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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:

Molybdenum (Mo) 2 atoms
Iron (Fe) 30 atoms
Chlorine (Cl) 2 atoms

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 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 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 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 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 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 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 site 7 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 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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