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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: Wed Dec 16 02:05:32 2020

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