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Magnesium in PDB 1h1l: Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant

Enzymatic activity of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant

All present enzymatic activity of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant, PDB code: 1h1l was solved by S.M.Mayer, C.A.Gormal, B.E.Smith, D.M.Lawson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 204.060, 75.060, 164.260, 90.00, 123.95, 90.00
R / Rfree (%) 17.6 / 23.6

Other elements in 1h1l:

The structure of Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant 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, Nifv Mutant (pdb code 1h1l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant, PDB code: 1h1l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1h1l

Go back to Magnesium Binding Sites List in 1h1l
Magnesium binding site 1 out of 4 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant


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, Nifv Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:28.9
occ:1.00
 O A:HOH2070 2.1 23.9 1.0
O B:HOH2041 2.2 29.4 1.0
O B:HOH2045 2.3 36.9 1.0
O A:HOH2072 2.3 22.2 1.0
O A:HOH2076 2.3 27.2 1.0
O D:HOH2460 4.1 31.0 1.0
OD2 A:ASP106 4.1 25.4 1.0
O B:HOH2049 4.1 36.0 1.0
CA A:GLY101 4.1 21.3 1.0
O A:THR100 4.2 23.6 1.0
OG1 A:THR100 4.2 23.8 1.0
O B:HOH2037 4.3 27.9 1.0
OE1 B:GLU30 4.3 29.6 1.0
C A:THR100 4.5 21.2 1.0
O A:HOH2077 4.6 28.1 1.0
N A:GLY101 4.6 20.3 1.0
NE B:ARG27 4.6 26.1 1.0
O B:HOH2044 4.7 43.7 1.0
O B:HOH2021 4.7 27.4 1.0
NZ A:LYS75 4.7 17.6 1.0
CD B:ARG27 4.7 26.1 1.0
CG B:ARG27 4.8 31.7 1.0

Magnesium binding site 2 out of 4 in 1h1l

Go back to Magnesium Binding Sites List in 1h1l
Magnesium binding site 2 out of 4 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant


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, Nifv Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:37.3
occ:1.00
 O D:HOH2015 2.2 32.4 1.0
O C:HOH2076 2.2 21.6 1.0
O C:HOH2082 2.2 29.3 1.0
O D:HOH2014 2.2 37.2 1.0
O C:THR100 4.0 22.1 1.0
O B:HOH2465 4.0 37.5 1.0
CA C:GLY101 4.0 21.0 1.0
OD2 C:ASP106 4.2 27.9 1.0
OG1 C:THR100 4.2 27.8 1.0
OE1 D:GLU30 4.3 25.9 1.0
NZ C:LYS75 4.4 16.3 1.0
O D:HOH2027 4.4 28.4 1.0
C C:THR100 4.4 20.5 1.0
O C:HOH2081 4.5 27.1 1.0
N C:GLY101 4.5 20.8 1.0
O D:HOH2029 4.8 39.7 1.0
O D:HOH2016 4.9 35.3 1.0
CG D:ARG27 4.9 39.1 1.0
CG C:ASP106 5.0 32.1 1.0

Magnesium binding site 3 out of 4 in 1h1l

Go back to Magnesium Binding Sites List in 1h1l
Magnesium binding site 3 out of 4 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant


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, Nifv Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1522

b:23.6
occ:1.00
 O B:HOH2323 2.1 23.0 1.0
O D:LYS106 2.1 11.8 1.0
OD2 B:ASP353 2.1 21.0 1.0
OE2 D:GLU107 2.1 22.9 1.0
O D:HOH2100 2.3 17.4 1.0
OD2 B:ASP349 2.3 22.0 1.0
CG B:ASP353 3.1 23.7 1.0
CG B:ASP349 3.2 19.1 1.0
OD1 B:ASP353 3.3 19.0 1.0
CD D:GLU107 3.3 27.3 1.0
C D:LYS106 3.3 15.8 1.0
OD1 B:ASP349 3.4 21.7 1.0
CG D:GLU107 3.8 23.7 1.0
CB D:LYS106 4.0 18.4 1.0
O B:HOH2324 4.1 29.0 1.0
N D:GLU107 4.2 13.4 1.0
NZ C:LYS431 4.2 21.6 1.0
CA D:GLU107 4.3 19.3 1.0
OE1 D:GLU107 4.3 29.2 1.0
O D:PHE105 4.3 14.5 1.0
CA D:LYS106 4.3 16.4 1.0
CB B:ASP353 4.5 15.6 1.0
CD1 C:TYR427 4.5 17.2 1.0
CB B:ASP349 4.6 15.9 1.0
O B:ASP349 4.6 13.2 1.0
CB D:GLU107 4.6 16.5 1.0
O D:HOH2238 4.7 21.3 1.0
O B:HOH2325 4.8 27.0 1.0
O D:HOH2239 4.9 21.4 1.0
CE C:LYS431 4.9 19.9 1.0
C B:ASP349 4.9 14.7 1.0
O D:HOH2426 4.9 32.8 1.0

Magnesium binding site 4 out of 4 in 1h1l

Go back to Magnesium Binding Sites List in 1h1l
Magnesium binding site 4 out of 4 in the Nitrogenase Mo-Fe Protein From Klebsiella Pneumoniae, Nifv Mutant


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, Nifv Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1523

b:21.3
occ:1.00
 O D:HOH2335 2.0 20.2 1.0
OD2 D:ASP353 2.0 19.4 1.0
O B:LYS106 2.2 14.2 1.0
OD2 D:ASP349 2.2 18.3 1.0
OE2 B:GLU107 2.2 20.0 1.0
O B:HOH2121 2.3 19.1 1.0
CG D:ASP353 3.0 28.0 1.0
OD1 D:ASP353 3.1 23.7 1.0
CG D:ASP349 3.2 21.7 1.0
CD B:GLU107 3.3 26.4 1.0
C B:LYS106 3.4 15.8 1.0
OD1 D:ASP349 3.4 21.0 1.0
CG B:GLU107 3.9 25.5 1.0
CB B:LYS106 4.0 16.9 1.0
O D:HOH2333 4.2 30.9 1.0
CA B:GLU107 4.3 19.7 1.0
O B:PHE105 4.3 15.5 1.0
CA B:LYS106 4.3 14.3 1.0
NZ A:LYS431 4.3 24.7 1.0
N B:GLU107 4.3 17.2 1.0
O D:ASP349 4.4 12.6 1.0
CB D:ASP353 4.4 18.1 1.0
OE1 B:GLU107 4.4 31.3 1.0
CD1 A:TYR427 4.4 16.1 1.0
CB D:ASP349 4.5 14.9 1.0
O D:HOH2334 4.6 31.0 1.0
O B:HOH2238 4.6 23.7 1.0
O B:HOH2239 4.6 28.1 1.0
CB B:GLU107 4.7 17.1 1.0
O B:HOH2432 4.8 23.3 1.0
C D:ASP349 4.8 15.4 1.0
CE1 A:TYR427 4.9 15.9 1.0
CE A:LYS431 5.0 20.5 1.0

Reference:

S.M.Mayer, C.A.Gormal, B.E.Smith, D.M.Lawson. Crystallographic Analysis of the Mofe Protein of Nitrogenase From A Nifv Mutant of Klebsiella Pneumoniae Identifies Citrate As A Ligand to the Molybdenum of Iron Molybdenum Cofactor (Femoco). J.Biol.Chem. V. 277 35263 2002.
ISSN: ISSN 0021-9258
PubMed: 12133839
DOI: 10.1074/JBC.M205888200
Page generated: Tue Aug 13 03:52:39 2024

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