Atomistry » Molybdenum » PDB 4c80-5koj » 5bvh
Atomistry »
  Molybdenum »
    PDB 4c80-5koj »
      5bvh »

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

Go back to Molybdenum Binding Sites List in 5bvh
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

Go back to Molybdenum Binding Sites List in 5bvh
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

Go back to Molybdenum Binding Sites List in 5bvh
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: Tue Dec 15 05:19:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy