Atomistry » Platinum » PDB 5yky-7bpr » 6e2b
Atomistry »
  Platinum »
    PDB 5yky-7bpr »
      6e2b »

Platinum in PDB 6e2b: Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3)

Protein crystallography data

The structure of Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3), PDB code: 6e2b was solved by V.A.Zhemkov, M.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.26 / 1.45
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 140.381, 140.381, 62.447, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.7

Platinum Binding Sites:

The binding sites of Platinum atom in the Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3) (pdb code 6e2b). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3), PDB code: 6e2b:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 6e2b

Go back to Platinum Binding Sites List in 6e2b
Platinum binding site 1 out of 3 in the Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt105

b:13.3
occ:1.00
PT20 A:PT7105 0.0 13.3 1.0
ND1 A:HIS68 2.1 12.1 1.0
C3 A:PT7105 2.2 15.3 1.0
N19 A:PT7105 2.2 14.1 1.0
P1 A:PT7105 2.3 14.6 1.0
CE1 A:HIS68 3.0 12.6 1.0
C2 A:PT7105 3.0 14.7 1.0
C14 A:PT7105 3.0 14.4 1.0
C18 A:PT7105 3.2 16.3 1.0
CG A:HIS68 3.2 12.4 1.0
C4 A:PT7105 3.3 13.3 1.0
C25 A:PT7105 3.3 13.3 1.0
C19 A:PT7105 3.4 13.4 1.0
C8 A:PT7105 3.4 13.5 1.0
C20 A:PT7105 3.5 12.8 1.0
C9 A:PT7105 3.5 15.0 1.0
CB A:HIS68 3.7 13.0 1.0
C30 A:PT7105 4.0 13.1 1.0
NE2 A:HIS68 4.2 13.0 1.0
C26 A:PT7105 4.2 13.4 1.0
OE1 P:GLN49 4.3 20.0 1.0
CD2 A:HIS68 4.3 13.4 1.0
C15 A:PT7105 4.3 15.2 1.0
C7 A:PT7105 4.3 14.5 1.0
C17 A:PT7105 4.4 16.1 1.0
CD P:GLN49 4.5 21.9 1.0
CG2 A:ILE44 4.6 15.2 1.0
C5 A:PT7105 4.6 13.9 1.0
CB A:ILE44 4.7 15.8 1.0
C13 A:PT7105 4.7 15.3 1.0
C24 A:PT7105 4.8 14.8 1.0
C10 A:PT7105 4.8 16.1 1.0
C21 A:PT7105 4.8 13.6 1.0
C16 A:PT7105 4.9 15.8 1.0
C6 A:PT7105 4.9 14.4 1.0
NE2 P:GLN49 4.9 22.5 1.0
CG P:GLN49 5.0 20.4 1.0

Platinum binding site 2 out of 3 in 6e2b

Go back to Platinum Binding Sites List in 6e2b
Platinum binding site 2 out of 3 in the Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt103

b:13.7
occ:1.00
PT20 C:PT7103 0.0 13.7 1.0
C3 C:PT7103 2.2 13.8 1.0
ND1 C:HIS68 2.2 15.6 1.0
N19 C:PT7103 2.2 12.7 1.0
P1 C:PT7103 2.3 15.1 1.0
C2 C:PT7103 3.0 13.7 1.0
CE1 C:HIS68 3.0 13.4 1.0
C18 C:PT7103 3.1 14.0 1.0
C14 C:PT7103 3.1 14.2 1.0
C4 C:PT7103 3.3 13.8 1.0
CG C:HIS68 3.3 12.8 1.0
C25 C:PT7103 3.4 13.3 1.0
C19 C:PT7103 3.4 15.1 1.0
C8 C:PT7103 3.4 15.6 1.0
C20 C:PT7103 3.5 16.0 1.0
C9 C:PT7103 3.6 16.1 1.0
CB C:HIS68 3.7 11.9 1.0
C30 C:PT7103 4.0 13.7 1.0
NE2 C:HIS68 4.2 14.2 1.0
C26 C:PT7103 4.3 14.5 1.0
OE1 A:GLN49 4.3 23.4 1.0
C7 C:PT7103 4.3 12.6 1.0
C15 C:PT7103 4.3 13.6 1.0
C17 C:PT7103 4.4 14.9 1.0
CD2 C:HIS68 4.4 13.5 1.0
CG2 C:ILE44 4.5 15.0 0.4
CG2 C:ILE44 4.5 16.4 0.6
C5 C:PT7103 4.5 13.7 1.0
CD A:GLN49 4.6 22.8 1.0
C13 C:PT7103 4.7 18.5 1.0
C24 C:PT7103 4.8 15.7 1.0
CB C:ILE44 4.8 15.2 0.4
C21 C:PT7103 4.8 16.2 1.0
C16 C:PT7103 4.9 14.9 1.0
C10 C:PT7103 4.9 16.9 1.0
C6 C:PT7103 4.9 14.3 1.0
CG A:GLN49 5.0 22.2 1.0
O A:HOH230 5.0 18.6 1.0
CB C:ILE44 5.0 16.7 0.6

