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Sodium in PDB 4kvk: Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase

Protein crystallography data

The structure of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase, PDB code: 4kvk was solved by G.Zhu, M.Koszelak-Rosenblum, M.G.Malkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 106.27 / 1.98
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 72.460, 128.583, 188.740, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.2

Other elements in 4kvk:

The structure of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 4 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase (pdb code 4kvk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase, PDB code: 4kvk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4kvk

Go back to Sodium Binding Sites List in 4kvk
Sodium binding site 1 out of 2 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na717

b:51.3
occ:1.00
O A:HOH981 2.4 43.0 1.0
O A:HOH980 2.4 62.3 1.0
O A:HOH1117 2.6 49.9 1.0
O A:ASP505 2.7 35.0 1.0
OH3 A:1PE705 3.1 47.0 1.0
OH4 A:1PE705 3.3 46.3 1.0
OH2 A:1PE705 3.3 48.5 1.0
C A:ASP505 3.6 34.6 1.0
O A:HOH1029 3.6 40.9 1.0
C13 A:1PE705 3.9 44.5 1.0
CA A:ASP505 3.9 35.0 1.0
C12 A:1PE705 3.9 49.5 1.0
C23 A:1PE705 3.9 44.6 1.0
C22 A:1PE705 4.1 47.8 1.0
C14 A:1PE705 4.2 45.0 1.0
CB A:ASP505 4.2 35.1 1.0
C24 A:1PE705 4.3 47.5 1.0
N A:LEU506 4.9 34.5 1.0
OD1 A:ASP505 4.9 37.6 1.0
CG A:ASP505 4.9 37.2 1.0

Sodium binding site 2 out of 2 in 4kvk

Go back to Sodium Binding Sites List in 4kvk
Sodium binding site 2 out of 2 in the Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Oryza Sativa Fatty Acid Alpha-Dioxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na718

b:54.1
occ:1.00
O A:HOH1228 2.7 45.0 1.0
O4 A:PG4707 3.0 45.9 1.0
O2 A:PG4707 3.1 51.3 1.0
OG A:SER608 3.1 28.3 0.5
O3 A:PG4707 3.3 48.2 1.0
O1 A:PG4707 3.4 61.7 1.0
O5 A:PG4707 3.4 57.4 1.0
CB A:SER608 3.8 23.9 0.5
C5 A:PG4707 3.8 45.7 1.0
C4 A:PG4707 3.9 50.0 1.0
C1 A:PG4707 3.9 58.1 1.0
C7 A:PG4707 3.9 52.7 1.0
CB A:SER608 4.0 25.0 0.5
C8 A:PG4707 4.0 54.0 1.0
C3 A:PG4707 4.0 49.2 1.0
C6 A:PG4707 4.0 45.3 1.0
C2 A:PG4707 4.1 54.7 1.0
CA A:SER608 4.7 24.9 0.5
CA A:SER608 4.7 24.0 0.5
OG A:SER608 4.7 21.8 0.5

Reference:

G.Zhu, M.Koszelak-Rosenblum, M.G.Malkowski. Crystal Structures of Alpha-Dioxygenase From Oryza Sativa: Insights Into Substrate Binding and Activation By Hydrogen Peroxide. Protein Sci. V. 22 1432 2013.
ISSN: ISSN 0961-8368
PubMed: 23934749
DOI: 10.1002/PRO.2327
Page generated: Tue Dec 15 06:50:43 2020

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