Barium in PDB 7ecf: Crystal Structure of D(G4C2)2-Ba in C2221 Space Group
Protein crystallography data
The structure of Crystal Structure of D(G4C2)2-Ba in C2221 Space Group, PDB code: 7ecf
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)
|
38.84 /
1.60
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.841,
110.076,
56.675,
90,
90,
90
|
R / Rfree (%)
|
14.1 /
17.1
|
Barium Binding Sites:
The binding sites of Barium atom in the Crystal Structure of D(G4C2)2-Ba in C2221 Space Group
(pdb code 7ecf). This binding sites where shown within
5.0 Angstroms radius around Barium atom.
In total 7 binding sites of Barium where determined in the
Crystal Structure of D(G4C2)2-Ba in C2221 Space Group, PDB code: 7ecf:
Jump to Barium binding site number:
1;
2;
3;
4;
5;
6;
7;
Barium binding site 1 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 1 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 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 C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba101
b:27.0
occ:1.00
|
O6
|
A:DG3
|
2.7
|
27.2
|
1.0
|
O6
|
B:DG10
|
2.7
|
27.7
|
1.0
|
O6
|
B:DG3
|
2.7
|
26.4
|
1.0
|
O6
|
A:DG10
|
2.7
|
30.1
|
1.0
|
O6
|
A:DG9
|
2.7
|
27.8
|
1.0
|
O6
|
A:DG4
|
2.8
|
25.1
|
1.0
|
O6
|
B:DG9
|
2.8
|
25.1
|
1.0
|
O6
|
B:DG4
|
2.8
|
26.1
|
1.0
|
C6
|
A:DG9
|
3.6
|
27.6
|
1.0
|
C6
|
B:DG9
|
3.6
|
27.1
|
1.0
|
C6
|
A:DG3
|
3.6
|
26.6
|
1.0
|
C6
|
B:DG3
|
3.6
|
28.8
|
1.0
|
C6
|
B:DG10
|
3.7
|
29.2
|
1.0
|
C6
|
A:DG10
|
3.7
|
28.3
|
1.0
|
C6
|
A:DG4
|
3.7
|
29.9
|
1.0
|
C6
|
B:DG4
|
3.8
|
27.0
|
1.0
|
N1
|
A:DG9
|
3.9
|
28.2
|
1.0
|
N1
|
B:DG9
|
3.9
|
27.2
|
1.0
|
N1
|
A:DG3
|
3.9
|
30.6
|
1.0
|
N1
|
B:DG3
|
4.0
|
29.8
|
1.0
|
N1
|
B:DG10
|
4.0
|
28.4
|
1.0
|
N1
|
A:DG10
|
4.0
|
28.8
|
1.0
|
N1
|
A:DG4
|
4.1
|
28.2
|
1.0
|
N1
|
B:DG4
|
4.1
|
32.2
|
1.0
|
N4
|
E:DC12
|
4.7
|
39.9
|
1.0
|
C5
|
A:DG9
|
4.8
|
26.6
|
1.0
|
C5
|
B:DG9
|
4.8
|
27.1
|
1.0
|
C5
|
A:DG3
|
4.8
|
30.8
|
1.0
|
C5
|
B:DG3
|
4.8
|
28.7
|
1.0
|
C5
|
B:DG10
|
5.0
|
28.7
|
1.0
|
C5
|
A:DG10
|
5.0
|
29.9
|
1.0
|
C5
|
A:DG4
|
5.0
|
33.1
|
1.0
|
|
Barium binding site 2 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 2 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 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 C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba102
b:25.5
occ:1.00
|
O6
|
A:DG7
