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Magnesium in PDB 1qh1: Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized State

Enzymatic activity of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized State

All present enzymatic activity of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized State:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized State, PDB code: 1qh1 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 (°) 204.180, 75.220, 162.840, 90.00, 122.88, 90.00
R / Rfree (%) 15.8 / 19.9

Other elements in 1qh1:

The structure of Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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 Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized State (pdb code 1qh1). 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, Phenosafranin Oxidized State, PDB code: 1qh1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1qh1

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Magnesium binding site 1 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:18.3
occ:1.00
 O A:HOH3588 2.3 21.2 1.0
O A:HOH3587 2.3 19.8 1.0
O A:HOH3590 2.3 18.9 1.0
O B:HOH3727 2.4 21.2 1.0
O A:HOH3589 2.4 25.1 1.0
O B:HOH3728 2.5 29.1 1.0
OD2 A:ASP106 4.0 21.4 1.0
O A:THR100 4.1 18.6 1.0
CA A:GLY101 4.1 14.3 1.0
O D:HOH3229 4.2 24.3 1.0
O B:HOH3488 4.2 39.0 1.0
O B:HOH3222 4.2 25.5 1.0
OE1 B:GLU30 4.3 18.1 1.0
O B:HOH3281 4.3 29.6 1.0
OG1 A:THR100 4.3 16.5 1.0
O1 A:EDO2774 4.3 23.2 1.0
C A:THR100 4.5 16.4 1.0
O A:HOH3055 4.5 18.3 1.0
N A:GLY101 4.5 16.0 1.0
NZ A:LYS75 4.6 14.3 1.0
O A:HOH3579 4.8 40.6 1.0
CG A:ASP106 4.9 23.1 1.0
NE B:ARG27 4.9 29.5 1.0
O B:HOH3208 4.9 25.4 1.0
OD1 A:ASP106 5.0 18.2 1.0
O B:HOH3213 5.0 25.4 1.0

Magnesium binding site 2 out of 7 in 1qh1

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Magnesium binding site 2 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:12.7
occ:1.00
 OD2 B:ASP353 2.2 10.7 1.0
OE2 D:GLU107 2.2 12.4 1.0
OD2 B:ASP349 2.2 12.5 1.0
O D:LYS106 2.2 11.8 1.0
O D:HOH3755 2.2 13.8 1.0
O B:HOH3729 2.2 12.0 1.0
CG B:ASP353 3.2 11.8 1.0
CG B:ASP349 3.2 12.7 1.0
CD D:GLU107 3.3 12.0 1.0
C D:LYS106 3.4 12.6 1.0
OD1 B:ASP353 3.4 12.2 1.0
OD1 B:ASP349 3.5 14.2 1.0
O B:HOH3038 3.8 15.7 1.0
CG D:GLU107 3.8 13.4 1.0
CB D:LYS106 4.1 11.7 1.0
NZ C:LYS431 4.2 13.3 1.0
N D:GLU107 4.2 12.8 1.0
O D:PHE105 4.2 10.4 1.0
CA D:GLU107 4.3 10.1 1.0
OE1 D:GLU107 4.3 13.8 1.0
CA D:LYS106 4.3 11.9 1.0
CB B:ASP353 4.5 11.4 1.0
O D:HOH3023 4.5 12.1 1.0
CB B:ASP349 4.5 12.2 1.0
O B:ASP349 4.5 11.4 1.0
CD1 C:TYR427 4.6 12.3 1.0
CB D:GLU107 4.7 10.7 1.0
C B:ASP349 4.8 13.1 1.0
O C:HOH1321 4.8 14.1 1.0
CE C:LYS431 4.8 14.6 1.0
CG C:TYR427 5.0 11.7 1.0

Magnesium binding site 3 out of 7 in 1qh1

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Magnesium binding site 3 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:27.5
occ:1.00
 O B:HOH3732 2.4 29.7 1.0
O B:HOH3730 2.4 27.6 1.0
O B:HOH3731 2.5 29.0 1.0
O B:HOH3733 2.5 33.1 1.0
O B:HOH3735 2.6 44.4 1.0
O B:HOH3734 2.7 45.7 1.0
O B:HOH3439 3.9 36.2 1.0
O B:HOH3682 4.0 54.5 1.0
O B:ALA457 4.1 17.9 1.0
O B:HOH3252 4.2 27.8 1.0
O B:HOH3155 4.2 23.0 1.0
O B:GLU459 4.2 17.5 1.0
O B:PRO435 4.3 14.6 1.0
OD1 B:ASP436 4.3 15.9 1.0
O B:HOH3511 4.4 45.0 1.0
O B:HOH3522 4.4 40.2 1.0
OE1 B:GLN434 4.5 21.7 1.0
CA B:ASP436 4.6 14.2 1.0
O B:ASP436 4.9 14.9 1.0

Magnesium binding site 4 out of 7 in 1qh1

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Magnesium binding site 4 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3004

b:25.9
occ:1.00
 OD1 B:ASP407 2.3 20.0 1.0
O B:HOH3737 2.3 23.4 1.0
O B:HOH3739 2.4 28.2 1.0
O B:HOH3736 2.4 20.3 1.0
O B:HOH3738 2.4 25.1 1.0
O B:HOH3740 2.5 28.3 1.0
CG B:ASP407 3.5 23.7 1.0
O B:HOH3231 3.9 25.3 1.0
O B:HOH3148 4.0 22.1 1.0
OD2 B:ASP407 4.1 19.7 1.0
CA B:ASP407 4.2 18.1 1.0
O B:HOH3113 4.2 20.3 1.0
O B:GLY412 4.2 15.4 1.0
O B:HOH3194 4.3 24.7 1.0
CB B:ASP407 4.3 15.4 1.0
O B:HOH3274 4.5 30.2 1.0
N B:ASP407 4.6 15.4 1.0
O B:ARG413 4.7 21.8 1.0
CA B:ARG413 4.9 15.3 1.0

Magnesium binding site 5 out of 7 in 1qh1

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Magnesium binding site 5 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3005

b:19.9
occ:1.00
 O C:HOH3027 2.3 18.9 1.0
O D:HOH3757 2.3 24.4 1.0
O D:HOH3758 2.3 22.5 1.0
O C:HOH3028 2.4 20.9 1.0
O C:HOH3029 2.4 23.9 1.0
O D:HOH3756 2.4 27.0 1.0
OD2 C:ASP106 4.0 20.8 1.0
O C:THR100 4.1 18.0 1.0
OE1 D:GLU30 4.2 21.1 1.0
CA C:GLY101 4.2 15.6 1.0
O D:HOH3671 4.2 46.9 1.0
O B:HOH3303 4.2 29.5 1.0
O D:HOH3014 4.3 46.4 1.0
O D:HOH3583 4.4 42.9 1.0
OG1 C:THR100 4.4 21.0 1.0
O D:HOH3191 4.4 22.8 1.0
O C:HOH1364 4.5 18.0 1.0
O D:HOH3627 4.5 45.3 1.0
NZ C:LYS75 4.5 16.0 1.0
O D:HOH3694 4.6 49.5 1.0
C C:THR100 4.6 16.7 1.0
N C:GLY101 4.6 16.0 1.0
O C:HOH1508 4.7 28.7 1.0
CG D:ARG27 4.9 26.0 1.0
CG C:ASP106 4.9 23.8 1.0
O D:HOH3473 5.0 35.7 1.0
OD1 C:ASP106 5.0 18.1 1.0

Magnesium binding site 6 out of 7 in 1qh1

Go back to Magnesium Binding Sites List in 1qh1
Magnesium binding site 6 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3006

b:12.3
occ:1.00
 O B:HOH3741 2.2 12.2 1.0
OE2 B:GLU107 2.2 13.1 1.0
OD2 D:ASP349 2.2 12.6 1.0
O D:HOH3759 2.2 12.7 1.0
OD2 D:ASP353 2.2 13.8 1.0
O B:LYS106 2.2 12.7 1.0
CG D:ASP349 3.2 14.2 1.0
CG D:ASP353 3.2 15.3 1.0
CD B:GLU107 3.3 14.2 1.0
C B:LYS106 3.4 12.3 1.0
OD1 D:ASP353 3.4 12.4 1.0
OD1 D:ASP349 3.4 13.2 1.0
CG B:GLU107 3.8 11.8 1.0
O D:HOH3041 3.9 14.1 1.0
CB B:LYS106 4.1 10.7 1.0
CA B:GLU107 4.1 10.6 1.0
N B:GLU107 4.2 11.0 1.0
NZ A:LYS431 4.2 13.3 1.0
CA B:LYS106 4.3 11.3 1.0
OE1 B:GLU107 4.3 15.0 1.0
O B:PHE105 4.3 11.1 1.0
CB D:ASP353 4.5 12.7 1.0
CB D:ASP349 4.5 11.9 1.0
O D:ASP349 4.5 11.3 1.0
O B:HOH3023 4.6 13.0 1.0
CD1 A:TYR427 4.6 11.1 1.0
CB B:GLU107 4.6 11.1 1.0
O D:HOH3049 4.7 14.3 1.0
C D:ASP349 4.8 11.4 1.0
CE A:LYS431 4.9 15.4 1.0
CG A:TYR427 5.0 12.1 1.0

Magnesium binding site 7 out of 7 in 1qh1

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Magnesium binding site 7 out of 7 in the Nitrogenase Mofe Protein From Klebsiella Pneumoniae, Phenosafranin Oxidized 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, Phenosafranin Oxidized State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3007

b:29.5
occ:1.00
 O D:HOH3760 2.5 26.9 1.0
O D:HOH3762 2.5 31.0 1.0
O D:HOH3761 2.5 33.2 1.0
O D:HOH3763 2.6 39.4 1.0
O D:HOH3765 2.6 44.5 1.0
O D:HOH3764 2.6 37.0 1.0
O D:HOH3468 3.9 37.4 1.0
O D:HOH3204 4.1 24.0 1.0
O D:ALA457 4.1 16.7 1.0
O D:HOH3422 4.1 32.7 1.0
O D:PRO435 4.2 14.7 1.0
O D:GLU459 4.2 16.9 1.0
CG D:GLN434 4.3 33.0 1.0
OD1 D:ASP436 4.3 15.7 1.0
OE1 D:GLN434 4.5 21.9 1.0
O D:HOH3697 4.6 36.3 1.0
CA D:ASP436 4.6 11.2 1.0
CD D:GLN434 4.9 36.2 1.0
O D:ASP436 4.9 15.2 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 11:50:47 2024

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