Platinum binding site 3 out of 3 in 6e2b

Go back to Platinum Binding Sites List in 6e2b
Platinum binding site 3 out of 3 in the Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3)


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Ubiquitin in Complex with Pt(2-Phenilpyridine)(PPH3) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Pt104

b:13.1
occ:1.00
PT20 P:PT7104 0.0 13.1 1.0
ND1 P:HIS68 2.1 11.7 1.0
C3 P:PT7104 2.2 12.4 1.0
N19 P:PT7104 2.2 15.1 1.0
P1 P:PT7104 2.3 14.6 1.0
C2 P:PT7104 3.0 13.9 1.0
C14 P:PT7104 3.0 13.8 1.0
CE1 P:HIS68 3.0 14.8 1.0
C18 P:PT7104 3.1 15.4 1.0
CG P:HIS68 3.2 11.6 1.0
C4 P:PT7104 3.2 13.9 1.0
C25 P:PT7104 3.3 13.9 1.0
C8 P:PT7104 3.4 14.3 1.0
C19 P:PT7104 3.4 14.9 1.0
C9 P:PT7104 3.6 13.4 1.0
C20 P:PT7104 3.6 19.1 1.0
CB P:HIS68 3.7 11.3 1.0
C30 P:PT7104 4.0 14.3 1.0
OE1 C:GLN49 4.1 27.0 1.0
NE2 P:HIS68 4.2 14.1 1.0
C26 P:PT7104 4.3 14.2 1.0
C7 P:PT7104 4.3 12.8 1.0
CD2 P:HIS68 4.3 14.1 1.0
C15 P:PT7104 4.3 14.1 1.0
C17 P:PT7104 4.4 14.5 1.0
C5 P:PT7104 4.4 13.9 1.0
CD C:GLN49 4.4 22.8 1.0
CG2 P:ILE44 4.5 14.0 1.0
C13 P:PT7104 4.6 14.1 1.0
CB P:ILE44 4.7 15.5 1.0
C24 P:PT7104 4.7 16.5 1.0
C16 P:PT7104 4.9 16.7 1.0
C10 P:PT7104 4.9 13.9 1.0
C6 P:PT7104 4.9 13.4 1.0
NE2 C:GLN49 4.9 25.2 1.0
CG C:GLN49 4.9 19.3 1.0
C21 P:PT7104 4.9 20.6 1.0

Reference:

A.I.Solomatina, P.S.Chelushkin, T.O.Abakumova, V.A.Zhemkov, M.Kim, I.Bezprozvanny, V.V.Gurzhiy, A.S.Melnikov, Y.A.Anufrikov, I.O.Koshevoy, S.H.Su, P.T.Chou, S.P.Tunik. Reactions of Cyclometalated Platinum(II) [Pt(N∧C)(PR3)Cl] Complexes with Imidazole and Imidazole-Containing Biomolecules: Fine-Tuning of Reactivity and Photophysical Properties Via Ligand Design. Inorg Chem V. 58 204 2019.
ISSN: ISSN 1520-510X
PubMed: 30376305
DOI: 10.1021/ACS.INORGCHEM.8B02204
Page generated: Thu Oct 10 11:41:56 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