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Platinum in PDB 6xcl: Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.

Protein crystallography data

The structure of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex., PDB code: 6xcl was solved by C.E.Miron, L.M.Van Staalduinen, Z.Jia, A.Petitjean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.60 / 2.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 64.030, 64.030, 42.230, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 24.3

Other elements in 6xcl:

The structure of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. also contains other interesting chemical elements:

Potassium (K) 5 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. (pdb code 6xcl). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex., PDB code: 6xcl:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in 6xcl

Go back to Platinum Binding Sites List in 6xcl
Platinum binding site 1 out of 3 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt101

b:57.7
occ:1.00
PT A:V4A101 0.0 57.7 1.0
N3 A:V4A101 1.6 24.1 1.0
NAJ A:V4A101 1.6 25.3 1.0
NBD A:V4A101 2.0 25.2 1.0
CAF A:V4A101 2.3 28.1 1.0
N4 A:V4A101 2.4 25.6 1.0
C6 A:V4A101 2.5 28.9 1.0
CAE A:V4A101 2.5 31.6 1.0
N2 A:V4A101 2.6 31.6 1.0
NAI A:V4A101 2.8 36.5 1.0
C5 A:V4A101 2.9 31.4 1.0
CAA A:V4A101 3.2 34.3 1.0
NAG A:V4A101 3.5 38.2 1.0
C1 A:V4A101 3.6 35.5 1.0
N1 A:V4A101 3.6 43.0 1.0
C7 A:V4A101 3.7 41.9 1.0
CAH A:V4A101 3.8 42.9 1.0
O6 A:DG22 3.8 33.9 1.0
CAD A:V4A101 3.9 40.5 1.0
O6 A:DG16 3.9 33.2 1.0
O6 A:DG4 4.1 25.8 1.0
O6 A:DG10 4.2 28.0 1.0
C4 A:V4A101 4.2 35.6 1.0
C6 A:DG22 4.3 33.8 1.0
CAB A:V4A101 4.4 40.4 1.0
N1 A:DG22 4.5 36.4 1.0
C6 A:DG16 4.5 32.8 1.0
K A:K105 4.5 35.6 1.0
N1 A:DG16 4.6 28.3 1.0
C6 A:DG10 4.6 32.7 1.0
CAC A:V4A101 4.7 41.6 1.0
C6 A:DG4 4.7 28.2 1.0
N1 A:DG10 4.8 34.6 1.0
CAK A:V4A101 4.8 46.0 1.0
C2 A:V4A101 4.8 34.6 1.0
N1 A:DG4 4.8 26.6 1.0
C8 A:V4A101 4.9 45.5 1.0

Platinum binding site 2 out of 3 in 6xcl

Go back to Platinum Binding Sites List in 6xcl
Platinum binding site 2 out of 3 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt103

