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Molybdenum in PDB 5vq3: Nitrogenase CP1 at pH 6.5

Enzymatic activity of Nitrogenase CP1 at pH 6.5

All present enzymatic activity of Nitrogenase CP1 at pH 6.5:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase CP1 at pH 6.5, PDB code: 5vq3 was solved by C.N.Morrison, T.Spatzal, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.477, 147.963, 116.694, 90.00, 103.51, 90.00
R / Rfree (%) 15.9 / 18.5

Other elements in 5vq3:

The structure of Nitrogenase CP1 at pH 6.5 also contains other interesting chemical elements:

Iron (Fe) 32 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Nitrogenase CP1 at pH 6.5 (pdb code 5vq3). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Nitrogenase CP1 at pH 6.5, PDB code: 5vq3:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 5vq3

Go back to Molybdenum Binding Sites List in 5vq3
Molybdenum binding site 1 out of 2 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo602

b:18.5
occ:1.00
MO1 A:ICS602 0.0 18.5 1.0
O7 A:HCA601 2.1 18.1 1.0
O6 A:HCA601 2.2 17.8 1.0
S4B A:ICS602 2.4 18.8 1.0
S1B A:ICS602 2.4 19.6 1.0
ND1 A:HIS482 2.4 22.2 1.0
S3B A:ICS602 2.4 19.5 1.0
FE7 A:ICS602 2.7 19.4 1.0
FE5 A:ICS602 2.7 18.5 1.0
FE6 A:ICS602 2.7 18.9 1.0
C7 A:HCA601 3.0 18.7 1.0
C3 A:HCA601 3.1 19.2 1.0
CE1 A:HIS482 3.2 22.0 1.0
CG A:HIS482 3.4 17.0 1.0
CX A:ICS602 3.5 19.6 1.0
CB A:HIS482 3.8 17.7 1.0
C2 A:HCA601 4.0 21.1 1.0
O2 A:HCA601 4.1 21.1 1.0
O A:HOH797 4.2 20.8 1.0
O5 A:HCA601 4.2 20.0 1.0
C4 A:HCA601 4.2 20.5 1.0
C5 A:HCA601 4.2 21.3 1.0
NE2 A:HIS482 4.4 22.8 1.0
CD2 A:HIS482 4.5 20.3 1.0
C1 A:HCA601 4.6 22.9 1.0
CA A:HIS482 4.7 16.9 1.0
S5A A:ICS602 4.8 21.7 1.0
S2B A:ICS602 4.8 19.7 1.0
S3A A:ICS602 4.8 19.7 1.0

Molybdenum binding site 2 out of 2 in 5vq3

Go back to Molybdenum Binding Sites List in 5vq3
Molybdenum binding site 2 out of 2 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo602

b:16.9
occ:1.00
MO1 C:ICS602 0.0 16.9 1.0
O7 C:HCA601 2.2 16.2 1.0
O5 C:HCA601 2.2 14.5 1.0
S4B C:ICS602 2.3 17.0 1.0
S1B C:ICS602 2.3 18.5 1.0
ND1 C:HIS482 2.3 18.0 1.0
S3B C:ICS602 2.4 17.0 1.0
FE5 C:ICS602 2.7 17.6 1.0
FE7 C:ICS602 2.7 18.1 1.0
FE6 C:ICS602 2.7 17.6 1.0
C7 C:HCA601 3.0 15.7 1.0
C3 C:HCA601 3.1 17.2 1.0
CE1 C:HIS482 3.2 18.0 1.0
CG C:HIS482 3.4 15.8 1.0
CX C:ICS602 3.5 18.9 1.0
CB C:HIS482 3.8 16.4 1.0
C2 C:HCA601 4.0 18.8 1.0
O C:HOH825 4.2 19.8 1.0
O1 C:HCA601 4.2 22.3 1.0
C5 C:HCA601 4.2 18.8 1.0
C4 C:HCA601 4.2 17.6 1.0
O6 C:HCA601 4.2 17.2 1.0
NE2 C:HIS482 4.4 18.7 1.0
CD2 C:HIS482 4.5 17.6 1.0
C1 C:HCA601 4.6 22.3 1.0
CA C:HIS482 4.7 15.3 1.0
S5A C:ICS602 4.8 18.9 1.0
S2B C:ICS602 4.8 18.9 1.0
S3A C:ICS602 4.8 19.2 1.0

Reference:

C.N.Morrison, T.Spatzal, D.C.Rees. Reversible Protonated Resting State of the Nitrogenase Active Site. J. Am. Chem. Soc. V. 139 10856 2017.
ISSN: ESSN 1520-5126
PubMed: 28692802
DOI: 10.1021/JACS.7B05695
Page generated: Tue Dec 15 05:20:05 2020

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