Molybdenum in PDB 2afi: Crystal Structure of Mgadp Bound AV2-AV1 Complex
Enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex
All present enzymatic activity of Crystal Structure of Mgadp Bound AV2-AV1 Complex:
1.18.6.1;
Protein crystallography data
The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi
was solved by
F.A.Tezcan,
J.T.Kaiser,
D.Mustafi,
M.Y.Walton,
J.B.Howard,
D.C.Rees,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.43 /
3.10
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.915,
141.432,
165.549,
73.69,
79.37,
76.58
|
R / Rfree (%)
|
22.9 /
27
|
Other elements in 2afi:
The structure of Crystal Structure of Mgadp Bound AV2-AV1 Complex also contains other interesting chemical elements:
Molybdenum Binding Sites:
The binding sites of Molybdenum atom in the Crystal Structure of Mgadp Bound AV2-AV1 Complex
(pdb code 2afi). This binding sites where shown within
5.0 Angstroms radius around Molybdenum atom.
In total 4 binding sites of Molybdenum where determined in the
Crystal Structure of Mgadp Bound AV2-AV1 Complex, PDB code: 2afi:
Jump to Molybdenum binding site number:
1;
2;
3;
4;
Molybdenum binding site 1 out
of 4 in 2afi
Go back to
Molybdenum Binding Sites List in 2afi
Molybdenum binding site 1 out
of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 1 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mo496
b:19.2
occ:1.00
|
MO1
|
A:CFN496
|
0.0
|
19.2
|
1.0
|
O5
|
A:HCA494
|
2.1
|
22.9
|
1.0
|
O7
|
A:HCA494
|
2.2
|
21.2
|
1.0
|
ND1
|
A:HIS442
|
2.3
|
19.1
|
1.0
|
S3B
|
A:CFN496
|
2.3
|
17.9
|
1.0
|
S4B
|
A:CFN496
|
2.3
|
16.7
|
1.0
|
S1B
|
A:CFN496
|
2.4
|
19.4
|
1.0
|
FE7
|
A:CFN496
|
2.7
|
14.5
|
1.0
|
FE5
|
A:CFN496
|
2.7
|
19.6
|
1.0
|
FE6
|
A:CFN496
|
2.8
|
15.9
|
1.0
|
C7
|
A:HCA494
|
2.9
|
24.3
|
1.0
|
C3
|
A:HCA494
|
3.0
|
24.0
|
1.0
|
CE1
|
A:HIS442
|
3.1
|
18.8
|
1.0
|
CG
|
A:HIS442
|
3.4
|
22.1
|
1.0
|
NX
|
A:CFN496
|
3.6
|
19.8
|
1.0
|
CB
|
A:HIS442
|
3.8
|
23.3
|
1.0
|
C2
|
A:HCA494
|
3.9
|
25.1
|
1.0
|
O6
|
A:HCA494
|
4.1
|
25.5
|
1.0
|
C4
|
A:HCA494
|
4.2
|
26.9
|
1.0
|
C5
|
A:HCA494
|
4.2
|
27.8
|
1.0
|
NE2
|
A:HIS442
|
4.2
|
22.4
|
1.0
|
O2
|
A:HCA494
|
4.3
|
30.8
|
1.0
|
CD2
|
A:HIS442
|
4.4
|
21.2
|
1.0
|
CA
|
A:HIS442
|
4.5
|
23.6
|
1.0
