Magnesium in PDB 1qgu: Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Enzymatic activity of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
All present enzymatic activity of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State:
1.18.6.1;
Protein crystallography data
The structure of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State, PDB code: 1qgu
was solved by
S.M.Mayer,
D.M.Lawson,
C.A.Gormal,
S.M.Roe,
B.E.Smith,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
1.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
204.030,
75.300,
163.010,
90.00,
122.61,
90.00
|
R / Rfree (%)
|
15.6 /
19.9
|
Other elements in 1qgu:
The structure of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
(pdb code 1qgu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State, PDB code: 1qgu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 1 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3001
b:17.1
occ:1.00
|
O
|
A:HOH3606
|
2.3
|
15.6
|
1.0
|
O
|
A:HOH3605
|
2.3
|
17.1
|
1.0
|
O
|
B:HOH3784
|
2.3
|
17.3
|
1.0
|
O
|
A:HOH3607
|
2.4
|
18.7
|
1.0
|
O
|
B:HOH3783
|
2.4
|
24.9
|
1.0
|
O
|
B:HOH3785
|
2.5
|
26.8
|
1.0
|
OD2
|
A:ASP106
|
4.0
|
17.8
|
1.0
|
O
|
A:THR100
|
4.1
|
14.8
|
1.0
|
O
|
D:HOH3243
|
4.1
|
21.4
|
1.0
|
CA
|
A:GLY101
|
4.1
|
11.1
|
1.0
|
O
|
B:HOH3256
|
4.2
|
23.2
|
1.0
|
O
|
B:HOH3312
|
4.2
|
28.1
|
1.0
|
OE1
|
B:GLU30
|
4.2
|
15.6
|
1.0
|
OG1
|
A:THR100
|
4.3
|
17.2
|
1.0
|
O1
|
A:EDO2774
|
4.3
|
18.4
|
1.0
|
O
|
B:HOH3575
|
4.4
|
38.2
|
1.0
|
O
|
A:HOH3600
|
4.5
|
35.2
|
1.0
|
C
|
A:THR100
|
4.5
|
13.4
|
1.0
|
NZ
|
A:LYS75
|
4.6
|
10.7
|
1.0
|
O
|
A:HOH3070
|
4.6
|
16.1
|
1.0
|
N
|
A:GLY101
|
4.6
|
12.4
|
1.0
|
O
|
B:HOH3622
|
4.7
|
42.0
|
1.0
|
O
|
B:HOH3192
|
4.8
|
21.0
|
1.0
|
NE
|
B:ARG27
|
4.9
|
23.1
|
1.0
|
CG
|
A:ASP106
|
4.9
|
17.1
|
1.0
|
O
|
B:HOH3007
|
4.9
|
21.6
|
1.0
|
CG
|
B:ARG27
|
5.0
|
18.8
|
1.0
|
CD
|
B:ARG27
|
5.0
|
19.3
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 2 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg3002
b:9.7
occ:1.00
|
OD2
|
B:ASP353
|
2.2
|
9.8
|
1.0
|
OE2
|
D:GLU107
|
2.2
|
10.0
|
1.0
|
O
|
B:HOH3786
|
2.2
|
9.0
|
1.0
|
OD2
|
B:ASP349
|
2.2
|
10.4
|
1.0
|
O
|
D:HOH3796
|
2.2
|
10.5
|
1.0
|
O
|
D:LYS106
|
2.3
|
9.9
|
1.0
|
CG
|
B:ASP353
|
3.2
|
11.1
|
1.0
|
CG
|
B:ASP349
|
3.2
|
10.1
|
1.0
|
CD
|
D:GLU107
|
3.3
|
11.6
|
1.0
|
C
|
D:LYS106
|
3.4
|
10.2
|
1.0
|
OD1
|
B:ASP353
|
3.5
|
10.8
|
1.0
|
OD1
|
B:ASP349
|
3.5
|
10.5
|
1.0
|
CG
|
D:GLU107
|
3.8
|
10.0
|
1.0
|
O
|
B:HOH3054
|
3.9
|
13.9
|
1.0
|
CB
|
D:LYS106
|
4.1
|
9.9
|
1.0
|
NZ
|
C:LYS431
|
4.1
|
10.0
|
1.0
|
N
|
D:GLU107
|
4.2
|
9.0
|
1.0
|
CA
|
D:GLU107
|
4.2
|
8.5
|
1.0
|
O
|
D:PHE105
|
4.3
|
8.3
|
1.0
|
OE1
|
D:GLU107
|
4.3
|
11.8
|
1.0
|
CA
|
D:LYS106
|
4.4
|
9.3
|
1.0
|
CB
|
B:ASP353
|
4.5
|
11.2
|
1.0
|
O
|
D:HOH3039
|
4.5
|
10.4
|
1.0
|
CB
|
B:ASP349
|
4.5
|
8.2
|
1.0
|
O
|
B:ASP349
|
4.5
|
8.3
|
1.0
|
CB
|
D:GLU107
|
4.6
|
9.6
|
1.0
|
CD1
|
C:TYR427
|
4.6
|
9.4
|
1.0
|
CE
|
C:LYS431
|
4.7
|
11.8
|
1.0
|
O
|
B:HOH3037
|
4.7
|
12.1
|
1.0
|
C
|
B:ASP349
|
4.8
|
10.0
|
1.0
|
CG
|
C:TYR427
|
5.0
|
8.4
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 3 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg3003
b:20.2
occ:1.00
|
O
|
B:HOH3789
|
2.4
|
26.7
|
1.0
|
O
|
B:HOH3787
|
2.5
|
22.6
|
1.0
|
O
|
B:HOH3788
|
2.5
|
24.4
|
1.0
|
O
|
B:HOH3792
|
2.6
|
38.2
|
1.0
|
O
|
B:HOH3790
|
2.6
|
32.7
|
1.0
|
O
|
B:HOH3791
|
2.6
|
37.1
|
1.0
|
O
|
B:HOH3362
|
4.0
|
29.0
|
1.0
|
O
|
B:HOH3250
|
4.0
|
24.0
|
1.0
|
O
|
B:HOH3685
|
4.1
|
45.8
|
1.0
|
O
|
B:ALA457
|
4.2
|
15.2
|
1.0
|
O
|
B:HOH3175
|
4.2
|
19.5
|
1.0
|
O
|
B:GLU459
|
4.2
|
14.3
|
1.0
|
OD1
|
B:ASP436
|
4.3
|
13.7
|
1.0
|
O
|
B:PRO435
|
4.3
|
12.1
|
1.0
|
CA
|
B:ASP436
|
4.5
|
10.9
|
1.0
|
OE1
|
B:GLN434
|
4.6
|
18.6
|
1.0
|
O
|
B:HOH3757
|
4.6
|
37.7
|
1.0
|
O
|
B:HOH3356
|
4.6
|
29.4
|
1.0
|
O
|
B:HOH3653
|
4.6
|
42.1
|
1.0
|
O
|
B:ASP436
|
4.8
|
10.9
|
1.0
|
O
|
B:GLN434
|
5.0
|
14.0
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 4 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg3004
b:19.7
occ:1.00
|
OD1
|
B:ASP407
|
2.3
|
15.9
|
1.0
|
O
|
B:HOH3797
|
2.3
|
15.7
|
1.0
|
O
|
B:HOH3794
|
2.4
|
18.0
|
1.0
|
O
|
B:HOH3793
|
2.4
|
23.0
|
1.0
|
O
|
B:HOH3795
|
2.4
|
23.2
|
1.0
|
O
|
B:HOH3796
|
2.5
|
25.1
|
1.0
|
CG
|
B:ASP407
|
3.5
|
14.0
|
1.0
|
O
|
B:HOH3172
|
3.8
|
19.8
|
1.0
|
O
|
B:HOH3184
|
4.1
|
19.5
|
1.0
|
OD2
|
B:ASP407
|
4.1
|
15.2
|
1.0
|
CA
|
B:ASP407
|
4.2
|
12.6
|
1.0
|
O
|
B:HOH3132
|
4.3
|
19.1
|
1.0
|
O
|
B:GLY412
|
4.3
|
12.5
|
1.0
|
CB
|
B:ASP407
|
4.3
|
12.4
|
1.0
|
O
|
B:HOH3235
|
4.4
|
22.9
|
1.0
|
O
|
B:HOH3310
|
4.5
|
26.3
|
1.0
|
O
|
B:HOH3217
|
4.5
|
22.6
|
1.0
|
N
|
B:ASP407
|
4.6
|
12.3
|
1.0
|
O
|
B:ARG413
|
4.7
|
17.8
|
1.0
|
CA
|
B:ARG413
|
4.9
|
13.4
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 5 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg3005
b:16.9
occ:1.00
|
O
|
C:HOH3029
|
2.3
|
17.4
|
1.0
|
O
|
C:HOH3027
|
2.4
|
19.2
|
1.0
|
O
|
C:HOH3028
|
2.4
|
20.0
|
1.0
|
O
|
D:HOH3798
|
2.4
|
18.3
|
1.0
|
O
|
D:HOH3797
|
2.4
|
23.3
|
1.0
|
O
|
C:HOH3031
|
2.5
|
28.9
|
1.0
|
OD2
|
C:ASP106
|
4.0
|
16.7
|
1.0
|
O
|
C:THR100
|
4.1
|
15.1
|
1.0
|
O
|
D:HOH3578
|
4.1
|
38.5
|
1.0
|
O
|
B:HOH3233
|
4.1
|
23.2
|
1.0
|
CA
|
C:GLY101
|
4.2
|
11.4
|
1.0
|
OE1
|
D:GLU30
|
4.3
|
17.8
|
1.0
|
O
|
D:HOH3679
|
4.3
|
43.5
|
1.0
|
OG1
|
C:THR100
|
4.4
|
15.9
|
1.0
|
O
|
C:HOH1433
|
4.4
|
16.4
|
1.0
|
O
|
D:HOH3614
|
4.5
|
38.9
|
1.0
|
O
|
D:HOH3214
|
4.5
|
20.8
|
1.0
|
NZ
|
C:LYS75
|
4.6
|
13.9
|
1.0
|
C
|
C:THR100
|
4.6
|
14.3
|
1.0
|
N
|
C:GLY101
|
4.6
|
13.3
|
1.0
|
O
|
C:HOH1575
|
4.7
|
28.4
|
1.0
|
O
|
D:HOH3698
|
4.8
|
40.1
|
1.0
|
CG
|
C:ASP106
|
4.9
|
20.1
|
1.0
|
CG
|
D:ARG27
|
5.0
|
22.4
|
1.0
|
O
|
D:HOH3326
|
5.0
|
26.6
|
1.0
|
OD1
|
C:ASP106
|
5.0
|
16.8
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 6 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg3006
b:10.2
occ:1.00
|
OD2
|
D:ASP353
|
2.2
|
10.1
|
1.0
|
OD2
|
D:ASP349
|
2.2
|
10.5
|
1.0
|
O
|
D:HOH3799
|
2.2
|
9.9
|
1.0
|
O
|
B:HOH3798
|
2.2
|
10.5
|
1.0
|
OE2
|
B:GLU107
|
2.2
|
10.3
|
1.0
|
O
|
B:LYS106
|
2.3
|
9.0
|
1.0
|
CG
|
D:ASP353
|
3.1
|
10.3
|
1.0
|
CG
|
D:ASP349
|
3.2
|
11.9
|
1.0
|
CD
|
B:GLU107
|
3.3
|
11.2
|
1.0
|
OD1
|
D:ASP353
|
3.4
|
10.3
|
1.0
|
OD1
|
D:ASP349
|
3.4
|
11.3
|
1.0
|
C
|
B:LYS106
|
3.4
|
9.5
|
1.0
|
CG
|
B:GLU107
|
3.8
|
10.4
|
1.0
|
O
|
D:HOH3094
|
3.8
|
14.2
|
1.0
|
CB
|
B:LYS106
|
4.1
|
8.6
|
1.0
|
NZ
|
A:LYS431
|
4.2
|
10.5
|
1.0
|
CA
|
B:GLU107
|
4.3
|
7.2
|
1.0
|
N
|
B:GLU107
|
4.3
|
8.3
|
1.0
|
O
|
B:PHE105
|
4.3
|
7.9
|
1.0
|
CA
|
B:LYS106
|
4.3
|
9.0
|
1.0
|
OE1
|
B:GLU107
|
4.3
|
12.0
|
1.0
|
CB
|
D:ASP353
|
4.4
|
9.5
|
1.0
|
CB
|
D:ASP349
|
4.5
|
9.4
|
1.0
|
O
|
B:HOH3033
|
4.5
|
11.7
|
1.0
|
O
|
D:ASP349
|
4.5
|
9.6
|
1.0
|
CB
|
B:GLU107
|
4.6
|
9.1
|
1.0
|
CD1
|
A:TYR427
|
4.6
|
8.5
|
1.0
|
O
|
D:HOH3009
|
4.7
|
11.4
|
1.0
|
C
|
D:ASP349
|
4.8
|
10.8
|
1.0
|
CE
|
A:LYS431
|
4.9
|
12.1
|
1.0
|
O
|
B:HOH3050
|
5.0
|
13.5
|
1.0
|
CG
|
A:TYR427
|
5.0
|
9.0
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 1qgu
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Magnesium Binding Sites List in 1qgu
Magnesium binding site 7 out
of 7 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State
Mono view
Stereo pair view
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A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Dithionite-Reduced State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg3007
b:25.6
occ:1.00
|
O
|
D:HOH3800
|
2.4
|
20.7
|
1.0
|
O
|
D:HOH3802
|
2.4
|
26.4
|
1.0
|
O
|
D:HOH3801
|
2.5
|
24.6
|
1.0
|
O
|
D:HOH3805
|
2.6
|
42.9
|
1.0
|
O
|
D:HOH3803
|
2.7
|
27.7
|
1.0
|
O
|
D:HOH3804
|
2.7
|
41.1
|
1.0
|
O
|
D:HOH3784
|
3.7
|
39.4
|
1.0
|
OE1
|
D:GLN434
|
3.7
|
41.0
|
1.0
|
O
|
D:HOH3604
|
3.9
|
38.1
|
1.0
|
O
|
D:ALA457
|
4.1
|
14.5
|
1.0
|
O
|
D:HOH3194
|
4.2
|
19.8
|
1.0
|
O
|
D:PRO435
|
4.2
|
12.8
|
1.0
|
O
|
D:HOH3351
|
4.3
|
28.8
|
1.0
|
OD1
|
D:ASP436
|
4.3
|
13.2
|
1.0
|
O
|
D:GLU459
|
4.3
|
13.3
|
1.0
|
CA
|
D:ASP436
|
4.5
|
9.3
|
1.0
|
CD
|
D:GLN434
|
4.5
|
26.3
|
1.0
|
NE2
|
D:GLN434
|
4.6
|
25.9
|
1.0
|
O
|
D:HOH3267
|
4.7
|
23.8
|
1.0
|
O
|
D:ASP436
|
4.8
|
12.3
|
1.0
|
C
|
D:PRO435
|
5.0
|
10.0
|
1.0
|
O
|
D:GLN434
|
5.0
|
13.8
|
1.0
|
|
Reference:
S.M.Mayer,
D.M.Lawson,
C.A.Gormal,
S.M.Roe,
B.E.Smith.
New Insights Into Structure-Function Relationships in Nitrogenase: A 1.6 A Resolution X-Ray Crystallographic Study of Klebsiella Pneumoniae Mofe-Protein. J.Mol.Biol. V. 292 871 1999.
ISSN: ISSN 0022-2836
PubMed: 10525412
DOI: 10.1006/JMBI.1999.3107
Page generated: Tue Aug 13 11:50:30 2024
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