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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:

Molybdenum (Mo) 2 atoms
Iron (Fe) 34 atoms
Chlorine (Cl) 2 atoms

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

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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

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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 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 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 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

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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: Sun Aug 10 03:02:37 2025

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