|
C1
|
A:HCA494
|
4.7
|
29.5
|
1.0
|
S5A
|
A:CFN496
|
4.8
|
15.0
|
1.0
|
S3A
|
A:CFN496
|
4.9
|
28.1
|
1.0
|
S2B
|
A:CFN496
|
4.9
|
23.6
|
1.0
|
FE3
|
A:CFN496
|
5.0
|
21.0
|
1.0
|
|
Molybdenum binding site 2 out
of 4 in 2afi
Go back to
Molybdenum Binding Sites List in 2afi
Molybdenum binding site 2 out
of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 2 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mo496
b:14.9
occ:1.00
|
MO1
|
C:CFN496
|
0.0
|
14.9
|
1.0
|
O5
|
C:HCA494
|
2.2
|
18.6
|
1.0
|
O7
|
C:HCA494
|
2.2
|
18.7
|
1.0
|
S1B
|
C:CFN496
|
2.3
|
9.1
|
1.0
|
ND1
|
C:HIS442
|
2.3
|
9.6
|
1.0
|
S3B
|
C:CFN496
|
2.3
|
14.0
|
1.0
|
S4B
|
C:CFN496
|
2.4
|
16.4
|
1.0
|
FE6
|
C:CFN496
|
2.7
|
12.5
|
1.0
|
FE5
|
C:CFN496
|
2.7
|
13.4
|
1.0
|
FE7
|
C:CFN496
|
2.8
|
13.7
|
1.0
|
C7
|
C:HCA494
|
2.9
|
18.6
|
1.0
|
C3
|
C:HCA494
|
3.0
|
19.2
|
1.0
|
CE1
|
C:HIS442
|
3.0
|
14.6
|
1.0
|
CG
|
C:HIS442
|
3.4
|
12.9
|
1.0
|
NX
|
C:CFN496
|
3.6
|
15.8
|
1.0
|
C2
|
C:HCA494
|
3.8
|
22.9
|
1.0
|
CB
|
C:HIS442
|
3.9
|
16.7
|
1.0
|
O6
|
C:HCA494
|
4.1
|
19.2
|
1.0
|
C5
|
C:HCA494
|
4.2
|
25.1
|
1.0
|
C4
|
C:HCA494
|
4.2
|
18.7
|
1.0
|
O2
|
C:HCA494
|
4.2
|
27.2
|
1.0
|
NE2
|
C:HIS442
|
4.2
|
17.4
|
1.0
|
CD2
|
C:HIS442
|
4.4
|
16.8
|
1.0
|
C1
|
C:HCA494
|
4.5
|
25.2
|
1.0
|
CA
|
C:HIS442
|
4.7
|
22.2
|
1.0
|
S2B
|
C:CFN496
|
4.8
|
18.5
|
1.0
|
S3A
|
C:CFN496
|
4.8
|
18.5
|
1.0
|
S5A
|
C:CFN496
|
4.9
|
17.6
|
1.0
|
|
Molybdenum binding site 3 out
of 4 in 2afi
Go back to
Molybdenum Binding Sites List in 2afi
Molybdenum binding site 3 out
of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 3 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mo496
b:24.6
occ:1.00
|
MO1
|
I:CFN496
|
0.0
|
24.6
|
1.0
|
O5
|
I:HCA494
|
2.1
|
27.8
|
1.0
|
O7
|
I:HCA494
|
2.2
|
22.4
|
1.0
|
ND1
|
I:HIS442
|
2.3
|
16.2
|
1.0
|
S3B
|
I:CFN496
|
2.3
|
17.9
|
1.0
|
S4B
|
I:CFN496
|
2.3
|
22.0
|
1.0
|
S1B
|
I:CFN496
|
2.3
|
20.8
|
1.0
|
FE7
|
I:CFN496
|
2.7
|
18.6
|
1.0
|
FE6
|
I:CFN496
|
2.7
|
18.6
|
1.0
|
FE5
|
I:CFN496
|
2.7
|
24.5
|
1.0
|
C7
|
I:HCA494
|
2.9
|
24.3
|
1.0
|
CE1
|
I:HIS442
|
3.0
|
18.7
|
1.0
|
C3
|
I:HCA494
|
3.1
|
21.3
|
1.0
|
CG
|
I:HIS442
|
3.4
|
19.4
|
1.0
|
NX
|
I:CFN496
|
3.5
|
20.8
|
1.0
|
CB
|
