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Ruthenium in PDB 4j8v: X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II)

Protein crystallography data

The structure of X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II), PDB code: 4j8v was solved by Z.Adhireksan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.07 / 2.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.800, 109.810, 182.380, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 27.3

Other elements in 4j8v:

The structure of X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II) (pdb code 4j8v). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 2 binding sites of Ruthenium where determined in the X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II), PDB code: 4j8v:
Jump to Ruthenium binding site number: 1; 2;

Ruthenium binding site 1 out of 2 in 4j8v

Go back to Ruthenium Binding Sites List in 4j8v
Ruthenium binding site 1 out of 2 in the X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ru1102

b:0.9
occ:1.00
RU1 D:RU71102 0.0 0.9 1.0
C6 D:RU71102 2.2 0.3 1.0
C2 D:RU71102 2.2 0.2 1.0
C5 D:RU71102 2.2 0.1 1.0
NE2 D:HIS79 2.2 66.4 1.0
C1 D:RU71102 2.2 0.2 1.0
C3 D:RU71102 2.2 0.3 1.0
C4 D:RU71102 2.2 0.1 1.0
CD2 D:HIS79 3.0 65.0 1.0
CE1 D:HIS79 3.2 66.1 1.0
C7 D:RU71102 3.4 1.0 1.0
C8 D:RU71102 3.4 0.9 1.0
C9 D:RU71102 4.1 0.7 1.0
CG D:HIS79 4.2 62.9 1.0
ND1 D:HIS79 4.3 65.4 1.0
C10 D:RU71102 4.6 1.0 1.0

Ruthenium binding site 2 out of 2 in 4j8v

Go back to Ruthenium Binding Sites List in 4j8v
Ruthenium binding site 2 out of 2 in the X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II)


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Structure of NCP145 with Bound Chlorido(Eta-6-P-Cymene)(N- Phenyl-2-Pyridinecarbothioamide)Ruthenium(II) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ru203

b:0.5
occ:1.00
RU1 H:RU7203 0.0 0.5 1.0
NE2 H:HIS79 2.0 65.9 1.0
C2 H:RU7203 2.2 0.2 1.0
C6 H:RU7203 2.2 0.2 1.0
C5 H:RU7203 2.2 0.1 1.0
C1 H:RU7203 2.2 0.2 1.0
C3 H:RU7203 2.2 0.9 1.0
C4 H:RU7203 2.2 0.9 1.0
CE1 H:HIS79 2.8 64.3 1.0
CD2 H:HIS79 3.1 63.5 1.0
C7 H:RU7203 3.4 0.0 1.0
C8 H:RU7203 3.4 0.8 1.0
NZ C:LYS36 3.9 67.4 1.0
ND1 H:HIS79 4.0 62.3 1.0
C9 H:RU7203 4.0 0.9 1.0
CG H:HIS79 4.2 60.4 1.0
C10 H:RU7203 4.6 1.0 1.0

Reference:

S.M.Meier, M.Hanif, Z.Adhireksan, V.Pichler, M.Novak, E.Jirkovsky, M.A.Jakupec, V.B.Arion, C.A.Davey, B.K.Keppler, C.G.Hartinger. Novel Metal(II) Arene 2-Pyridinecarbothioamides: A Rationale to Orally Active Organometallic Anticancer Agents Chem Sci V. 4 1837 2013.
ISSN: ISSN 2041-6520
DOI: 10.1039/C3SC22294B
Page generated: Wed Dec 16 02:08:14 2020

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