|
2.7
|
21.7
|
1.0
|
O6
|
B:DG7
|
2.7
|
23.1
|
1.0
|
O6
|
B:DG1
|
2.7
|
26.4
|
1.0
|
O6
|
A:DG8
|
2.7
|
24.1
|
1.0
|
O6
|
B:DG2
|
2.7
|
24.5
|
1.0
|
O6
|
B:DG8
|
2.8
|
23.5
|
1.0
|
O6
|
A:DG2
|
2.8
|
27.9
|
1.0
|
O6
|
A:DG1
|
2.8
|
26.4
|
1.0
|
C6
|
B:DG1
|
3.6
|
27.0
|
1.0
|
C6
|
A:DG7
|
3.6
|
28.2
|
1.0
|
C6
|
A:DG1
|
3.6
|
27.6
|
1.0
|
C6
|
B:DG7
|
3.7
|
29.1
|
1.0
|
C6
|
A:DG2
|
3.7
|
28.6
|
1.0
|
C6
|
B:DG2
|
3.7
|
31.9
|
1.0
|
C6
|
B:DG8
|
3.7
|
25.0
|
1.0
|
C6
|
A:DG8
|
3.7
|
25.9
|
1.0
|
N1
|
A:DG7
|
3.9
|
28.6
|
1.0
|
N1
|
B:DG7
|
4.0
|
25.7
|
1.0
|
N1
|
A:DG2
|
4.0
|
25.4
|
1.0
|
N1
|
B:DG1
|
4.0
|
25.4
|
1.0
|
N1
|
A:DG1
|
4.0
|
28.1
|
1.0
|
N1
|
B:DG2
|
4.0
|
29.0
|
1.0
|
N1
|
B:DG8
|
4.0
|
28.0
|
1.0
|
N1
|
A:DG8
|
4.1
|
29.9
|
1.0
|
C5
|
B:DG1
|
4.8
|
27.8
|
1.0
|
C5
|
A:DG1
|
4.9
|
26.9
|
1.0
|
C5
|
A:DG7
|
4.9
|
27.2
|
1.0
|
C5
|
B:DG7
|
4.9
|
27.2
|
1.0
|
C5
|
A:DG8
|
4.9
|
26.1
|
1.0
|
C5
|
A:DG2
|
4.9
|
25.8
|
1.0
|
C5
|
B:DG8
|
4.9
|
29.6
|
1.0
|
C5
|
B:DG2
|
5.0
|
25.5
|
1.0
|
|
Barium binding site 3 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 3 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 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 C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba103
b:39.7
occ:0.50
|
O
|
C:HOH213
|
2.5
|
44.8
|
1.0
|
O
|
A:HOH214
|
2.6
|
41.3
|
1.0
|
O
|
C:HOH203
|
2.7
|
49.5
|
1.0
|
O
|
C:HOH212
|
2.8
|
43.2
|
1.0
|
O
|
A:HOH211
|
2.9
|
49.8
|
1.0
|
O
|
E:HOH205
|
3.0
|
41.1
|
1.0
|
O
|
C:HOH210
|
4.1
|
36.8
|
1.0
|
OP2
|
C:DC5
|
4.7
|
55.7
|
1.0
|
OP2
|
A:DG9
|
4.7
|
42.3
|
1.0
|
O
|
A:HOH204
|
4.8
|
33.9
|
1.0
|
|
Barium binding site 4 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 4 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 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 C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ba101
b:30.3
occ:1.00
|
O6
|
C:DG9
|
2.7
|
28.7
|
1.0
|
O6
|
C:DG3
|
2.7
|
32.9
|
1.0
|
O6
|
D:DG4
|
2.7
|
32.5
|
1.0
|
O6
|
D:DG10
|
2.7
|
29.6
|
1.0
|
O6
|
D:DG3
|
2.7
|
27.8
|
1.0
|
O6
|
D:DG9
|
2.7
|
30.1
|
1.0
|
O6
|
C:DG10
|
2.7
|
31.0
|
1.0
|
O6
|
C:DG4
|
2.8
|
33.5
|
1.0
|
C6
|
C:DG9
|
3.6
|
31.0
|
1.0
|
C6
|
C:DG3
|
3.6
|
33.6
|
1.0
|
C6
|
D:DG9
|
3.6
|
31.6
|
1.0
|
C6
|
D:DG3
|
3.6
|
29.2
|
1.0
|
C6
|
D:DG4
|
3.7
|
28.8
|
1.0
|
C6
|
D:DG10
|
3.7
|
34.4
|
1.0
|
C6
|
C:DG10
|
