Barium in PDB 7ecg: Crystal Structure of D(G4C2)2-Ba in F222 Space Group

Protein crystallography data

The structure of Crystal Structure of D(G4C2)2-Ba in F222 Space Group, PDB code: 7ecg was solved by Y.Geng, C.Liu, Q.Cai, Z.Luo, G.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.81 / 1.97
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.613, 60.817, 109.605, 90, 90, 90
R / Rfree (%) 23.6 / 25.4

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group (pdb code 7ecg). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 5 binding sites of Barium where determined in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group, PDB code: 7ecg:
Jump to Barium binding site number: 1; 2; 3; 4; 5;

Barium binding site 1 out of 5 in 7ecg

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Barium binding site 1 out of 5 in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of D(G4C2)2-Ba in F222 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:49.4
occ:0.50
O6 A:DG9 2.6 37.9 1.0
O6 A:DG3 2.8 34.7 1.0
O6 A:DG10 2.8 42.1 1.0
O6 A:DG4 2.9 56.8 1.0
C6 A:DG9 3.6 36.4 1.0
C6 A:DG3 3.6 31.9 1.0
C6 A:DG4 3.8 44.7 1.0
C6 A:DG10 3.8 44.0 1.0
N1 A:DG3 3.8 34.4 1.0
N1 A:DG9 4.0 37.8 1.0
N1 A:DG4 4.0 47.2 1.0
N1 A:DG10 4.1 46.7 1.0
N4 C:DC12 4.6 55.6 1.0
C5 A:DG9 4.8 36.0 1.0
C5 A:DG3 4.8 39.5 1.0

Barium binding site 2 out of 5 in 7ecg

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Barium binding site 2 out of 5 in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of D(G4C2)2-Ba in F222 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba102

b:44.2
occ:0.50
O6 A:DG1 2.6 34.2 1.0
O6 A:DG2 2.7 35.1 1.0
O6 A:DG8 2.8 36.2 1.0
O6 A:DG7 2.8 36.0 1.0
C6 A:DG1 3.5 37.9 1.0
C6 A:DG2 3.6 31.6 1.0
C6 A:DG8 3.7 37.6 1.0
C6 A:DG7 3.7 36.9 1.0
N1 A:DG1 3.9 38.8 1.0
N1 A:DG2 4.0 34.8 1.0
N1 A:DG7 4.0 37.8 1.0
N1 A:DG8 4.0 44.1 1.0
C5 A:DG1 4.7 38.3 1.0
C5 A:DG2 4.9 34.4 1.0
C5 A:DG8 4.9 37.5 1.0
C5 A:DG7 5.0 35.9 1.0

Barium binding site 3 out of 5 in 7ecg

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Barium binding site 3 out of 5 in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of D(G4C2)2-Ba in F222 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba103

b:61.6
occ:0.30
N2 A:DG4 4.4 45.4 1.0
N4 C:DC11 4.4 62.4 1.0
N3 A:DG4 4.7 39.7 1.0
C2' A:DG9 4.9 53.1 1.0

Barium binding site 4 out of 5 in 7ecg

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Barium binding site 4 out of 5 in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of D(G4C2)2-Ba in F222 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba101

b:59.7
occ:1.00
O6 C:DG9 2.5 47.4 1.0
O6 C:DG10 2.6 49.6 1.0
O6 B:DG3 2.6 29.7 1.0
O6 C:DG4 2.7 56.2 1.0
O6 C:DG3 2.8 44.2 1.0
O6 B:DG4 2.8 38.4 1.0
O6 B:DG9 3.0 57.1 1.0
O6 B:DG10 3.3 61.6 1.0
C6 C:DG9 3.4 45.3 1.0
C6 C:DG3 3.5 51.2 1.0
C6 B:DG3 3.5 34.5 1.0
N1 C:DG3 3.5 41.5 1.0
C6 C:DG4 3.5 48.4 1.0
C6 C:DG10 3.6 42.3 1.0
C6 B:DG4 3.7 40.0 1.0
N1 C:DG4 3.7 44.9 1.0
N1 B:DG3 3.8 34.5 1.0
N1 C:DG9 3.8 40.6 1.0
C6 B:DG9 3.9 45.4 1.0
N1 C:DG10 3.9 42.0 1.0
N1 B:DG4 4.0 51.7 1.0
N1 B:DG9 4.2 44.2 1.0
C6 B:DG10 4.2 42.4 1.0
N4 A:DC12 4.4 56.1 1.0
N1 B:DG10 4.4 37.8 1.0
C5 C:DG9 4.6 46.9 1.0
C5 B:DG3 4.7 34.0 1.0
C2 C:DG3 4.7 55.0 1.0
C5 C:DG3 4.7 47.5 1.0
C5 C:DG4 4.8 59.7 1.0
C5 C:DG10 4.9 43.1 1.0
C4 A:DC12 5.0 53.6 1.0
C5 B:DG4 5.0 46.1 1.0

Barium binding site 5 out of 5 in 7ecg

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Barium binding site 5 out of 5 in the Crystal Structure of D(G4C2)2-Ba in F222 Space Group


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of D(G4C2)2-Ba in F222 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba102

b:52.5
occ:1.00
O6 C:DG8 2.5 56.7 1.0
O6 B:DG1 2.7 44.8 1.0
O6 B:DG2 2.7 35.2 1.0
O6 C:DG7 2.8 36.1 1.0
O6 B:DG7 2.8 35.0 1.0
O6 B:DG8 2.8 51.7 1.0
O6 C:DG2 2.8 40.5 1.0
O6 C:DG1 3.0 51.2 1.0
C6 C:DG8 3.4 39.4 1.0
C6 B:DG1 3.5 32.0 1.0
C6 C:DG7 3.6 45.4 1.0
C6 B:DG2 3.6 36.6 1.0
C6 B:DG7 3.7 35.2 1.0
C6 C:DG2 3.7 55.0 1.0
C6 B:DG8 3.7 48.9 1.0
N1 C:DG7 3.7 33.9 1.0
N1 C:DG8 3.8 53.6 1.0
C6 C:DG1 3.9 38.3 1.0
N1 C:DG2 3.9 56.1 1.0
N1 B:DG1 3.9 34.7 1.0
N1 B:DG2 3.9 36.5 1.0
N1 B:DG7 4.0 41.8 1.0
N1 B:DG8 4.0 48.9 1.0
N1 C:DG1 4.1 40.3 1.0
C5 C:DG8 4.7 48.8 1.0
C5 B:DG1 4.8 39.0 1.0
C5 C:DG7 4.8 52.7 1.0
C5 B:DG2 4.9 38.8 1.0
C5 B:DG7 4.9 38.9 1.0
C5 B:DG8 5.0 47.0 1.0
C5 C:DG2 5.0 40.6 1.0
C2 C:DG7 5.0 41.0 1.0

Reference:

Y.Geng, C.Liu, Q.Cai, Z.Luo, H.Miao, X.Shi, N.Xu, C.P.Fung, T.T.Choy, B.Yan, N.Li, P.Qian, B.Zhou, G.Zhu. Crystal Structure of Parallel G-Quadruplex Formed By the Two-Repeat Als- and Ftd-Related Ggggcc Sequence. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34048588
DOI: 10.1093/NAR/GKAB302
Page generated: Sat Jul 10 09:48:27 2021

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