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Molybdenum in PDB 6cdk: Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster

Enzymatic activity of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster

All present enzymatic activity of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster:
1.18.6.1;

Protein crystallography data

The structure of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster, PDB code: 6cdk was solved by S.M.Keable, O.A.Zadvornyy, A.J.Rasmussen, K.Danyal, B.J.Eilers, G.A.Prussia, A.X.Levan, L.C.Seefeldt, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.01 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.880, 130.780, 80.789, 90.00, 110.85, 90.00
R / Rfree (%) 23.2 / 26.3

Other elements in 6cdk:

The structure of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster also contains other interesting chemical elements:

Iron (Fe) 32 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster (pdb code 6cdk). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 2 binding sites of Molybdenum where determined in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster, PDB code: 6cdk:
Jump to Molybdenum binding site number: 1; 2;

Molybdenum binding site 1 out of 2 in 6cdk

Go back to Molybdenum Binding Sites List in 6cdk
Molybdenum binding site 1 out of 2 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo502

b:29.6
occ:1.00
MO1 A:ICS502 0.0 29.6 1.0
O7 A:HCA501 1.9 29.8 1.0
O5 A:HCA501 2.0 31.0 1.0
ND1 A:HIS442 2.2 28.0 1.0
S4B A:ICS502 2.2 30.0 1.0
S3B A:ICS502 2.2 28.2 1.0
S1B A:ICS502 2.3 28.7 1.0
FE7 A:ICS502 2.6 30.2 1.0
FE6 A:ICS502 2.6 29.4 1.0
FE5 A:ICS502 2.7 30.4 1.0
C7 A:HCA501 2.9 32.1 1.0
CE1 A:HIS442 3.0 29.2 1.0
C3 A:HCA501 3.0 32.7 1.0
CG A:HIS442 3.3 28.1 1.0
CX A:ICS502 3.5 29.9 1.0
CB A:HIS442 3.8 29.1 1.0
O A:HOH650 4.0 33.7 1.0
C2 A:HCA501 4.0 35.0 1.0
O6 A:HCA501 4.1 29.6 1.0
C4 A:HCA501 4.1 33.3 1.0
NE2 A:HIS442 4.2 26.8 1.0
CD2 A:HIS442 4.4 26.4 1.0
O2 A:HCA501 4.4 36.5 1.0
CA A:HIS442 4.6 30.3 1.0
S5A A:ICS502 4.8 28.1 1.0
C1 A:HCA501 4.8 36.2 1.0
S2B A:ICS502 4.8 32.3 1.0
C5 A:HCA501 4.9 32.2 1.0
S3A A:ICS502 4.9 32.8 1.0
FE2 A:ICS502 5.0 31.2 1.0
FE3 A:ICS502 5.0 29.7 1.0

Molybdenum binding site 2 out of 2 in 6cdk

Go back to Molybdenum Binding Sites List in 6cdk
Molybdenum binding site 2 out of 2 in the Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Characterization of the P1+ Intermediate State of Nitrogenase P- Cluster within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo502

b:30.1
occ:1.00
MO1 C:ICS502 0.0 30.1 1.0
O7 C:HCA501 1.9 31.1 1.0
O5 C:HCA501 2.0 31.2 1.0
S4B C:ICS502 2.2 30.8 1.0
S1B C:ICS502 2.3 31.1 1.0
S3B C:ICS502 2.3 27.6 1.0
FE7 C:ICS502 2.6 32.2 1.0
FE6 C:ICS502 2.6 29.8 1.0
FE5 C:ICS502 2.6 33.4 1.0
ND1 C:HIS442 2.7 27.6 1.0
C7 C:HCA501 2.7 30.6 1.0
C3 C:HCA501 2.9 29.9 1.0
CE1 C:HIS442 3.2 31.1 1.0
CG C:HIS442 3.3 30.3 1.0
CX C:ICS502 3.5 29.2 1.0
CB C:HIS442 3.7 30.7 1.0
O C:HOH614 3.9 42.2 1.0
C2 C:HCA501 3.9 31.2 1.0
O6 C:HCA501 4.0 30.9 1.0
C4 C:HCA501 4.0 29.2 1.0
NE2 C:HIS442 4.0 29.4 1.0
CD2 C:HIS442 4.1 29.4 1.0
C5 C:HCA501 4.2 28.4 1.0
O1 C:HCA501 4.4 35.0 1.0
CA C:HIS442 4.6 30.9 1.0
C1 C:HCA501 4.7 31.4 1.0
S5A C:ICS502 4.8 28.4 1.0
S2B C:ICS502 4.8 32.4 1.0
S3A C:ICS502 4.8 34.4 1.0
FE2 C:ICS502 5.0 31.6 1.0
FE3 C:ICS502 5.0 29.6 1.0

Reference:

S.M.Keable, O.A.Zadvornyy, L.E.Johnson, B.Ginovska, A.J.Rasmussen, K.Danyal, B.J.Eilers, G.A.Prussia, A.X.Levan, S.Raugei, L.C.Seefeldt, J.W.Peters. Structural Characterization of the P1+Intermediate State of the P-Cluster of Nitrogenase. J. Biol. Chem. V. 293 9629 2018.
ISSN: ESSN 1083-351X
PubMed: 29720402
DOI: 10.1074/JBC.RA118.002435
Page generated: Tue Dec 15 05:20:12 2020

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