3.7
|
30.9
|
1.0
|
C6
|
C:DG4
|
3.8
|
33.5
|
1.0
|
N1
|
C:DG9
|
3.9
|
28.0
|
1.0
|
N1
|
C:DG3
|
3.9
|
31.3
|
1.0
|
N1
|
D:DG9
|
3.9
|
32.0
|
1.0
|
N1
|
D:DG3
|
3.9
|
34.8
|
1.0
|
N1
|
D:DG4
|
4.0
|
38.1
|
1.0
|
N1
|
D:DG10
|
4.0
|
39.0
|
1.0
|
N1
|
C:DG10
|
4.1
|
36.4
|
1.0
|
N1
|
C:DG4
|
4.1
|
35.0
|
1.0
|
C5
|
C:DG9
|
4.8
|
32.7
|
1.0
|
C5
|
D:DG9
|
4.8
|
34.1
|
1.0
|
C5
|
C:DG3
|
4.8
|
33.0
|
1.0
|
C5
|
D:DG3
|
4.8
|
28.1
|
1.0
|
C5
|
D:DG4
|
5.0
|
34.2
|
1.0
|
C5
|
D:DG10
|
5.0
|
39.5
|
1.0
|
|
Barium binding site 5 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 5 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 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 C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ba102
b:29.9
occ:1.00
|
O6
|
D:DG8
|
2.7
|
31.5
|
1.0
|
O6
|
D:DG2
|
2.7
|
27.5
|
1.0
|
O6
|
D:DG1
|
2.7
|
29.3
|
1.0
|
O6
|
C:DG7
|
2.7
|
31.3
|
1.0
|
O6
|
D:DG7
|
2.7
|
29.3
|
1.0
|
O6
|
C:DG8
|
2.7
|
27.3
|
1.0
|
O6
|
C:DG2
|
2.8
|
31.4
|
1.0
|
O6
|
C:DG1
|
2.8
|
33.6
|
1.0
|
C6
|
D:DG7
|
3.6
|
32.5
|
1.0
|
C6
|
D:DG1
|
3.6
|
30.9
|
1.0
|
C6
|
C:DG1
|
3.6
|
29.8
|
1.0
|
C6
|
C:DG7
|
3.7
|
35.1
|
1.0
|
C6
|
D:DG8
|
3.7
|
34.7
|
1.0
|
C6
|
D:DG2
|
3.7
|
29.0
|
1.0
|
C6
|
C:DG2
|
3.7
|
33.2
|
1.0
|
C6
|
C:DG8
|
3.7
|
31.0
|
1.0
|
N1
|
D:DG7
|
3.9
|
34.5
|
1.0
|
N1
|
D:DG1
|
3.9
|
29.7
|
1.0
|
N1
|
C:DG7
|
4.0
|
34.6
|
1.0
|
N1
|
C:DG1
|
4.0
|
31.7
|
1.0
|
N1
|
D:DG8
|
4.0
|
30.4
|
1.0
|
N1
|
C:DG2
|
4.0
|
36.9
|
1.0
|
N1
|
D:DG2
|
4.0
|
32.5
|
1.0
|
N1
|
C:DG8
|
4.0
|
30.7
|
1.0
|
C5
|
D:DG7
|
4.8
|
29.7
|
1.0
|
C5
|
C:DG1
|
4.9
|
33.2
|
1.0
|
C5
|
D:DG1
|
4.9
|
29.2
|
1.0
|
C5
|
C:DG7
|
4.9
|
34.0
|
1.0
|
C5
|
D:DG2
|
4.9
|
32.0
|
1.0
|
C5
|
C:DG2
|
4.9
|
33.5
|
1.0
|
C5
|
D:DG8
|
4.9
|
27.8
|
1.0
|
C5
|
C:DG8
|
5.0
|
29.7
|
1.0
|
|
Barium binding site 6 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 6 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 Space Group
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 6 of Crystal Structure of D(G4C2)2-Ba in C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ba101
b:26.5
occ:1.00
|
O6
|
F:DG8
|
2.6
|
28.6
|
1.0
|
O6
|
E:DG7
|
2.7
|
27.7
|
1.0
|
O6
|
E:DG8
|
2.7
|
27.5
|
1.0
|
O6
|
F:DG2
|
2.7
|
27.6
|
1.0
|
O6
|
E:DG2
|
2.7
|
28.5
|
1.0
|
O6
|
F:DG1
|
2.7
|
25.5
|
1.0
|
O6
|
E:DG1
|
2.7
|
24.0
|
1.0
|
O6
|
F:DG7
|
2.8
