Magnesium in PDB 1qh8: Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Enzymatic activity of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
All present enzymatic activity of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State:
1.18.6.1;
Protein crystallography data
The structure of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State, PDB code: 1qh8
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 (°)
|
203.030,
74.900,
162.120,
90.00,
122.80,
90.00
|
R / Rfree (%)
|
15.5 /
19.7
|
Other elements in 1qh8:
The structure of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
(pdb code 1qh8). 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 Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State, PDB code: 1qh8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 1qh8
Go back to
Magnesium Binding Sites List in 1qh8
Magnesium binding site 1 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg3001
b:16.5
occ:1.00
|
O
|
A:HOH3612
|
2.3
|
16.7
|
1.0
|
O
|
A:HOH3611
|
2.3
|
17.0
|
1.0
|
O
|
A:HOH3609
|
2.4
|
23.0
|
1.0
|
O
|
A:HOH3610
|
2.4
|
17.6
|
1.0
|
O
|
B:HOH3800
|
2.4
|
19.3
|
1.0
|
O
|
B:HOH3799
|
2.5
|
29.5
|
1.0
|
OD2
|
A:ASP106
|
4.0
|
17.9
|
1.0
|
O
|
A:THR100
|
4.1
|
14.8
|
1.0
|
CA
|
A:GLY101
|
4.1
|
11.3
|
1.0
|
O
|
D:HOH3244
|
4.2
|
21.8
|
1.0
|
O
|
B:HOH3256
|
4.2
|
24.3
|
1.0
|
O
|
B:HOH3449
|
4.2
|
35.2
|
1.0
|
OE1
|
B:GLU30
|
4.2
|
15.5
|
1.0
|
O
|
B:HOH3273
|
4.3
|
26.0
|
1.0
|
O1
|
A:EDO2909
|
4.3
|
18.9
|
1.0
|
OG1
|
A:THR100
|
4.3
|
14.3
|
1.0
|
C
|
A:THR100
|
4.5
|
12.9
|
1.0
|
NZ
|
A:LYS75
|
4.5
|
11.0
|
1.0
|
O
|
A:HOH3065
|
4.5
|
15.9
|
1.0
|
N
|
A:GLY101
|
4.6
|
13.1
|
1.0
|
NE
|
B:ARG27
|
4.8
|
24.1
|
1.0
|
O
|
A:HOH3602
|
4.9
|
39.3
|
1.0
|
CG
|
A:ASP106
|
4.9
|
19.1
|
1.0
|
O
|
B:HOH3230
|
4.9
|
23.1
|
1.0
|
O
|
B:HOH3224
|
4.9
|
22.4
|
1.0
|
CD
|
B:ARG27
|
5.0
|
19.9
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 1qh8
Go back to
Magnesium Binding Sites List in 1qh8
Magnesium binding site 2 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg3002
b:10.0
occ:1.00
|
OE2
|
D:GLU107
|
2.2
|
10.1
|
1.0
|
OD2
|
B:ASP353
|
2.2
|
9.1
|
1.0
|
O
|
D:LYS106
|
2.2
|
9.3
|
1.0
|
O
|
D:HOH3825
|
2.2
|
10.7
|
1.0
|
OD2
|
B:ASP349
|
2.2
|
8.5
|
1.0
|
O
|
B:HOH3801
|
2.2
|
9.0
|
1.0
|
CG
|
B:ASP353
|
3.2
|
10.5
|
1.0
|
CG
|
B:ASP349
|
3.2
|
10.9
|
1.0
|
CD
|
D:GLU107
|
3.3
|
10.6
|
1.0
|
C
|
D:LYS106
|
3.4
|
9.3
|
1.0
|
OD1
|
B:ASP353
|
3.4
|
10.0
|
1.0
|
OD1
|
B:ASP349
|
3.5
|
11.7
|
1.0
|
CG
|
D:GLU107
|
3.8
|
11.0
|
1.0
|
O
|
B:HOH3038
|
3.8
|
11.9
|
1.0
|
CB
|
D:LYS106
|
4.0
|
8.7
|
1.0
|
NZ
|
C:LYS431
|
4.1
|
10.4
|
1.0
|
N
|
D:GLU107
|
4.2
|
9.0
|
1.0
|
CA
|
D:GLU107
|
4.2
|
8.4
|
1.0
|
O
|
D:PHE105
|
4.2
|
7.9
|
1.0
|
OE1
|
D:GLU107
|
4.3
|
12.5
|
1.0
|
CA
|
D:LYS106
|
4.3
|
9.4
|
1.0
|
O
|
D:HOH3039
|
4.4
|
9.9
|
1.0
|
CB
|
B:ASP353
|
4.5
|
9.3
|
1.0
|
CB
|
B:ASP349
|
4.5
|
9.2
|
1.0
|
O
|
B:ASP349
|
4.5
|
8.7
|
1.0
|
CD1
|
C:TYR427
|
4.6
|
8.9
|
1.0
|
CB
|
D:GLU107
|
4.6
|
7.0
|
1.0
|
O
|
B:HOH3043
|
4.7
|
11.9
|
1.0
|
C
|
B:ASP349
|
4.8
|
10.4
|
1.0
|
CE
|
C:LYS431
|
4.8
|
12.4
|
1.0
|
CG
|
C:TYR427
|
5.0
|
9.5
|
1.0
|
O
|
D:HOH3049
|
5.0
|
10.6
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 1qh8
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Magnesium Binding Sites List in 1qh8
Magnesium binding site 3 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg3003
b:27.4
occ:1.00
|
O
|
B:HOH3804
|
2.4
|
27.6
|
1.0
|
O
|
B:HOH3806
|
2.5
|
24.2
|
1.0
|
O
|
B:HOH3805
|
2.5
|
26.0
|
1.0
|
O
|
B:HOH3803
|
2.6
|
26.9
|
1.0
|
O
|
B:HOH3802
|
2.7
|
44.9
|
1.0
|
O
|
B:HOH3776
|
3.6
|
56.8
|
1.0
|
O
|
B:PRO435
|
4.1
|
12.8
|
1.0
|
O
|
B:HOH3376
|
4.1
|
30.0
|
1.0
|
OD1
|
B:ASP436
|
4.2
|
13.8
|
1.0
|
O
|
B:ALA457
|
4.2
|
15.2
|
1.0
|
O
|
B:HOH3272
|
4.2
|
25.3
|
1.0
|
O
|
B:HOH3760
|
4.3
|
37.5
|
1.0
|
O
|
B:HOH3175
|
4.4
|
20.4
|
1.0
|
O
|
B:GLU459
|
4.4
|
13.8
|
1.0
|
OE1
|
B:GLN434
|
4.4
|
19.4
|
1.0
|
CA
|
B:ASP436
|
4.4
|
11.2
|
1.0
|
O
|
B:GLN434
|
4.7
|
13.8
|
1.0
|
O
|
B:ASP436
|
4.8
|
12.4
|
1.0
|
C
|
B:PRO435
|
4.9
|
10.7
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 1qh8
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Magnesium Binding Sites List in 1qh8
Magnesium binding site 4 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg3004
b:24.2
occ:1.00
|
OD1
|
B:ASP407
|
2.3
|
17.1
|
1.0
|
O
|
B:HOH3811
|
2.3
|
22.1
|
1.0
|
O
|
B:HOH3807
|
2.4
|
18.1
|
1.0
|
O
|
B:HOH3808
|
2.4
|
21.1
|
1.0
|
O
|
B:HOH3810
|
2.4
|
25.1
|
1.0
|
O
|
B:HOH3809
|
2.5
|
23.0
|
1.0
|
CG
|
B:ASP407
|
3.5
|
18.3
|
1.0
|
O
|
B:HOH3213
|
3.9
|
22.0
|
1.0
|
O
|
B:HOH3193
|
4.1
|
21.3
|
1.0
|
OD2
|
B:ASP407
|
4.1
|
16.4
|
1.0
|
CA
|
B:ASP407
|
4.1
|
13.8
|
1.0
|
O
|
B:GLY412
|
4.2
|
12.3
|
1.0
|
O
|
B:HOH3164
|
4.2
|
19.9
|
1.0
|
O
|
B:HOH3228
|
4.3
|
22.4
|
1.0
|
CB
|
B:ASP407
|
4.3
|
11.8
|
1.0
|
N
|
B:ASP407
|
4.5
|
13.0
|
1.0
|
O
|
B:HOH3252
|
4.5
|
24.2
|
1.0
|
O
|
B:ARG413
|
4.6
|
20.4
|
1.0
|
O
|
B:HOH3673
|
4.7
|
42.8
|
1.0
|
CA
|
B:ARG413
|
4.9
|
14.0
|
1.0
|
|
Magnesium binding site 5 out
of 7 in 1qh8
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Magnesium Binding Sites List in 1qh8
Magnesium binding site 5 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) 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
|
17.6
|
1.0
|
O
|
C:HOH3030
|
2.4
|
20.2
|
1.0
|
O
|
C:HOH3026
|
2.4
|
25.9
|
1.0
|
O
|
C:HOH3028
|
2.4
|
20.8
|
1.0
|
O
|
D:HOH3827
|
2.4
|
22.1
|
1.0
|
O
|
D:HOH3826
|
2.4
|
19.0
|
1.0
|
OD2
|
C:ASP106
|
4.0
|
17.5
|
1.0
|
O
|
C:THR100
|
4.1
|
14.4
|
1.0
|
O
|
D:HOH3712
|
4.2
|
40.7
|
1.0
|
CA
|
C:GLY101
|
4.2
|
13.1
|
1.0
|
O
|
B:HOH3260
|
4.2
|
24.6
|
1.0
|
OE1
|
D:GLU30
|
4.2
|
16.6
|
1.0
|
O
|
D:HOH3556
|
4.3
|
36.7
|
1.0
|
O
|
D:HOH3668
|
4.3
|
44.6
|
1.0
|
OG1
|
C:THR100
|
4.4
|
15.5
|
1.0
|
O
|
D:HOH3228
|
4.4
|
20.9
|
1.0
|
O
|
C:HOH1465
|
4.4
|
15.1
|
1.0
|
NZ
|
C:LYS75
|
4.5
|
13.1
|
1.0
|
C
|
C:THR100
|
4.6
|
14.4
|
1.0
|
N
|
C:GLY101
|
4.6
|
13.4
|
1.0
|
O
|
C:HOH1685
|
4.7
|
30.0
|
1.0
|
CG
|
C:ASP106
|
4.8
|
21.3
|
1.0
|
O
|
D:HOH3447
|
4.9
|
30.9
|
1.0
|
CG
|
D:ARG27
|
4.9
|
24.0
|
1.0
|
OD1
|
C:ASP106
|
4.9
|
16.9
|
1.0
|
|
Magnesium binding site 6 out
of 7 in 1qh8
Go back to
Magnesium Binding Sites List in 1qh8
Magnesium binding site 6 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg3006
b:10.0
occ:1.00
|
OE2
|
B:GLU107
|
2.2
|
9.7
|
1.0
|
OD2
|
D:ASP349
|
2.2
|
8.7
|
1.0
|
O
|
D:HOH3828
|
2.2
|
9.3
|
1.0
|
O
|
B:HOH3812
|
2.2
|
9.5
|
1.0
|
OD2
|
D:ASP353
|
2.2
|
9.9
|
1.0
|
O
|
B:LYS106
|
2.2
|
9.0
|
1.0
|
CG
|
D:ASP349
|
3.1
|
11.7
|
1.0
|
CG
|
D:ASP353
|
3.2
|
13.2
|
1.0
|
CD
|
B:GLU107
|
3.3
|
10.7
|
1.0
|
OD1
|
D:ASP349
|
3.4
|
10.4
|
1.0
|
C
|
B:LYS106
|
3.4
|
9.2
|
1.0
|
OD1
|
D:ASP353
|
3.4
|
9.7
|
1.0
|
CG
|
B:GLU107
|
3.8
|
9.2
|
1.0
|
O
|
D:HOH3082
|
3.8
|
12.4
|
1.0
|
CB
|
B:LYS106
|
4.1
|
8.2
|
1.0
|
CA
|
B:GLU107
|
4.2
|
7.8
|
1.0
|
NZ
|
A:LYS431
|
4.2
|
10.0
|
1.0
|
N
|
B:GLU107
|
4.2
|
8.8
|
1.0
|
O
|
B:PHE105
|
4.3
|
9.0
|
1.0
|
CA
|
B:LYS106
|
4.3
|
9.0
|
1.0
|
OE1
|
B:GLU107
|
4.3
|
12.2
|
1.0
|
CB
|
D:ASP353
|
4.4
|
10.1
|
1.0
|
CB
|
D:ASP349
|
4.5
|
8.0
|
1.0
|
O
|
B:HOH3033
|
4.5
|
11.2
|
1.0
|
O
|
D:ASP349
|
4.5
|
8.1
|
1.0
|
CD1
|
A:TYR427
|
4.6
|
8.3
|
1.0
|
CB
|
B:GLU107
|
4.6
|
7.6
|
1.0
|
O
|
D:HOH3059
|
4.7
|
11.3
|
1.0
|
CE
|
A:LYS431
|
4.8
|
12.7
|
1.0
|
C
|
D:ASP349
|
4.8
|
9.9
|
1.0
|
CG
|
A:TYR427
|
4.9
|
8.8
|
1.0
|
O
|
B:HOH3035
|
5.0
|
11.8
|
1.0
|
|
Magnesium binding site 7 out
of 7 in 1qh8
Go back to
Magnesium Binding Sites List in 1qh8
Magnesium binding site 7 out
of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, As-Crystallized (Mixed Oxidation) State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg3007
b:29.0
occ:1.00
|
O
|
D:HOH3831
|
2.4
|
24.3
|
1.0
|
O
|
D:HOH3830
|
2.5
|
24.7
|
1.0
|
OE1
|
D:GLN434
|
2.5
|
31.1
|
1.0
|
O
|
B:HOH3814
|
2.5
|
35.8
|
1.0
|
O
|
B:HOH3813
|
2.7
|
33.0
|
1.0
|
O
|
D:HOH3829
|
2.7
|
44.9
|
1.0
|
CD
|
D:GLN434
|
3.4
|
30.6
|
1.0
|
CG
|
D:GLN434
|
3.9
|
27.0
|
1.0
|
O
|
D:HOH3524
|
3.9
|
36.0
|
1.0
|
O
|
B:HOH3795
|
3.9
|
39.2
|
1.0
|
O
|
D:ALA457
|
4.0
|
13.7
|
1.0
|
O
|
D:HOH3217
|
4.1
|
20.0
|
1.0
|
O
|
D:PRO435
|
4.1
|
12.1
|
1.0
|
O
|
D:GLU459
|
4.2
|
14.3
|
1.0
|
O
|
D:HOH3366
|
4.2
|
27.4
|
1.0
|
OD1
|
D:ASP436
|
4.4
|
13.8
|
1.0
|
O
|
B:HOH3791
|
4.4
|
40.0
|
1.0
|
NE2
|
D:GLN434
|
4.5
|
16.7
|
1.0
|
CA
|
D:ASP436
|
4.6
|
8.3
|
1.0
|
O
|
D:HOH3498
|
4.7
|
33.6
|
1.0
|
O
|
D:ASP436
|
4.9
|
11.3
|
1.0
|
C
|
D:PRO435
|
5.0
|
9.2
|
1.0
|
O
|
D:GLN434
|
5.0
|
13.7
|
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 11:51:10 2024
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