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Molybdenum in PDB 5cx1: Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant

Enzymatic activity of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant

All present enzymatic activity of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant, PDB code: 5cx1 was solved by C.P.Owens, M.A.Luca, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.68 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 175.502, 144.595, 177.747, 90.00, 114.27, 90.00
R / Rfree (%) 19.8 / 24.5

Other elements in 5cx1:

The structure of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant also contains other interesting chemical elements:

Iron (Fe) 120 atoms
Calcium (Ca) 8 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant (pdb code 5cx1). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 8 binding sites of Molybdenum where determined in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant, PDB code: 5cx1:
Jump to Molybdenum binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Molybdenum binding site 1 out of 8 in 5cx1

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Molybdenum binding site 1 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo502

b:12.8
occ:1.00
MO1 A:ICS502 0.0 12.8 1.0
S1B A:ICS502 2.3 10.5 1.0
O6 A:HCA501 2.4 14.1 1.0
S4B A:ICS502 2.4 11.6 1.0
S3B A:ICS502 2.4 12.0 1.0
FE7 A:ICS502 2.6 11.9 1.0
FE6 A:ICS502 2.7 13.5 1.0
O7 A:HCA501 2.7 12.8 1.0
ND1 A:HIS442 2.7 14.3 1.0
FE5 A:ICS502 2.7 12.9 1.0
C7 A:HCA501 3.2 10.2 1.0
C3 A:HCA501 3.4 12.3 1.0
CX A:ICS502 3.5 12.2 1.0
CG A:HIS442 3.6 12.7 1.0
CE1 A:HIS442 3.6 11.8 1.0
CB A:HIS442 3.8 12.3 1.0
C5 A:HCA501 4.2 12.2 1.0
C2 A:HCA501 4.3 14.4 1.0
O5 A:HCA501 4.3 13.6 1.0
O A:HOH924 4.4 14.4 1.0
O2 A:HCA501 4.4 12.5 1.0
C4 A:HCA501 4.5 12.1 1.0
CA A:HIS442 4.6 11.8 1.0
S2B A:ICS502 4.7 13.9 1.0
S5A A:ICS502 4.8 13.5 1.0
NE2 A:HIS442 4.8 13.0 1.0
CD2 A:HIS442 4.8 11.3 1.0
C1 A:HCA501 4.9 18.4 1.0
S3A A:ICS502 4.9 13.3 1.0

Molybdenum binding site 2 out of 8 in 5cx1

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Molybdenum binding site 2 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo502

b:12.4
occ:1.00
MO1 C:ICS502 0.0 12.4 1.0
S1B C:ICS502 2.3 9.2 1.0
O5 C:HCA501 2.4 10.2 1.0
S4B C:ICS502 2.4 13.0 1.0
S3B C:ICS502 2.4 11.3 1.0
FE7 C:ICS502 2.6 10.6 1.0
FE6 C:ICS502 2.6 10.7 1.0
O7 C:HCA501 2.7 17.0 1.0
FE5 C:ICS502 2.7 12.2 1.0
ND1 C:HIS442 2.7 13.6 1.0
C7 C:HCA501 3.1 14.9 1.0
C3 C:HCA501 3.3 11.2 1.0
CX C:ICS502 3.5 10.3 1.0
CG C:HIS442 3.6 11.7 1.0
CE1 C:HIS442 3.7 10.8 1.0
CB C:HIS442 3.7 9.2 1.0
C2 C:HCA501 4.2 12.2 1.0
O C:HOH828 4.2 11.2 1.0
C5 C:HCA501 4.2 9.7 1.0
O1 C:HCA501 4.3 13.5 1.0
O6 C:HCA501 4.3 11.6 1.0
C4 C:HCA501 4.4 12.1 1.0
CA C:HIS442 4.6 11.8 1.0
S2B C:ICS502 4.8 14.0 1.0
S5A C:ICS502 4.8 14.2 1.0
CD2 C:HIS442 4.8 10.6 1.0
NE2 C:HIS442 4.8 14.6 1.0
C1 C:HCA501 4.8 14.1 1.0
S3A C:ICS502 4.9 13.2 1.0
FE2 C:ICS502 5.0 12.3 1.0

Molybdenum binding site 3 out of 8 in 5cx1

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Molybdenum binding site 3 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mo502

