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Calcium in PDB 1m34: Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate

Enzymatic activity of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate

All present enzymatic activity of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate, PDB code: 1m34 was solved by B.Schmid, O.Einsle, H.-J.Chiu, A.Willing, M.Yoshida, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 326.100, 75.800, 312.200, 90.00, 102.60, 90.00
R / Rfree (%) 20 / 23.6

Other elements in 1m34:

The structure of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate also contains other interesting chemical elements:

Fluorine (F) 32 atoms
Molybdenum (Mo) 4 atoms
Magnesium (Mg) 8 atoms
Aluminium (Al) 8 atoms
Iron (Fe) 76 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate (pdb code 1m34). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate, PDB code: 1m34:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1m34

Go back to Calcium Binding Sites List in 1m34
Calcium binding site 1 out of 4 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2299

b:34.3
occ:1.00
 OE2 D:GLU109 2.2 41.3 1.0
OD2 B:ASP357 2.2 28.1 1.0
OD2 B:ASP353 2.3 32.4 1.0
O D:ARG108 2.3 33.6 1.0
O B:HOH2477 2.5 34.3 1.0
OD1 B:ASP353 2.9 34.2 1.0
CG B:ASP353 2.9 33.8 1.0
CG B:ASP357 3.1 29.9 1.0
CD D:GLU109 3.2 41.7 1.0
OD1 B:ASP357 3.3 28.8 1.0
C D:ARG108 3.5 34.5 1.0
CG D:GLU109 3.6 40.8 1.0
CD1 C:PHE429 4.0 30.0 1.0
CA D:GLU109 4.1 36.0 1.0
NZ C:LYS433 4.1 40.4 1.0
N D:GLU109 4.2 34.9 1.0
O D:HOH2461 4.2 48.7 1.0
OE1 D:GLU109 4.3 43.1 1.0
CB B:ASP353 4.4 32.8 1.0
CB D:GLU109 4.4 38.0 1.0
CB B:ASP357 4.5 29.7 1.0
O B:ASP353 4.6 32.8 1.0
CE1 C:PHE429 4.6 29.4 1.0
O D:PHE107 4.6 29.7 1.0
CB D:ARG108 4.6 35.0 1.0
CG C:PHE429 4.6 31.9 1.0
CE C:LYS433 4.6 40.5 1.0
CA D:ARG108 4.7 34.1 1.0
O B:HOH2452 4.8 42.4 1.0
CB C:PHE429 4.9 31.7 1.0
C B:ASP353 4.9 32.8 1.0
O D:HOH2347 4.9 30.8 1.0

Calcium binding site 2 out of 4 in 1m34

Go back to Calcium Binding Sites List in 1m34
Calcium binding site 2 out of 4 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2099

b:61.4
occ:1.00
 OD2 D:ASP357 2.1 35.7 1.0
OE2 B:GLU109 2.1 45.4 1.0
OD2 D:ASP353 2.2 26.3 1.0
O B:ARG108 2.4 34.0 1.0
O D:HOH2469 2.5 30.9 1.0
CG D:ASP353 3.0 25.7 1.0
CG D:ASP357 3.1 34.6 1.0
OD1 D:ASP353 3.1 25.5 1.0
CD B:GLU109 3.3 44.4 1.0
OD1 D:ASP357 3.4 38.9 1.0
C B:ARG108 3.6 31.8 1.0
CG B:GLU109 3.9 41.4 1.0
NZ A:LYS433 4.1 30.8 1.0
CA B:GLU109 4.2 32.4 1.0
OE1 B:GLU109 4.3 46.2 1.0
O D:HOH2442 4.3 44.0 1.0
N B:GLU109 4.3 32.7 1.0
CD1 A:PHE429 4.3 28.1 1.0
O B:PHE107 4.4 25.5 1.0
CB D:ASP357 4.4 33.6 1.0
CB D:ASP353 4.5 20.5 1.0
CB B:ARG108 4.5 30.7 1.0
O D:ASP353 4.6 21.6 1.0
CB B:GLU109 4.6 35.2 1.0
CA B:ARG108 4.6 31.1 1.0
CE A:LYS433 4.7 32.4 1.0
CE1 A:PHE429 4.7 29.2 1.0
C D:ASP353 4.8 21.9 1.0
O B:HOH2405 4.9 37.3 1.0
CG A:PHE429 5.0 27.4 1.0

Calcium binding site 3 out of 4 in 1m34

Go back to Calcium Binding Sites List in 1m34
Calcium binding site 3 out of 4 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca4299

b:56.4
occ:1.00
 OD2 J:ASP357 2.0 37.2 1.0
OE2 L:GLU109 2.1 44.5 1.0
O L:ARG108 2.2 27.4 1.0
OD2 J:ASP353 2.3 33.9 1.0
O J:HOH4506 2.6 35.1 1.0
CG J:ASP357 3.1 36.2 1.0
CD L:GLU109 3.1 42.2 1.0
CG J:ASP353 3.2 31.6 1.0
C L:ARG108 3.4 29.8 1.0
OD1 J:ASP353 3.4 34.6 1.0
OD1 J:ASP357 3.4 38.9 1.0
CG L:GLU109 3.6 40.0 1.0
O L:PHE107 4.1 24.8 1.0
N L:GLU109 4.2 30.4 1.0
CA L:GLU109 4.2 31.9 1.0
CB L:ARG108 4.2 33.1 1.0
OE1 L:GLU109 4.2 43.1 1.0
CD1 K:PHE429 4.2 28.1 1.0
CA L:ARG108 4.4 30.1 1.0
CB J:ASP357 4.4 33.8 1.0
O J:HOH4478 4.4 44.9 1.0
CB L:GLU109 4.5 34.1 1.0
CE1 K:PHE429 4.6 29.9 1.0
NZ K:LYS433 4.6 29.1 1.0
O J:ASP353 4.6 23.8 1.0
CB J:ASP353 4.6 28.9 1.0
O L:HOH4383 4.7 35.9 1.0
O L:HOH4382 4.8 35.8 1.0
C J:ASP353 4.9 23.6 1.0
CG K:PHE429 5.0 29.1 1.0

Calcium binding site 4 out of 4 in 1m34

Go back to Calcium Binding Sites List in 1m34
Calcium binding site 4 out of 4 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca4099

b:53.2
occ:1.00
 OE2 J:GLU109 2.1 37.9 1.0
OD2 L:ASP357 2.1 31.8 1.0
O J:ARG108 2.2 27.3 1.0
OD2 L:ASP353 2.4 32.7 1.0
O J:HOH4505 2.5 36.3 1.0
CG L:ASP357 3.1 29.1 1.0
CG L:ASP353 3.2 31.1 1.0
CD J:GLU109 3.2 39.6 1.0
OD1 L:ASP353 3.3 31.6 1.0
C J:ARG108 3.4 27.5 1.0
OD1 L:ASP357 3.4 32.4 1.0
CG J:GLU109 3.7 37.2 1.0
CA J:GLU109 4.1 29.7 1.0
N J:GLU109 4.1 28.1 1.0
CD1 I:PHE429 4.2 27.0 1.0
OE1 J:GLU109 4.2 39.1 1.0
CB J:ARG108 4.3 28.1 1.0
O J:PHE107 4.4 25.6 1.0
CB L:ASP357 4.5 26.1 1.0
CA J:ARG108 4.5 27.1 1.0
CB J:GLU109 4.5 31.9 1.0
NZ I:LYS433 4.5 28.6 1.0
O L:ASP353 4.6 26.1 1.0
CB L:ASP353 4.6 29.1 1.0
CE1 I:PHE429 4.7 28.4 1.0
CG I:PHE429 4.8 28.0 1.0
CE I:LYS433 4.8 33.5 1.0
C L:ASP353 5.0 27.9 1.0

Reference:

B.Schmid, O.Einsle, H.-J.Chiu, A.Willing, M.Yoshida, J.B.Howard, D.C.Rees. Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the Adp-ALF4 Stabilized Structure Biochemistry V. 41 15557 2002.
ISSN: ISSN 0006-2960
PubMed: 12501184
DOI: 10.1021/BI026642B
Page generated: Thu Jul 11 12:14:30 2024

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