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Barium in PDB 1kd4: The Crystal Structure of R(Ggucacagccc)2, Barium Form

Protein crystallography data

The structure of The Crystal Structure of R(Ggucacagccc)2, Barium Form, PDB code: 1kd4 was solved by V.Kacer, S.A.Scaringe, J.N.Scarsdale, J.P.Rife, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.85
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 39.990, 39.990, 52.620, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 22.2

Barium Binding Sites:

The binding sites of Barium atom in the The Crystal Structure of R(Ggucacagccc)2, Barium Form (pdb code 1kd4). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the The Crystal Structure of R(Ggucacagccc)2, Barium Form, PDB code: 1kd4:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 1kd4

Go back to Barium Binding Sites List in 1kd4
Barium binding site 1 out of 2 in the The Crystal Structure of R(Ggucacagccc)2, Barium Form


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of The Crystal Structure of R(Ggucacagccc)2, Barium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba502

b:27.1
occ:1.00
O B:HOH75 2.7 24.0 1.0
O4 A:U3 2.7 26.3 1.0
O A:HOH70 2.7 23.4 1.0
O B:HOH141 2.7 41.1 1.0
O B:HOH72 2.7 23.5 1.0
O A:HOH147 2.8 29.1 1.0
O6 A:G2 2.8 23.4 1.0
O B:HOH82 2.8 32.8 1.0
O6 B:G8 2.9 21.0 1.0
C4 A:U3 3.7 27.7 1.0
C6 A:G2 3.8 22.5 1.0
N3 A:U3 4.0 26.1 1.0
C6 B:G8 4.1 19.3 1.0
N4 B:C9 4.1 23.1 1.0
O A:HOH98 4.4 29.1 1.0
C5 A:G2 4.6 22.2 1.0
N7 B:G8 4.6 21.6 1.0
N7 A:G2 4.6 23.6 1.0
OP2 B:C6 4.6 28.6 1.0
O A:HOH102 4.6 38.8 1.0
C5 B:G8 4.7 19.1 1.0
OP2 B:A7 4.8 35.2 1.0
N7 B:A7 4.8 24.6 1.0
N1 A:G2 4.8 23.6 1.0

Barium binding site 2 out of 2 in 1kd4

Go back to Barium Binding Sites List in 1kd4
Barium binding site 2 out of 2 in the The Crystal Structure of R(Ggucacagccc)2, Barium Form


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of The Crystal Structure of R(Ggucacagccc)2, Barium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba501

b:26.9
occ:1.00
O B:HOH84 2.7 26.6 1.0
O A:HOH73 2.7 24.8 1.0
O A:HOH175 2.7 39.6 1.0
O4 B:U3 2.7 26.5 1.0
O B:HOH134 2.7 26.9 1.0
O A:HOH174 2.8 35.4 1.0
O A:HOH81 2.8 24.7 1.0
O6 B:G2 2.8 23.1 1.0
O6 A:G8 2.9 23.4 1.0
C4 B:U3 3.7 27.4 1.0
C6 B:G2 3.9 22.7 1.0
N3 B:U3 4.0 26.9 1.0
C6 A:G8 4.1 21.1 1.0
N4 A:C9 4.1 22.4 1.0
C5 B:G2 4.6 22.4 1.0
N7 B:G2 4.6 23.4 1.0
N7 A:G8 4.6 21.7 1.0
O B:HOH95 4.6 32.2 1.0
OP2 A:C6 4.7 28.2 1.0
O B:HOH99 4.7 30.9 1.0
C5 A:G8 4.7 20.3 1.0
O A:HOH158 4.7 43.9 1.0
N7 A:A7 4.9 23.4 1.0
N1 B:G2 4.9 24.2 1.0
C5 B:U3 5.0 28.6 1.0

Reference:

V.Kacer, S.A.Scaringe, J.N.Scarsdale, J.P.Rife. Crystal Structures of R(Ggucacagccc)2. Acta Crystallogr.,Sect.D V. 59 423 2003.
ISSN: ISSN 0907-4449
PubMed: 12595698
DOI: 10.1107/S0907444902021911
Page generated: Sat Dec 12 01:54:58 2020

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