b:14.0
occ:1.00
MO1 E:ICS502 0.0 14.0 1.0
S1B E:ICS502 2.4 11.8 1.0
S4B E:ICS502 2.4 16.5 1.0
O7 E:HCA501 2.4 17.1 1.0
S3B E:ICS502 2.4 12.8 1.0
O6 E:HCA501 2.6 17.2 1.0
FE6 E:ICS502 2.7 14.0 1.0
FE7 E:ICS502 2.7 13.5 1.0
ND1 E:HIS442 2.7 18.6 1.0
FE5 E:ICS502 2.7 14.6 1.0
C7 E:HCA501 3.3 16.8 1.0
C3 E:HCA501 3.3 13.9 1.0
CX E:ICS502 3.5 11.2 1.0
CG E:HIS442 3.6 14.5 1.0
CE1 E:HIS442 3.7 14.5 1.0
CB E:HIS442 3.7 16.3 1.0
C2 E:HCA501 4.2 15.8 1.0
O E:HOH715 4.2 13.3 1.0
C5 E:HCA501 4.2 15.0 1.0
C4 E:HCA501 4.3 11.8 1.0
O2 E:HCA501 4.3 17.9 1.0
O5 E:HCA501 4.4 14.0 1.0
CA E:HIS442 4.5 15.1 1.0
S2B E:ICS502 4.7 17.6 1.0
CD2 E:HIS442 4.7 17.2 1.0
S5A E:ICS502 4.7 11.5 1.0
NE2 E:HIS442 4.8 16.1 1.0
C1 E:HCA501 4.8 13.6 1.0
S3A E:ICS502 4.9 15.5 1.0

Molybdenum binding site 4 out of 8 in 5cx1

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Molybdenum binding site 4 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mo502

b:11.6
occ:1.00
MO1 G:ICS502 0.0 11.6 1.0
O5 G:HCA501 2.3 9.7 1.0
S4B G:ICS502 2.3 8.4 1.0
S1B G:ICS502 2.3 10.0 1.0
S3B G:ICS502 2.4 9.8 1.0
FE6 G:ICS502 2.6 10.5 1.0
FE7 G:ICS502 2.6 11.8 1.0
O7 G:HCA501 2.7 12.7 1.0
ND1 G:HIS442 2.7 12.6 1.0
FE5 G:ICS502 2.7 11.7 1.0
C7 G:HCA501 3.1 9.3 1.0
C3 G:HCA501 3.3 10.3 1.0
CX G:ICS502 3.5 12.6 1.0
CG G:HIS442 3.6 8.4 1.0
CE1 G:HIS442 3.6 12.0 1.0
CB G:HIS442 3.7 9.5 1.0
C2 G:HCA501 4.1 9.9 1.0
O G:HOH827 4.2 11.2 1.0
C5 G:HCA501 4.2 10.1 1.0
O6 G:HCA501 4.2 11.9 1.0
O1 G:HCA501 4.3 10.7 1.0
C4 G:HCA501 4.4 9.5 1.0
CA G:HIS442 4.6 9.8 1.0
S5A G:ICS502 4.7 9.3 1.0
C1 G:HCA501 4.7 11.7 1.0
S2B G:ICS502 4.7 10.5 1.0
NE2 G:HIS442 4.8 7.3 1.0
CD2 G:HIS442 4.8 9.3 1.0
S3A G:ICS502 4.9 10.4 1.0

Molybdenum binding site 5 out of 8 in 5cx1

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Molybdenum binding site 5 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mo502

b:12.8
occ:1.00
MO1 I:ICS502 0.0 12.8 1.0
S1B I:ICS502 2.3 10.4 1.0
S4B I:ICS502 2.3 13.2 1.0
S3B I:ICS502 2.3 13.5 1.0
O7 I:HCA501 2.4 14.8 1.0
FE6 I:ICS502 2.6 12.2 1.0
O5 I:HCA501 2.7 16.6 1.0
FE7 I:ICS502 2.7 12.8 1.0
FE5 I:ICS502 2.7 14.0 1.0
ND1 I:HIS442 2.7 19.6 1.0
C7 I:HCA501 3.3 12.9 1.0
C3 I:HCA501 3.3 11.1 1.0
CX I:ICS502 3.5 16.5 1.0
CG I:HIS442 3.6 13.1 1.0
CE1 I:HIS442 3.6 14.7 1.0
CB I:HIS442 3.7 10.4 1.0
O I:HOH788 4.2 11.5 1.0
C2 I:HCA501 4.3 12.1 1.0
O1 I:HCA501 4.3 14.1 1.0
C5 I:HCA501 4.3 17.3 1.0
C4 I:HCA501 4.4 14.8 1.0
O6 I:HCA501 4.4 13.4 1.0
CA I:HIS442 4.6 12.9 1.0
S2B I:ICS502 4.7 13.2 1.0
NE2 I:HIS442 4.8 12.8 1.0
CD2 I:HIS442 4.8 11.9 1.0
S5A I:ICS502 4.8 13.4 1.0
C1 I:HCA501 4.8 15.1 1.0
S3A I:ICS502 4.9 14.0 1.0

