Atomistry » Sodium » PDB 5o8n-5opd » 5ohe
Atomistry »
  Sodium »
    PDB 5o8n-5opd »
      5ohe »

Sodium in PDB 5ohe: Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide

Enzymatic activity of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide

All present enzymatic activity of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide:
2.7.13.3;

Protein crystallography data

The structure of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, PDB code: 5ohe was solved by T.Skalova, P.Kolenko, J.Dohnalek, M.Stranava, M.Martinkova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.82 / 1.85
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.069, 78.069, 441.819, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.1

Other elements in 5ohe:

The structure of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide (pdb code 5ohe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide, PDB code: 5ohe:

Sodium binding site 1 out of 1 in 5ohe

Go back to Sodium Binding Sites List in 5ohe
Sodium binding site 1 out of 1 in the Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Globin Sensor Domain of Afgchk (Feiii Form) in Complex with Cyanide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na203

b:35.6
occ:1.00
 O E:HOH412 2.2 29.6 1.0
O E:LEU58 2.7 20.6 1.0
O E:ARG55 2.7 25.4 1.0
O E:HOH429 2.8 36.5 1.0
C E:ARG55 3.6 27.6 1.0
C E:LEU58 3.8 20.9 1.0
O E:HOH370 4.1 24.0 1.0
CG E:ARG55 4.2 27.4 1.0
CB E:ARG55 4.2 26.2 1.0
CB E:LEU58 4.3 21.4 1.0
N E:THR56 4.3 29.0 1.0
O E:HOH432 4.4 34.8 1.0
CA E:ARG55 4.5 26.6 1.0
CA E:LEU58 4.5 21.0 1.0
CA E:THR56 4.6 28.9 1.0
N E:LEU58 4.6 20.6 1.0
C E:THR56 4.8 27.1 1.0
CD E:ARG55 4.8 28.5 1.0
O E:THR56 4.9 27.2 1.0
N E:VAL59 4.9 20.4 1.0

Reference:

M.Stranava, P.Man, T.Skalova, P.Kolenko, J.Blaha, V.Fojtikova, V.Martinek, J.Dohnalek, A.Lengalova, M.Rosulek, T.Shimizu, M.Martinkova. Coordination and Redox State-Dependent Structural Changes of the Heme-Based Oxygen Sensor Afgchk Associated with Intraprotein Signal Transduction. J. Biol. Chem. V. 292 20921 2017.
ISSN: ESSN 1083-351X
PubMed: 29092908
DOI: 10.1074/JBC.M117.817023
Page generated: Mon Oct 7 23:11:51 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy