Magnesium in PDB 7aiz: Vanadium Nitrogenase Vfe Protein, High Co State
Enzymatic activity of Vanadium Nitrogenase Vfe Protein, High Co State
All present enzymatic activity of Vanadium Nitrogenase Vfe Protein, High Co State:
1.18.6.1;
Protein crystallography data
The structure of Vanadium Nitrogenase Vfe Protein, High Co State, PDB code: 7aiz
was solved by
M.Rohde,
O.Einsle,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.39 /
1.05
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.521,
80.041,
107.21,
84,
72.48,
75.03
|
R / Rfree (%)
|
12.4 /
14.6
|
Other elements in 7aiz:
The structure of Vanadium Nitrogenase Vfe Protein, High Co State also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Vanadium Nitrogenase Vfe Protein, High Co State
(pdb code 7aiz). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Vanadium Nitrogenase Vfe Protein, High Co State, PDB code: 7aiz:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7aiz
Go back to
Magnesium Binding Sites List in 7aiz
Magnesium binding site 1 out
of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg502
b:10.5
occ:1.00
|
OE2
|
B:GLU70
|
2.0
|
11.4
|
1.0
|
O
|
B:HOH668
|
2.0
|
11.6
|
1.0
|
OD2
|
E:ASP314
|
2.1
|
11.4
|
1.0
|
O
|
E:HOH674
|
2.1
|
10.7
|
1.0
|
O
|
B:HOH839
|
2.1
|
11.6
|
1.0
|
O
|
E:HOH979
|
2.1
|
11.1
|
1.0
|
CD
|
B:GLU70
|
3.2
|
11.0
|
1.0
|
CG
|
E:ASP314
|
3.2
|
10.4
|
1.0
|
CB
|
E:ASP314
|
3.9
|
10.1
|
1.0
|
CG
|
B:GLU70
|
4.0
|
10.2
|
1.0
|
O
|
B:LYS69
|
4.0
|
9.7
|
1.0
|
NZ
|
A:LYS414
|
4.1
|
11.8
|
1.0
|
OE1
|
B:GLU70
|
4.1
|
13.3
|
1.0
|
NZ
|
A:LYS413
|
4.1
|
11.8
|
1.0
|
O
|
A:HOH887
|
4.1
|
14.4
|
1.0
|
OD1
|
E:ASP314
|
4.2
|
12.3
|
1.0
|
O
|
B:HOH678
|
4.2
|
11.8
|
1.0
|
OD1
|
B:ASP222
|
4.2
|
12.3
|
1.0
|
OD2
|
E:ASP318
|
4.2
|
11.0
|
1.0
|
O
|
B:SER223
|
4.2
|
11.1
|
1.0
|
OH
|
B:TYR437
|
4.2
|
14.9
|
1.0
|
O
|
B:PHE68
|
4.4
|
10.5
|
1.0
|
O
|
E:ASP314
|
4.5
|
10.5
|
1.0
|
C
|
E:ASP314
|
4.6
|
9.5
|
1.0
|
N
|
B:SER223
|
4.8
|
11.2
|
1.0
|
C
|
B:LYS69
|
4.8
|
9.4
|
1.0
|
CA
|
E:ASP314
|
4.8
|
9.7
|
1.0
|
N
|
E:ALA315
|
4.9
|
9.5
|
1.0
|
CB
|
B:LYS69
|
5.0
|
11.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7aiz
Go back to
Magnesium Binding Sites List in 7aiz
Magnesium binding site 2 out
of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg503
b:9.8
occ:1.00
|
OE2
|
E:GLU70
|
2.0
|
10.9
|
1.0
|
O
|
E:HOH658
|
2.0
|
11.2
|
1.0
|
OD2
|
B:ASP314
|
2.0
|
11.3
|
1.0
|
O
|
B:HOH677
|
2.1
|
10.1
|
1.0
|
O
|
B:HOH947
|
2.1
|
11.1
|
1.0
|
O
|
E:HOH858
|
2.1
|
10.7
|
1.0
|
CG
|
B:ASP314
|
3.2
|
10.1
|
1.0
|
CD
|
E:GLU70
|
3.2
|
10.3
|
1.0
|
CB
|
B:ASP314
|
3.9
|
9.1
|
1.0
|
CG
|
E:GLU70
|
4.0
|
9.3
|
1.0
|
NZ
|
D:LYS414
|
4.0
|
11.3
|
1.0
|
O
|
E:LYS69
|
4.0
|
9.1
|
1.0
|
NZ
|
D:LYS413
|
4.1
|
11.0
|
1.0
|
OE1
|
E:GLU70
|
4.1
|
12.6
|
1.0
|
O
|
D:HOH865
|
4.1
|
12.5
|
1.0
|
OD1
|
B:ASP314
|
4.2
|
11.5
|
1.0
|
OD2
|
B:ASP318
|
4.2
|
10.6
|
1.0
|
O
|
E:HOH670
|
4.2
|
11.5
|
1.0
|
OD1
|
E:ASP222
|
4.2
|
11.6
|
1.0
|
OH
|
E:TYR437
|
4.2
|
14.7
|
1.0
|
O
|
E:SER223
|
4.2
|
10.1
|
1.0
|
O
|
E:PHE68
|
4.5
|
10.1
|
1.0
|
O
|
B:ASP314
|
4.6
|
9.8
|
1.0
|
C
|
B:ASP314
|
4.6
|
9.2
|
1.0
|
C
|
E:LYS69
|
4.8
|
8.6
|
1.0
|
N
|
E:SER223
|
4.8
|
10.1
|
1.0
|
CA
|
B:ASP314
|
4.8
|
9.7
|
1.0
|
N
|
B:ALA315
|
4.9
|
9.0
|
1.0
|
CB
|
E:LYS69
|
5.0
|
10.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7aiz
Go back to
Magnesium Binding Sites List in 7aiz
Magnesium binding site 3 out
of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg201
b:15.1
occ:1.00
|
O
|
C:HOH356
|
2.0
|
14.9
|
1.0
|
O
|
C:HOH440
|
2.0
|
15.5
|
1.0
|
O
|
A:HOH915
|
2.1
|
14.7
|
1.0
|
O
|
C:HOH451
|
2.1
|
16.8
|
1.0
|
O
|
C:HOH310
|
2.1
|
15.6
|
1.0
|
O
|
C:HOH463
|
2.1
|
17.1
|
1.0
|
OE1
|
C:GLU14
|
4.0
|
16.2
|
1.0
|
O
|
C:HOH448
|
4.2
|
18.4
|
1.0
|
O
|
A:HOH805
|
4.2
|
14.9
|
1.0
|
O
|
A:HOH755
|
4.2
|
18.4
|
1.0
|
O
|
A:HOH856
|
4.2
|
15.2
|
1.0
|
O
|
A:HOH1123
|
4.3
|
24.1
|
1.0
|
O
|
C:HOH452
|
4.3
|
20.5
|
1.0
|
OE2
|
C:GLU15
|
4.4
|
17.3
|
1.0
|
O
|
C:HOH436
|
4.4
|
16.8
|
1.0
|
O
|
C:HOH453
|
4.5
|
25.6
|
1.0
|
O
|
C:ALA11
|
4.6
|
13.9
|
1.0
|
CB
|
C:ALA11
|
4.6
|
15.3
|
1.0
|
O
|
A:ALA373
|
4.6
|
12.1
|
1.0
|
CA
|
C:ALA11
|
4.7
|
14.3
|
1.0
|
CD
|
C:GLU14
|
4.8
|
14.3
|
1.0
|
O
|
A:HOH885
|
4.9
|
17.0
|
1.0
|
CB
|
C:GLU14
|
4.9
|
13.0
|
1.0
|
CB
|
C:GLU15
|
4.9
|
15.0
|
1.0
|
CG
|
C:GLU14
|
4.9
|
14.1
|
1.0
|
O
|
A:HOH892
|
4.9
|
20.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7aiz
Go back to
Magnesium Binding Sites List in 7aiz
Magnesium binding site 4 out
of 4 in the Vanadium Nitrogenase Vfe Protein, High Co State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Vanadium Nitrogenase Vfe Protein, High Co State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg201
b:16.0
occ:1.00
|
O
|
F:HOH310
|
2.0
|
15.4
|
1.0
|
O
|
D:HOH904
|
2.1
|
16.2
|
1.0
|
O
|
F:HOH429
|
2.1
|
18.4
|
1.0
|
O
|
F:HOH332
|
2.1
|
15.7
|
1.0
|
O
|
F:HOH414
|
2.1
|
16.4
|
1.0
|
O
|
F:HOH435
|
2.1
|
18.1
|
1.0
|
OE1
|
F:GLU14
|
4.0
|
16.7
|
1.0
|
O
|
D:HOH909
|
4.1
|
19.0
|
1.0
|
O
|
F:HOH427
|
4.2
|
20.1
|
1.0
|
O
|
D:HOH793
|
4.2
|
15.3
|
1.0
|
O
|
D:HOH859
|
4.2
|
15.1
|
1.0
|
O
|
D:HOH1148
|
4.2
|
25.6
|
1.0
|
OE2
|
F:GLU15
|
4.4
|
18.1
|
1.0
|
O
|
F:HOH430
|
4.4
|
21.5
|
1.0
|
O
|
F:HOH412
|
4.4
|
16.1
|
1.0
|
O
|
F:HOH425
|
4.4
|
30.4
|
1.0
|
O
|
F:ALA11
|
4.5
|
15.3
|
1.0
|
O
|
D:ALA373
|
4.6
|
12.0
|
1.0
|
CB
|
F:ALA11
|
4.7
|
17.8
|
1.0
|
CD
|
F:GLU14
|
4.7
|
14.9
|
1.0
|
CA
|
F:ALA11
|
4.8
|
15.5
|
1.0
|
CB
|
F:GLU15
|
4.9
|
15.6
|
1.0
|
CG
|
F:GLU14
|
4.9
|
14.0
|
1.0
|
O
|
D:HOH874
|
4.9
|
16.8
|
1.0
|
O
|
D:HOH835
|
4.9
|
20.3
|
1.0
|
CB
|
F:GLU14
|
4.9
|
13.8
|
1.0
|
|
Reference:
M.Rohde,
K.Laun,
I.Zebger,
S.T.Stripp,
O.Einsle.
Two Ligand-Binding Sites in Co-Reducing V Nitrogenase Reveal A General Mechanistic Principle Sci Adv 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABG4474
Page generated: Wed Oct 2 10:06:37 2024
|