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Nickel 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:

Sodium (Na) 1 atom

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Thebaine 6-O-Demethylase (T6ODM) From Papaver Somniferum in Complex with 2-Oxoglutarate, PDB code: 5o9w:

Nickel binding site 1 out of 1 in 5o9w

Go back to Nickel Binding Sites List in 5o9w
Nickel 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 Nickel with other atoms in the Ni 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:Ni401

b:14.6
occ:1.00
 O1 A:AKG402 2.1 15.7 1.0
O A:HOH526 2.1 14.6 1.0
NE2 A:HIS295 2.1 13.7 1.0
NE2 A:HIS238 2.1 17.3 1.0
OD1 A:ASP240 2.2 12.8 1.0
O5 A:AKG402 2.2 15.0 1.0
C1 A:AKG402 2.8 16.4 1.0
C2 A:AKG402 2.9 15.6 1.0
CE1 A:HIS238 3.0 18.5 1.0
CD2 A:HIS295 3.0 13.3 1.0
CG A:ASP240 3.1 13.5 1.0
CE1 A:HIS295 3.1 13.6 1.0
CD2 A:HIS238 3.2 16.8 1.0
OD2 A:ASP240 3.3 12.5 1.0
O2 A:AKG402 4.0 15.3 1.0
ND1 A:HIS238 4.2 17.8 1.0
O A:HOH817 4.2 26.2 1.0
CG A:HIS295 4.2 13.2 1.0
ND1 A:HIS295 4.2 13.5 1.0
CG A:HIS238 4.3 17.5 1.0
C3 A:AKG402 4.3 15.6 1.0
O A:HOH702 4.3 34.1 1.0
CB A:ASP240 4.5 13.8 1.0
CD2 A:LEU235 4.7 19.3 1.0
CE1 A:PHE311 4.8 15.5 1.0
C4 A:AKG402 4.9 15.3 1.0
N A:ASP240 4.9 14.2 1.0
CA A:ASP240 4.9 14.2 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: Thu Oct 10 06:42:38 2024

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