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Calcium in PDB 4xpi: Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer

Enzymatic activity of Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer

All present enzymatic activity of Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer:
1.18.6.1;

Protein crystallography data

The structure of Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer, PDB code: 4xpi was solved by K.Danyal, A.J.Rasmusen, S.M.Keable, S.Shaw, O.Zadvornyy, S.Duval, D.R.Dean, S.Raugei, J.W.Peters, L.C.Seefeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.804, 130.830, 108.110, 90.00, 111.14, 90.00
R / Rfree (%) 21.3 / 26.4

Other elements in 4xpi:

The structure of Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer (pdb code 4xpi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer, PDB code: 4xpi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4xpi

Go back to Calcium Binding Sites List in 4xpi
Calcium binding site 1 out of 2 in the Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:41.1
occ:1.00
 O D:ARG108 2.0 30.3 1.0
O D:HOH730 2.1 36.9 1.0
OD2 B:ASP357 2.2 38.8 1.0
O B:HOH728 2.3 40.0 1.0
OE2 D:GLU109 2.3 30.0 0.6
OD2 B:ASP353 2.6 43.1 1.0
CG B:ASP357 3.0 34.8 1.0
OD1 B:ASP357 3.1 36.6 1.0
C D:ARG108 3.2 32.2 1.0
CG B:ASP353 3.3 34.7 1.0
OD1 B:ASP353 3.3 32.7 1.0
CD D:GLU109 3.4 31.2 0.5
CG D:GLU109 3.9 30.3 0.7
CB D:ARG108 4.0 33.1 1.0
N D:GLU109 4.2 30.3 1.0
CD1 C:PHE429 4.2 33.7 1.0
CA D:ARG108 4.2 30.0 1.0
O D:PHE107 4.2 31.2 1.0
CA D:GLU109 4.3 30.9 0.9
OE1 D:GLU109 4.4 29.7 0.6
O B:ASP353 4.5 29.5 1.0
CB B:ASP357 4.5 34.2 1.0
NZ C:LYS433 4.6 38.2 1.0
CE1 C:PHE429 4.6 29.3 1.0
CB D:GLU109 4.7 30.4 0.8
CB B:ASP353 4.7 32.4 1.0
O B:HOH809 4.8 36.4 1.0
O D:HOH813 4.8 27.7 1.0
CG C:PHE429 4.8 32.1 1.0
CE C:LYS433 4.9 37.9 1.0
O D:HOH899 4.9 24.0 1.0
C B:ASP353 5.0 28.9 1.0

Calcium binding site 2 out of 2 in 4xpi

Go back to Calcium Binding Sites List in 4xpi
Calcium binding site 2 out of 2 in the Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fe Protein Independent Substrate Reduction By Nitrogenase Variants Altered in Intramolecular Electron Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca609

b:42.6
occ:1.00
 O B:ARG108 2.1 31.5 1.0
OD2 D:ASP357 2.3 40.7 1.0
O D:HOH720 2.3 38.4 1.0
O B:HOH789 2.3 40.8 1.0
OE2 B:GLU109 2.4 29.9 0.8
OD2 D:ASP353 2.5 39.1 1.0
CG D:ASP357 3.0 33.6 1.0
OD1 D:ASP357 3.0 36.0 1.0
CG D:ASP353 3.2 34.6 1.0
OD1 D:ASP353 3.3 32.1 1.0
C B:ARG108 3.4 31.9 1.0
CD B:GLU109 3.4 32.6 0.6
O D:HOH702 3.9 34.7 1.0
CG B:GLU109 4.0 31.3 0.8
CB B:ARG108 4.0 33.4 1.0
CD1 A:PHE429 4.2 29.2 1.0
N B:GLU109 4.2 29.8 1.0
CA B:GLU109 4.3 29.8 1.0
CA B:ARG108 4.3 30.6 1.0
O B:PHE107 4.3 30.2 1.0
NZ A:LYS433 4.4 36.4 1.0
O D:ASP353 4.4 30.2 1.0
OE1 B:GLU109 4.4 31.3 0.7
CB D:ASP357 4.5 32.6 1.0
CB D:ASP353 4.6 33.3 1.0
CE1 A:PHE429 4.7 27.6 1.0
CE A:LYS433 4.7 36.3 1.0
CB B:GLU109 4.8 31.7 0.9
O B:HOH814 4.8 32.6 1.0
CG A:PHE429 4.9 29.6 1.0
C D:ASP353 4.9 29.7 1.0
O B:HOH828 5.0 28.3 1.0
O B:HOH878 5.0 29.0 1.0

Reference:

K.Danyal, A.J.Rasmussen, S.M.Keable, B.S.Inglet, S.Shaw, O.A.Zadvornyy, S.Duval, D.R.Dean, S.Raugei, J.W.Peters, L.C.Seefeldt. Fe Protein-Independent Substrate Reduction By Nitrogenase Mofe Protein Variants. Biochemistry V. 54 2456 2015.
ISSN: ISSN 0006-2960
PubMed: 25831270
DOI: 10.1021/ACS.BIOCHEM.5B00140
Page generated: Wed Jul 9 02:55:36 2025

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