICS502 5.0 7.7 0.7

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: Sun Oct 6 16:18:34 2024

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