b:44.1
occ:1.00
PT A:V4A103 0.0 44.1 1.0
N3 A:V4A103 1.5 23.6 1.0
NAJ A:V4A103 1.7 33.8 1.0
NBD A:V4A103 1.9 20.8 1.0
CAF A:V4A103 2.3 27.2 1.0
N2 A:V4A103 2.3 26.1 1.0
CAE A:V4A103 2.4 19.6 1.0
C6 A:V4A103 2.6 24.1 1.0
N4 A:V4A103 2.8 29.1 1.0
NAI A:V4A103 2.9 32.0 1.0
CAA A:V4A103 3.1 27.3 1.0
C5 A:V4A103 3.2 30.0 1.0
C7 A:V4A103 3.5 27.7 1.0
NAG A:V4A103 3.6 33.7 1.0
N1 A:V4A103 3.7 32.5 1.0
O6 B:DG14 3.8 33.1 1.0
O6 A:DG14 3.8 32.0 1.0
CAD A:V4A103 3.8 29.9 1.0
CAH A:V4A103 3.8 32.6 1.0
O6 A:DG8 3.9 27.1 1.0
O6 B:DG8 3.9 27.5 1.0
C1 A:V4A103 4.0 31.2 1.0
O6 B:DG20 4.1 30.2 1.0
O6 A:DG20 4.1 31.1 1.0
O6 A:DG2 4.2 31.4 1.0
O6 B:DG2 4.2 35.5 1.0
CAB A:V4A103 4.3 29.8 1.0
C6 B:DG14 4.4 29.6 1.0
N1 A:DG8 4.4 25.5 1.0
C6 A:DG14 4.4 28.5 1.0
C6 A:DG8 4.4 27.2 1.0
C6 B:DG8 4.5 26.5 1.0
N1 B:DG8 4.5 24.8 1.0
N1 B:DG14 4.6 29.3 1.0
CAC A:V4A103 4.6 32.0 1.0
K A:K104 4.6 38.5 1.0
C4 A:V4A103 4.6 30.0 1.0
N1 A:DG14 4.6 29.1 1.0
K B:K504 4.7 39.3 1.0
CAK A:V4A103 4.8 33.7 1.0
C6 B:DG20 4.8 31.5 1.0
C11 A:V4A103 4.8 28.4 1.0
C6 A:DG20 4.8 28.9 1.0
C6 B:DG2 4.9 33.4 1.0
C6 A:DG2 4.9 30.8 1.0
N1 B:DG2 5.0 32.9 1.0

Platinum binding site 3 out of 3 in 6xcl

Go back to Platinum Binding Sites List in 6xcl
Platinum binding site 3 out of 3 in the Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex.


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of Human Telomeric Dna G-Quadruplex in Complex with A Novel Platinum(II) Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt503

b:58.7
occ:1.00
PT B:V4A503 0.0 58.7 1.0
N3 B:V4A503 1.6 28.6 1.0
NAJ B:V4A503 1.6 25.4 1.0
N4 B:V4A503 2.0 27.1 1.0
C6 B:V4A503 2.2 29.3 1.0
C5 B:V4A503 2.4 33.2 1.0
NBD B:V4A503 2.5 30.2 1.0
CAF B:V4A503 2.5 25.6 1.0
NAI B:V4A503 2.6 32.1 1.0
N2 B:V4A503 2.8 36.9 1.0
CAE B:V4A503 2.9 33.8 1.0
C1 B:V4A503 3.2 33.0 1.0
N1 B:V4A503 3.5 41.4 1.0
CAA B:V4A503 3.6 39.9 1.0
NAG B:V4A503 3.7 39.6 1.0
CAH B:V4A503 3.7 40.8 1.0
C7 B:V4A503 3.7 46.7 1.0
C4 B:V4A503 3.8 42.2 1.0
O6 B:DG22 3.9 35.0 1.0
O6 B:DG16 4.0 34.0 1.0
O6 B:DG4 4.1 27.8 1.0
O6 B:DG10 4.2 25.3 1.0
CAD B:V4A503 4.3 39.0 1.0
K B:K502 4.3 37.4 1.0
C2 B:V4A503 4.3 39.4 1.0
C6 B:DG22 4.4 35.3 1.0
C6 B:DG16 4.5 36.4 1.0
N1 B:DG22 4.5 37.1 1.0
N1 B:DG16 4.6 35.5 1.0
C3 B:V4A503 4.6 42.3 1.0
C6 B:DG4 4.7 28.9 1.0
C6 B:DG10 4.7 29.7 1.0
C8 B:V4A503 4.7 44.3 1.0
N1 B:DG10 4.8 33.1 1.0
N1 B:DG4 4.8 26.0 1.0
CAB B:V4A503 4.8 37.3 1.0

Reference:

C.E.Miron, L.Van Staalduinen, A.M.M.Rangaswamy, M.Chen, Y.Liang, Z.Jia, J.L.Mergny, A.Petitjean. Going Platinum to the Tune of A Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 33090592
DOI: 10.1002/ANIE.202012520
Page generated: Wed Dec 16 02:05:41 2020

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