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Molybdenum in PDB 7mci: Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor

Enzymatic activity of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor

All present enzymatic activity of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor:
1.18.6.1;

Protein crystallography data

The structure of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor, PDB code: 7mci was solved by W.Kang, C.Lee, Y.Hu, M.W.Ribbe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.22 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 166.834, 73.995, 208.766, 90, 103.05, 90
R / Rfree (%) 17.2 / 19.5

Other elements in 7mci:

The structure of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Calcium (Ca) 2 atoms

Molybdenum Binding Sites:

The binding sites of Molybdenum atom in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor (pdb code 7mci). This binding sites where shown within 5.0 Angstroms radius around Molybdenum atom.
In total 8 binding sites of Molybdenum where determined in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor, PDB code: 7mci:
Jump to Molybdenum binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Molybdenum binding site 1 out of 8 in 7mci

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Molybdenum binding site 1 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 1 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo502

b:21.8
occ:1.00
 MO1 A:ICS502 0.0 21.8 1.0
O5 A:HCA501 2.2 19.8 1.0
O7 A:HCA501 2.3 20.3 1.0
S3B A:ICS502 2.3 19.7 1.0
S1B A:ICS502 2.3 19.2 1.0
S4B A:ICS502 2.4 19.8 1.0
ND1 A:HIS442 2.4 24.2 1.0
FE7 A:ICS502 2.7 20.3 1.0
FE6 A:ICS502 2.7 20.6 1.0
FE5 A:ICS502 2.7 20.4 1.0
C7 A:HCA501 3.0 20.9 1.0
C3 A:HCA501 3.1 19.4 1.0
CE1 A:HIS442 3.3 25.1 1.0
CG A:HIS442 3.5 23.0 1.0
CX A:ICS502 3.5 19.4 1.0
CB A:HIS442 3.8 22.1 1.0
C2 A:HCA501 4.0 19.2 1.0
O1 A:HCA501 4.2 20.5 1.0
O6 A:HCA501 4.2 19.9 1.0
O A:HOH738 4.2 19.3 1.0
C4 A:HCA501 4.3 23.1 1.0
C5 A:HCA501 4.3 21.3 1.0
NE2 A:HIS442 4.5 24.6 1.0
CD2 A:HIS442 4.6 23.3 1.0
C1 A:HCA501 4.6 24.1 1.0
CA A:HIS442 4.6 20.9 1.0
S2B A:ICS502 4.8 20.4 1.0
S5A A:ICS502 4.8 21.8 1.0
S3A A:ICS502 4.9 20.6 1.0

Molybdenum binding site 2 out of 8 in 7mci

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Molybdenum binding site 2 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 2 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo504

b:29.8
occ:0.60
 O A:HOH789 2.9 40.8 1.0
O A:ASN29 3.0 29.3 1.0
O A:LEU32 3.1 33.2 1.0
O A:CYS45 3.1 33.2 1.0
O A:HOH695 3.2 33.6 1.0
CA A:LYS30 4.0 28.7 1.0
C A:ASN29 4.1 29.0 1.0
C A:CYS45 4.1 34.5 1.0
O A:LYS30 4.2 28.7 1.0
C A:LYS30 4.2 28.1 1.0
C A:LEU32 4.2 29.3 1.0
N A:LYS30 4.5 28.7 1.0
N A:LEU32 4.7 28.3 1.0
CA A:CYS45 4.8 36.9 1.0
O A:HOH791 4.8 34.4 1.0
ND2 A:ASN29 4.8 39.9 1.0
CB A:ALA33 4.8 33.9 1.0
OD1 A:ASN29 4.9 34.0 1.0
O A:HOH855 4.9 40.2 1.0
CA A:ALA33 4.9 31.6 1.0
CG A:ASN29 4.9 35.8 1.0
N A:HIS31 5.0 28.1 1.0
N A:ILE46 5.0 32.2 1.0

Molybdenum binding site 3 out of 8 in 7mci

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Molybdenum binding site 3 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 3 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo505

b:48.4
occ:0.31
 O A:HOH846 2.5 43.5 1.0
CZ3 A:TRP205 3.5 36.7 1.0
O A:ASP204 3.5 29.4 1.0
CE3 A:TRP205 3.5 34.9 1.0
CH2 A:TRP205 3.6 40.0 1.0
CD2 A:TRP205 3.7 33.4 1.0
CZ2 A:TRP205 3.8 37.1 1.0
CE2 A:TRP205 3.8 32.5 1.0
C A:ASP204 4.5 28.4 1.0
CG A:TRP205 4.5 31.0 1.0
NE1 A:TRP205 4.6 32.0 1.0
CA A:TRP205 5.0 27.8 1.0
CD1 A:TRP205 5.0 30.1 1.0
NZ A:LYS168 5.0 51.9 1.0

Molybdenum binding site 4 out of 8 in 7mci

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Molybdenum binding site 4 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 4 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mo506

b:49.4
occ:0.40
 O A:HOH795 2.9 31.8 1.0
O A:TRP294 3.3 27.5 1.0
O A:HOH702 3.5 28.0 1.0
CE2 A:TRP294 3.7 31.4 1.0
CD2 A:TRP294 3.8 30.6 1.0
CZ2 A:TRP294 3.8 33.6 1.0
CH2 A:TRP294 4.0 33.5 1.0
CE3 A:TRP294 4.1 32.3 1.0
CZ3 A:TRP294 4.1 32.6 1.0
C A:TRP294 4.2 29.9 1.0
NE1 A:TRP294 4.2 28.4 1.0
CG A:TRP294 4.4 30.8 1.0
O A:HOH749 4.4 29.7 1.0
O A:HOH657 4.4 35.3 1.0
CD1 A:TRP294 4.5 30.2 1.0
CA A:MET295 4.7 26.8 1.0
N A:MET295 4.8 28.0 1.0

Molybdenum binding site 5 out of 8 in 7mci

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Molybdenum binding site 5 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 5 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo502

b:19.7
occ:1.00
 MO1 C:ICS502 0.0 19.7 1.0
O6 C:HCA501 2.2 16.5 1.0
O7 C:HCA501 2.3 18.6 1.0
S4B C:ICS502 2.3 17.0 1.0
S1B C:ICS502 2.3 16.5 1.0
S3B C:ICS502 2.3 18.1 1.0
ND1 C:HIS442 2.4 25.1 1.0
FE7 C:ICS502 2.6 17.8 1.0
FE6 C:ICS502 2.6 18.6 1.0
FE5 C:ICS502 2.7 19.1 1.0
C7 C:HCA501 3.0 18.9 1.0
C3 C:HCA501 3.2 19.6 1.0
CE1 C:HIS442 3.3 26.4 1.0
CG C:HIS442 3.5 23.1 1.0
CX C:ICS502 3.5 16.0 1.0
CB C:HIS442 3.8 21.8 1.0
C2 C:HCA501 4.0 18.5 1.0
O C:HOH703 4.2 16.7 1.0
O5 C:HCA501 4.2 19.4 1.0
O2 C:HCA501 4.2 21.1 1.0
C4 C:HCA501 4.3 22.1 1.0
C5 C:HCA501 4.3 19.9 1.0
NE2 C:HIS442 4.5 25.6 1.0
CD2 C:HIS442 4.6 23.8 1.0
CA C:HIS442 4.6 19.7 1.0
C1 C:HCA501 4.7 24.7 1.0
S5A C:ICS502 4.7 17.1 1.0
S2B C:ICS502 4.7 18.0 1.0
S3A C:ICS502 4.9 18.7 1.0

Molybdenum binding site 6 out of 8 in 7mci

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Molybdenum binding site 6 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 6 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo505

b:26.8
occ:0.71
 O C:LEU32 3.0 32.5 1.0
O C:CYS45 3.0 29.2 1.0
O C:ASN29 3.3 27.9 1.0
O C:HOH742 3.4 29.5 1.0
O C:HOH855 3.5 38.8 1.0
O C:HOH638 3.6 36.6 1.0
C C:CYS45 4.1 29.6 1.0
C C:LEU32 4.1 30.0 1.0
O C:LYS30 4.2 27.7 1.0
CA C:LYS30 4.3 28.7 1.0
C C:LYS30 4.4 29.5 1.0
C C:ASN29 4.4 28.3 1.0
CB C:ALA33 4.4 28.9 1.0
O C:HOH839 4.5 35.5 1.0
CA C:ALA33 4.6 28.2 1.0
N C:LEU32 4.8 24.7 1.0
N C:LYS30 4.8 27.3 1.0
CA C:ILE46 4.9 28.1 1.0
N C:ALA33 4.9 28.6 1.0
N C:ILE46 4.9 27.9 1.0

Molybdenum binding site 7 out of 8 in 7mci

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Molybdenum binding site 7 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 7 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo506

b:26.8
occ:0.70
 O C:TRP294 3.1 21.3 1.0
O C:HOH684 3.4 32.4 1.0
O C:HOH739 3.5 24.0 1.0
CE2 C:TRP294 3.6 26.3 1.0
CZ2 C:TRP294 3.7 27.2 1.0
CD2 C:TRP294 3.7 24.8 1.0
CH2 C:TRP294 3.9 29.1 1.0
O C:HOH677 4.0 30.9 1.0
CE3 C:TRP294 4.0 25.6 1.0
CZ3 C:TRP294 4.1 28.3 1.0
NE1 C:TRP294 4.1 24.0 1.0
C C:TRP294 4.2 21.8 1.0
CG C:TRP294 4.3 21.9 1.0
O C:HOH798 4.4 26.0 1.0
CD1 C:TRP294 4.5 25.9 1.0
N C:TRP294 5.0 21.9 1.0

Molybdenum binding site 8 out of 8 in 7mci

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Molybdenum binding site 8 out of 8 in the Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor


Mono view


Stereo pair view

A full contact list of Molybdenum with other atoms in the Mo binding site number 8 of Mofe Protein From Azotobacter Vinelandii with A Sulfur-Replenished Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mo507

b:42.4
occ:0.30
 O C:ASP204 3.4 26.6 1.0
CZ3 C:TRP205 3.5 38.4 1.0
CH2 C:TRP205 3.5 36.4 1.0
CE3 C:TRP205 3.6 32.3 1.0
CZ2 C:TRP205 3.6 35.6 1.0
CD2 C:TRP205 3.7 30.5 1.0
CE2 C:TRP205 3.7 29.6 1.0
O C:HOH907 4.0 48.6 1.0
C C:ASP204 4.3 27.4 1.0
NE1 C:TRP205 4.5 30.1 1.0
CG C:TRP205 4.5 27.9 1.0
CB C:ASP204 4.8 28.4 1.0
CD1 C:TRP205 4.9 29.1 1.0
CA C:TRP205 4.9 27.0 1.0

Reference:

C.C.Lee, W.Kang, A.J.Jasniewski, M.T.Stiebritz, K.Tanifuji, M.W.Ribbe, Y.Hu. Evidence of Substrate Binding and Product Release Via Belt-Sulfur Mobilization of the Nitrogenase Cofactor Nat Catal V. 5 443 2022.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-022-00782-7
Page generated: Sun Oct 6 16:57:59 2024

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