|
23.2
|
1.0
|
C6
|
F:DG8
|
3.6
|
33.4
|
1.0
|
C6
|
E:DG7
|
3.6
|
24.7
|
1.0
|
C6
|
E:DG8
|
3.7
|
29.6
|
1.0
|
C6
|
E:DG1
|
3.7
|
28.5
|
1.0
|
C6
|
F:DG2
|
3.7
|
31.9
|
1.0
|
C6
|
F:DG1
|
3.7
|
25.7
|
1.0
|
C6
|
E:DG2
|
3.7
|
30.0
|
1.0
|
C6
|
F:DG7
|
3.7
|
29.7
|
1.0
|
N1
|
F:DG2
|
4.0
|
31.9
|
1.0
|
N1
|
E:DG7
|
4.0
|
26.5
|
1.0
|
N1
|
F:DG1
|
4.0
|
25.8
|
1.0
|
N1
|
F:DG7
|
4.0
|
30.3
|
1.0
|
N1
|
E:DG1
|
4.0
|
27.5
|
1.0
|
N1
|
E:DG2
|
4.0
|
35.3
|
1.0
|
N1
|
E:DG8
|
4.0
|
34.2
|
1.0
|
N1
|
F:DG8
|
4.0
|
29.3
|
1.0
|
C5
|
E:DG1
|
4.9
|
30.8
|
1.0
|
C5
|
F:DG1
|
4.9
|
31.6
|
1.0
|
C5
|
F:DG8
|
4.9
|
35.1
|
1.0
|
C5
|
E:DG7
|
4.9
|
27.9
|
1.0
|
C5
|
E:DG8
|
4.9
|
31.5
|
1.0
|
C5
|
E:DG2
|
4.9
|
36.4
|
1.0
|
C5
|
F:DG2
|
4.9
|
32.1
|
1.0
|
C5
|
F:DG7
|
4.9
|
29.8
|
1.0
|
|
Barium binding site 7 out
of 7 in 7ecf
Go back to
Barium Binding Sites List in 7ecf
Barium binding site 7 out
of 7 in the Crystal Structure of D(G4C2)2-Ba in C2221 Space Group
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 7 of Crystal Structure of D(G4C2)2-Ba in C2221 Space Group within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ba102
b:27.7
occ:1.00
|
O6
|
E:DG9
|
2.7
|
23.4
|
1.0
|
O6
|
F:DG3
|
2.7
|
27.1
|
1.0
|
O6
|
E:DG4
|
2.7
|
29.8
|
1.0
|
O6
|
F:DG10
|
2.7
|
26.8
|
1.0
|
O6
|
F:DG4
|
2.7
|
28.7
|
1.0
|
O6
|
E:DG3
|
2.7
|
27.9
|
1.0
|
O6
|
F:DG9
|
2.7
|
25.8
|
1.0
|
O6
|
E:DG10
|
2.8
|
31.8
|
1.0
|
C6
|
E:DG9
|
3.6
|
29.4
|
1.0
|
C6
|
F:DG9
|
3.6
|
26.8
|
1.0
|
C6
|
F:DG3
|
3.6
|
27.6
|
1.0
|
C6
|
E:DG3
|
3.6
|
34.2
|
1.0
|
C6
|
E:DG4
|
3.7
|
28.4
|
1.0
|
C6
|
F:DG4
|
3.7
|
24.4
|
1.0
|
C6
|
F:DG10
|
3.7
|
27.9
|
1.0
|
C6
|
E:DG10
|
3.8
|
30.0
|
1.0
|
N1
|
E:DG9
|
3.9
|
27.2
|
1.0
|
N1
|
F:DG9
|
3.9
|
27.3
|
1.0
|
N1
|
E:DG3
|
3.9
|
28.2
|
1.0
|
N1
|
F:DG3
|
3.9
|
31.3
|
1.0
|
N1
|
F:DG4
|
4.0
|
31.3
|
1.0
|
N1
|
E:DG4
|
4.1
|
27.5
|
1.0
|
N1
|
F:DG10
|
4.1
|
28.4
|
1.0
|
N1
|
E:DG10
|
4.1
|
30.2
|
1.0
|
N4
|
B:DC12
|
4.1
|
33.1
|
1.0
|
C4
|
B:DC12
|
4.6
|
28.3
|
1.0
|
C5
|
E:DG9
|
4.8
|
29.6
|
1.0
|
C5
|
F:DG9
|
4.8
|
30.9
|
1.0
|
C5
|
F:DG3
|
4.8
|
27.1
|
1.0
|
C5
|
E:DG3
|
4.9
|
26.8
|
1.0
|
C5
|
E:DG4
|
5.0
|
33.2
|
1.0
|
N3
|
B:DC12
|
5.0
|
36.4
|
1.0
|
C5
|
F:DG4
|
5.0
|
29.5
|
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: Wed Jul 10 16:06:03 2024
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