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Barium in PDB 284d: The Bi-Loop, A New General Four-Stranded Dna Motif

Protein crystallography data

The structure of The Bi-Loop, A New General Four-Stranded Dna Motif, PDB code: 284d was solved by S.A.Salisbury, S.E.Wilson, H.R.Powell, O.Kennard, P.Lubini, G.M.Sheldrick, N.Escaja, E.Alazzouzi, A.Grandas, E.Pedroso, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.00 / 1.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 22.844, 27.676, 55.370, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / n/a

Other elements in 284d:

The structure of The Bi-Loop, A New General Four-Stranded Dna Motif also contains other interesting chemical elements:

Sodium (Na) 1 atom

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Barium atom in the The Bi-Loop, A New General Four-Stranded Dna Motif (pdb code 284d). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 11 binding sites of Barium where determined in the The Bi-Loop, A New General Four-Stranded Dna Motif, PDB code: 284d:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 11 in 284d

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Barium binding site 1 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba28

b:17.9
occ:0.29
 OP2 A:DT3 2.6 15.5 1.0
O A:HOH134 2.9 25.3 1.0
BA A:BA30 3.5 21.9 0.5
P A:DT3 3.9 12.6 1.0
OP1 A:DT3 4.0 16.6 1.0
H3' A:DT2 4.1 15.2 1.0
BA A:BA29 4.1 21.7 0.5
O B:HOH125 4.2 32.9 1.0
O A:HOH128 4.4 13.3 1.0
O A:HOH62 4.4 20.0 1.0
O3' A:DT2 4.6 11.1 1.0
C3' A:DT2 4.8 10.1 1.0
O A:HOH135 4.9 23.7 1.0
H2' A:DT2 4.9 15.4 1.0

Barium binding site 2 out of 11 in 284d

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Barium binding site 2 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba29

b:21.7
occ:0.49
 BA A:BA30 2.0 21.9 0.5
O A:HOH84 4.0 25.0 1.0
BA A:BA28 4.1 17.9 0.3
O A:HOH134 4.3 25.3 1.0
OP2 A:DT3 4.7 15.5 1.0
O A:HOH135 4.9 23.7 1.0

Barium binding site 3 out of 11 in 284d

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Barium binding site 3 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba30

b:21.9
occ:0.51
 BA A:BA29 2.0 21.7 0.5
OP2 A:DT3 3.1 15.5 1.0
BA A:BA28 3.5 17.9 0.3
O A:HOH84 3.5 25.0 1.0
P A:DT3 4.2 12.6 1.0
H2' A:DT3 4.2 13.4 1.0
O5' A:DT3 4.3 11.7 1.0
O A:HOH135 4.5 23.7 1.0
H3' A:DT3 4.6 13.8 1.0
O A:HOH134 4.8 25.3 1.0
OP1 A:DT3 4.8 16.6 1.0
C2' A:DT3 5.0 8.9 1.0

Barium binding site 4 out of 11 in 284d

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Barium binding site 4 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba20

b:12.2
occ:1.00
 O B:HOH93 2.7 16.6 1.0
O B:HOH94 2.7 12.6 1.0
O B:HOH38 2.7 9.7 1.0
O B:HOH35 2.8 15.3 1.0
OP1 B:DA15 2.9 8.1 1.0
O B:HOH36 2.9 12.6 1.0
O B:HOH92 2.9 13.4 1.0
O B:HOH95 2.9 12.3 1.0
O B:HOH68 3.0 16.0 1.0
O3' B:DC14 3.5 6.8 1.0
P B:DA15 3.9 6.9 1.0
H1' B:DC14 4.1 13.3 1.0
H5'' B:DA15 4.4 10.0 1.0
O B:HOH55 4.6 11.3 1.0
H2'' B:DC14 4.6 11.8 1.0
O B:HOH51 4.7 11.6 1.0
OP2 B:DA15 4.7 7.9 1.0
O B:HOH91 4.8 26.4 1.0
C3' B:DC14 4.8 7.3 1.0
C1' B:DC14 4.9 8.9 1.0
C2' B:DC14 5.0 7.8 1.0