I:HIS442
|
3.8
|
20.6
|
1.0
|
C2
|
I:HCA494
|
3.9
|
25.8
|
1.0
|
O6
|
I:HCA494
|
4.1
|
32.2
|
1.0
|
C5
|
I:HCA494
|
4.2
|
26.0
|
1.0
|
C4
|
I:HCA494
|
4.2
|
19.6
|
1.0
|
NE2
|
I:HIS442
|
4.2
|
23.2
|
1.0
|
O2
|
I:HCA494
|
4.3
|
37.2
|
1.0
|
CD2
|
I:HIS442
|
4.4
|
22.5
|
1.0
|
CA
|
I:HIS442
|
4.6
|
22.6
|
1.0
|
C1
|
I:HCA494
|
4.7
|
32.6
|
1.0
|
S3A
|
I:CFN496
|
4.8
|
27.9
|
1.0
|
S5A
|
I:CFN496
|
4.8
|
23.3
|
1.0
|
S2B
|
I:CFN496
|
4.9
|
24.7
|
1.0
|
FE4
|
I:CFN496
|
5.0
|
18.5
|
1.0
|
FE3
|
I:CFN496
|
5.0
|
25.8
|
1.0
|
|
Molybdenum binding site 4 out
of 4 in 2afi
Go back to
Molybdenum Binding Sites List in 2afi
Molybdenum binding site 4 out
of 4 in the Crystal Structure of Mgadp Bound AV2-AV1 Complex
Mono view
Stereo pair view
|
A full contact list of Molybdenum with other atoms in the Mo binding
site number 4 of Crystal Structure of Mgadp Bound AV2-AV1 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mo496
b:22.9
occ:1.00
|
MO1
|
K:CFN496
|
0.0
|
22.9
|
1.0
|
O5
|
K:HCA494
|
2.2
|
21.6
|
1.0
|
O7
|
K:HCA494
|
2.2
|
17.5
|
1.0
|
S3B
|
K:CFN496
|
2.3
|
26.2
|
1.0
|
S4B
|
K:CFN496
|
2.3
|
19.2
|
1.0
|
ND1
|
K:HIS442
|
2.3
|
21.2
|
1.0
|
S1B
|
K:CFN496
|
2.3
|
21.4
|
1.0
|
FE7
|
K:CFN496
|
2.7
|
16.5
|
1.0
|
FE5
|
K:CFN496
|
2.7
|
19.3
|
1.0
|
FE6
|
K:CFN496
|
2.7
|
23.3
|
1.0
|
C7
|
K:HCA494
|
2.9
|
21.2
|
1.0
|
C3
|
K:HCA494
|
3.0
|
21.2
|
1.0
|
CE1
|
K:HIS442
|
3.1
|
20.1
|
1.0
|
CG
|
K:HIS442
|
3.4
|
21.7
|
1.0
|
NX
|
K:CFN496
|
3.6
|
20.2
|
1.0
|
CB
|
K:HIS442
|
3.9
|
20.1
|
1.0
|
C2
|
K:HCA494
|
3.9
|
22.6
|
1.0
|
O6
|
K:HCA494
|
4.1
|
23.4
|
1.0
|
C5
|
K:HCA494
|
4.2
|
30.8
|
1.0
|
C4
|
K:HCA494
|
4.2
|
22.9
|
1.0
|
NE2
|
K:HIS442
|
4.2
|
20.2
|
1.0
|
O2
|
K:HCA494
|
4.2
|
29.6
|
1.0
|
CD2
|
K:HIS442
|
4.4
|
22.6
|
1.0
|
CA
|
K:HIS442
|
4.6
|
20.9
|
1.0
|
C1
|
K:HCA494
|
4.6
|
26.6
|
1.0
|
S5A
|
K:CFN496
|
4.8
|
25.2
|
1.0
|
S3A
|
K:CFN496
|
4.8
|
25.4
|
1.0
|
S2B
|
K:CFN496
|
4.9
|
22.2
|
1.0
|
|
Reference:
F.A.Tezcan,
J.T.Kaiser,
D.Mustafi,
M.Y.Walton,
J.B.Howard,
D.C.Rees.
Nitrogenase Complexes: Multiple Docking Sites For A Nucleotide Switch Protein Science V. 309 1377 2005.
ISSN: ISSN 0036-8075
PubMed: 16123301
DOI: 10.1126/SCIENCE.1115653
Page generated: Sun Oct 6 15:35:50 2024
|