Potassium in PDB 8edp: Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7

The structure of Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7, PDB code: 8edp was solved by M.Ye, L.A.Yatsunyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.01 / 2.01
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.583, 40.927, 56.018, 90, 90, 90
R / Rfree (%)	24.3 / 27.8

The structure of Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7 also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Potassium atom in the Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7 (pdb code 8edp). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7, PDB code: 8edp:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:K102 b:51.0 occ:1.00 O6 A:DG12 2.6 55.5 1.0 O6 A:DG16 2.6 50.7 1.0 O6 A:DG24 2.7 60.0 1.0 O6 A:DG4 2.7 49.6 1.0 O6 A:DG23 2.7 55.0 1.0 O6 A:DG15 2.7 44.2 1.0 O6 A:DG3 2.8 51.3 1.0 O6 A:DG11 3.0 58.8 1.0 K A:K103 3.4 51.2 1.0 C6 A:DG15 3.5 57.2 1.0 C6 A:DG23 3.6 55.7 1.0 C6 A:DG12 3.6 64.2 1.0 C6 A:DG3 3.6 57.5 1.0 C6 A:DG16 3.6 58.8 1.0 C6 A:DG24 3.6 60.0 1.0 C6 A:DG4 3.7 59.5 1.0 C6 A:DG11 3.8 54.8 1.0 N1 A:DG15 3.8 53.0 1.0 N1 A:DG3 3.9 54.0 1.0 N1 A:DG16 3.9 59.1 1.0 N1 A:DG23 3.9 57.6 1.0 N1 A:DG24 3.9 58.2 1.0 N1 A:DG12 3.9 61.2 1.0 N1 A:DG4 4.0 61.2 1.0 N1 A:DG11 4.1 58.9 1.0 C1 A:MMP106 4.3 73.2 1.0 C5 A:DG15 4.6 53.4 1.0 C5 A:DG3 4.8 58.9 1.0 C5 A:DG23 4.8 55.4 1.0 C5 A:DG12 4.9 64.8 1.0 C5 A:DG24 4.9 61.2 1.0 C5 A:DG16 4.9 60.5 1.0 C5 A:DG11 5.0 56.5 1.0 C5 A:DG4 5.0 63.6 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:K103 b:51.2 occ:1.00 O6 A:DG15 2.6 44.2 1.0 O6 A:DG3 2.7 51.3 1.0 O6 A:DG23 2.7 55.0 1.0 O6 A:DG11 2.7 58.8 1.0 O6 A:DG14 2.8 50.4 1.0 O6 A:DG22 2.8 51.0 1.0 O6 A:DG10 2.8 50.3 1.0 O6 A:DG2 2.9 46.1 1.0 K A:K102 3.4 51.0 1.0 K A:K104 3.4 47.8 1.0 C6 A:DG15 3.5 57.2 1.0 C6 A:DG23 3.6 55.7 1.0 C6 A:DG14 3.6 56.1 1.0 C6 A:DG22 3.6 54.4 1.0 C6 A:DG10 3.6 54.4 1.0 C6 A:DG3 3.7 57.5 1.0 C6 A:DG11 3.7 54.8 1.0 C6 A:DG2 3.7 56.4 1.0 N1 A:DG23 3.9 57.6 1.0 N1 A:DG15 3.9 53.0 1.0 N1 A:DG14 4.0 55.9 1.0 N1 A:DG11 4.0 58.9 1.0 N1 A:DG2 4.0 54.6 1.0 N1 A:DG22 4.0 53.1 1.0 N1 A:DG3 4.0 54.0 1.0 N1 A:DG10 4.0 53.8 1.0 C5 A:DG14 4.8 55.4 1.0 C5 A:DG15 4.8 53.4 1.0 C5 A:DG23 4.8 55.4 1.0 C5 A:DG10 4.8 57.9 1.0 C5 A:DG22 4.8 57.8 1.0 C5 A:DG2 4.9 52.0 1.0 C5 A:DG11 4.9 56.5 1.0 C5 A:DG3 4.9 58.9 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:K104 b:47.8 occ:1.00 O6 A:DG14 2.6 50.4 1.0 O6 A:DG21 2.6 52.9 1.0 O6 A:DG2 2.8 46.1 1.0 O6 A:DG22 2.8 51.0 1.0 O6 A:DG9 2.8 59.9 1.0 O6 A:DG10 3.0 50.3 1.0 K A:K103 3.4 51.2 1.0 C6 A:DG14 3.6 56.1 1.0 C6 A:DG21 3.6 55.1 1.0 C6 A:DG22 3.7 54.4 1.0 C6 A:DG2 3.7 56.4 1.0 C6 A:DG9 3.8 60.3 1.0 C6 A:DG10 3.9 54.4 1.0 N1 A:DG14 4.0 55.9 1.0 N1 A:DG22 4.0 53.1 1.0 N1 A:DG10 4.1 53.8 1.0 N1 A:DG2 4.2 54.6 1.0 N1 A:DG9 4.2 58.3 1.0 N1 A:DG21 4.2 56.1 1.0 C5 A:DG21 4.7 56.9 1.0 C5 A:DG14 4.8 55.4 1.0 C5 A:DG22 4.9 57.8 1.0 C5 A:DG2 4.9 52.0 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Three-Tetrad, Parallel, and K+ Stabilized Homopurine G-Quadruplex From Human Chromosome 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:K105 b:130.7 occ:0.50 O A:HOH203 3.0 124.3 1.0 O A:HOH202 3.0 127.9 1.0 OP2 A:DA6 4.4 156.4 1.0

M.Ye, E.V.Chen, S.H.Pfeil, K.N.Martin, T.Atrafi, S.Yun, Z.Martinez, L.A.Yatsunyk. Homopurine Guanine-Rich Sequences in Complex with N-Methyl Mesoporphyrin IX Form Parallel G-Quadruplex Dimers and Display A Unique Symmetry Tetrad. Bioorg.Med.Chem. V. 77 17112 2022.
ISSN: ESSN 1464-3391
PubMed: 36508994
DOI: 10.1016/J.BMC.2022.117112