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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

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