Atomistry » Sodium » PDB 5o8n-5opd » 5o9w
Atomistry »
  Sodium »
    PDB 5o8n-5opd »
      5o9w »

Sodium in PDB 5o9w: Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate

Enzymatic activity of Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate

All present enzymatic activity of Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate:
1.14.11.31;

Protein crystallography data

The structure of Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate, PDB code: 5o9w was solved by A.Kluza, E.Niedzialkowska, K.Kurpiewska, P.J.Porebski, T.Borowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.43 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.044, 87.424, 94.863, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 21.4

Other elements in 5o9w:

The structure of Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate (pdb code 5o9w). 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 Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate, PDB code: 5o9w:

Sodium binding site 1 out of 1 in 5o9w

Go back to Sodium Binding Sites List in 5o9w
Sodium binding site 1 out of 1 in the Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na423

b:29.1
occ:1.00
 O A:HOH818 2.4 35.1 1.0
O A:HOH813 2.4 41.6 1.0
O A:SER324 2.4 20.4 1.0
O A:ILE327 2.4 19.6 1.0
O A:HOH802 2.4 37.1 1.0
C A:SER324 3.4 19.5 1.0
C A:ILE327 3.5 17.9 1.0
CB A:ILE327 3.9 17.1 1.0
CA A:SER325 4.1 19.6 1.0
CA A:ILE327 4.1 16.9 1.0
N A:ILE327 4.1 16.9 1.0
O A:HOH832 4.1 45.7 1.0
N A:SER325 4.2 19.7 1.0
CA A:SER324 4.3 19.0 1.0
C A:SER325 4.4 17.9 1.0
O A:HOH532 4.4 40.4 1.0
CG2 A:ILE327 4.6 17.9 1.0
CB A:SER324 4.6 20.4 1.0
N A:THR328 4.6 17.3 1.0
O A:HOH559 4.7 33.9 1.0
O A:SER325 4.7 16.7 1.0
N A:LEU326 5.0 16.5 1.0
CA A:THR328 5.0 18.0 1.0
CG2 A:THR328 5.0 19.5 1.0

Reference:

A.Kluza, E.Niedzialkowska, K.Kurpiewska, Z.Wojdyla, M.Quesne, E.Kot, P.J.Porebski, T.Borowski. Crystal Structure of Thebaine 6-O-Demethylase From the Morphine Biosynthesis Pathway. J. Struct. Biol. V. 202 229 2018.
ISSN: ESSN 1095-8657
PubMed: 29408320
DOI: 10.1016/J.JSB.2018.01.007
Page generated: Mon Oct 7 23:09:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy