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:
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
Go back to
Molybdenum Binding Sites List in 7mci
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 Sites List in 7mci
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 Sites List in 7mci
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 Sites List in 7mci
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 Sites List in 7mci
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
Go back to
Molybdenum Binding Sites List in 7mci
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
Go back to
Molybdenum Binding Sites List in 7mci
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
Go back to
Molybdenum Binding Sites List in 7mci
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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