Molybdenum binding site 6 out of 8 in 5cx1

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Molybdenum binding site 6 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mo502

b:12.4
occ:1.00
MO1 K:ICS502 0.0 12.4 1.0
S3B K:ICS502 2.3 11.7 1.0
S1B K:ICS502 2.3 10.9 1.0
S4B K:ICS502 2.4 12.1 1.0
O7 K:HCA501 2.4 11.9 1.0
FE7 K:ICS502 2.6 10.6 1.0
FE6 K:ICS502 2.6 11.1 1.0
O6 K:HCA501 2.7 15.1 1.0
FE5 K:ICS502 2.7 12.5 1.0
ND1 K:HIS442 2.7 12.6 1.0
C7 K:HCA501 3.2 13.4 1.0
C3 K:HCA501 3.3 9.2 1.0
CX K:ICS502 3.5 13.9 1.0
CG K:HIS442 3.6 12.6 1.0
CE1 K:HIS442 3.6 11.8 1.0
CB K:HIS442 3.7 13.8 1.0
O K:HOH723 4.2 12.5 1.0
C2 K:HCA501 4.2 11.5 1.0
C5 K:HCA501 4.3 10.6 1.0
O2 K:HCA501 4.3 9.8 1.0
C4 K:HCA501 4.4 12.3 1.0
O5 K:HCA501 4.4 11.1 1.0
CA K:HIS442 4.6 15.3 1.0
NE2 K:HIS442 4.7 12.6 1.0
CD2 K:HIS442 4.7 12.3 1.0
S5A K:ICS502 4.8 11.8 1.0
S2B K:ICS502 4.8 12.6 1.0
C1 K:HCA501 4.8 14.2 1.0
S3A K:ICS502 4.9 13.0 1.0

Molybdenum binding site 7 out of 8 in 5cx1

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Molybdenum binding site 7 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mo502

b:11.4
occ:1.00
MO1 M:ICS502 0.0 11.4 1.0
O5 M:HCA501 2.3 6.6 1.0
S3B M:ICS502 2.3 9.4 1.0
S1B M:ICS502 2.3 10.5 1.0
S4B M:ICS502 2.3 9.0 1.0
FE6 M:ICS502 2.6 11.2 1.0
O7 M:HCA501 2.6 12.3 1.0
FE7 M:ICS502 2.6 9.6 1.0
ND1 M:HIS442 2.7 10.9 1.0
FE5 M:ICS502 2.7 10.6 1.0
C7 M:HCA501 3.0 9.7 1.0
C3 M:HCA501 3.2 7.4 1.0
CX M:ICS502 3.5 5.2 1.0
CG M:HIS442 3.6 8.1 1.0
CE1 M:HIS442 3.7 6.7 1.0
CB M:HIS442 3.7 9.8 1.0
C2 M:HCA501 4.1 8.8 1.0
O6 M:HCA501 4.2 9.8 1.0
O M:HOH755 4.2 8.8 1.0
C5 M:HCA501 4.2 9.6 1.0
C4 M:HCA501 4.3 9.6 1.0
O1 M:HCA501 4.4 12.8 1.0
CA M:HIS442 4.6 8.3 1.0
S5A M:ICS502 4.7 9.4 1.0
S2B M:ICS502 4.8 11.3 1.0
CD2 M:HIS442 4.8 10.5 1.0
C1 M:HCA501 4.8 10.8 1.0
NE2 M:HIS442 4.8 11.1 1.0
S3A M:ICS502 4.9 11.1 1.0
FE2 M:ICS502 5.0 10.4 1.0

Molybdenum binding site 8 out of 8 in 5cx1

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Molybdenum binding site 8 out of 8 in the Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Nitrogenase Molybdenum-Iron Protein Beta-K400E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Mo502

b:11.3
occ:1.00
MO1 O:ICS502 0.0 11.3 1.0
O6 O:HCA501 2.3 7.0 1.0
S4B O:ICS502 2.3 10.7 1.0
S1B O:ICS502 2.3 11.6 1.0
S3B O:ICS502 2.4 10.1 1.0
FE7 O:ICS502 2.7 12.3 1.0
O7 O:HCA501 2.7 15.3 1.0
ND1 O:HIS442 2.7 16.3 1.0
FE6 O:ICS502 2.7 10.4 1.0
FE5 O:ICS502 2.7 11.1 1.0
C7 O:HCA501 3.1 11.6 1.0
C3 O:HCA501 3.3 13.3 1.0
CX O:ICS502 3.5 8.2 1.0
CG O:HIS442 3.6 12.7 1.0
CE1 O:HIS442 3.6 14.6 1.0
CB O:HIS442 3.7 13.7 1.0
C2 O:HCA501 4.2 7.8 1.0
C5 O:HCA501 4.2 12.0 1.0
O5 O:HCA501 4.3 12.0 1.0
O O:HOH875 4.3 11.3 1.0
C4 O:HCA501 4.4 14.9 1.0
O2 O:HCA501 4.4 13.9 1.0
CA O:HIS442 4.6 9.9 1.0
NE2 O:HIS442 4.7 11.9 1.0
CD2 O:HIS442 4.7 10.8 1.0
S5A O:ICS502 4.7 10.8 1.0
S2B O:ICS502 4.8 10.4 1.0
C1 O:HCA501 4.8 15.2 1.0
S3A O:ICS502 4.9 14.2 1.0

Reference:

C.P.Owens, F.E.Katz, C.H.Carter, M.A.Luca, F.A.Tezcan. Evidence For Functionally Relevant Encounter Complexes in Nitrogenase Catalysis. J.Am.Chem.Soc. V. 137 12704 2015.
ISSN: ESSN 1520-5126
PubMed: 26360912
DOI: 10.1021/JACS.5B08310
Page generated: Tue Dec 15 05:19:43 2020

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