Barium binding site 5 out of 11 in 284d

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Barium binding site 5 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba21

b:11.4
occ:0.56
 OP2 B:DA11 2.7 13.0 1.0
O B:HOH124 2.8 23.0 1.0
O B:HOH99 2.9 15.4 1.0
O B:HOH98 2.9 18.5 1.0
O B:HOH96 3.1 19.5 1.0
O B:HOH100 3.1 26.3 1.0
O3' B:DC18 3.3 12.7 1.0
P B:DA11 3.6 12.7 1.0
H5'' B:DA11 4.0 15.7 1.0
H1' B:DC18 4.1 21.6 1.0
H2'' B:DC18 4.2 21.2 1.0
O B:HOH102 4.2 24.3 1.0
O B:HOH72 4.3 16.1 1.0
O B:HOH111 4.4 24.3 1.0
C3' B:DC18 4.5 13.3 1.0
OP1 B:DA11 4.6 14.8 1.0
C2' B:DC18 4.7 14.1 1.0
O B:HOH131 4.7 15.7 1.0
O B:HOH97 4.7 21.7 1.0
O5' B:DA11 4.8 12.2 1.0
C5' B:DA11 4.8 10.4 1.0
C1' B:DC18 4.9 14.4 1.0

Barium binding site 6 out of 11 in 284d

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Barium binding site 6 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba22

b:13.1
occ:0.44
 BA B:BA23 1.7 13.2 0.4
BA B:BA24 1.9 14.2 0.2
O B:HOH49 2.8 10.6 1.0
O B:HOH101 2.9 17.0 1.0
O B:HOH117 3.0 22.1 1.0
O B:HOH40 3.0 10.1 1.0
O B:HOH56 3.1 16.4 1.0
O B:HOH33 4.1 20.2 1.0
O B:HOH102 4.3 24.3 1.0
OP1 B:DT16 4.5 9.7 1.0
O B:HOH119 4.6 23.9 1.0
O B:HOH94 4.8 12.6 1.0
O B:HOH41 5.0 6.7 1.0
O B:HOH97 5.0 21.7 1.0

Barium binding site 7 out of 11 in 284d

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Barium binding site 7 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba23

b:13.2
occ:0.37
 BA B:BA22 1.7 13.1 0.4
BA B:BA24 1.9 14.2 0.2
O B:HOH40 2.7 10.1 1.0
O B:HOH49 2.7 10.6 1.0
O B:HOH102 2.8 24.3 1.0
O B:HOH101 3.3 17.0 1.0
O B:HOH117 3.4 22.1 1.0
O B:HOH97 3.6 21.7 1.0
O B:HOH119 4.3 23.9 1.0
O B:HOH56 4.3 16.4 1.0
O B:HOH33 4.5 20.2 1.0
O B:HOH72 4.5 16.1 1.0
OP1 B:DT16 4.6 9.7 1.0
O B:HOH109 4.6 26.0 1.0

Barium binding site 8 out of 11 in 284d

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Barium binding site 8 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba24

b:14.2
occ:0.17
 BA B:BA22 1.9 13.1 0.4
BA B:BA23 1.9 13.2 0.4
O B:HOH49 2.7 10.6 1.0
O B:HOH40 2.8 10.1 1.0
O B:HOH33 3.2 20.2 1.0
O B:HOH109 3.7 26.0 1.0
O B:HOH56 3.8 16.4 1.0
O B:HOH102 4.0 24.3 1.0
O B:HOH97 4.2 21.7 1.0
OP1 B:DT12 4.4 10.9 1.0
O B:HOH101 4.4 17.0 1.0
O B:HOH117 4.5 22.1 1.0
O B:HOH127 4.6 22.2 1.0
O B:HOH72 4.7 16.1 1.0
O B:HOH94 4.8 12.6 1.0

Barium binding site 9 out of 11 in 284d

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Barium binding site 9 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba25

b:13.6
occ:0.42
 BA B:BA26 2.3 14.5 0.3
BA B:BA27 2.3 15.8 0.2
O B:HOH53 2.7 19.9 1.0
O B:HOH106 2.7 19.2 1.0
O A:HOH107 2.8 17.1 1.0
O B:HOH71 2.9 17.3 1.0
O B:HOH70 2.9 12.4 1.0
O B:HOH104 3.1 15.5 1.0
O B:HOH113 3.2 33.4 1.0
H2' B:DT12 3.5 11.8 1.0
O B:HOH123 3.6 28.9 1.0
H3' B:DT12 4.2 11.7 1.0
C2' B:DT12 4.3 7.9 1.0
H6 B:DT12 4.4 11.8 1.0
H2'' B:DT12 4.5 11.8 1.0
O B:HOH121 4.6 15.1 1.0
O B:HOH74 4.7 19.6 1.0
O B:HOH83 4.7 19.9 1.0
H72 B:DT12 4.8 14.7 1.0
O B:HOH115 4.8 26.4 1.0
C3' B:DT12 4.8 7.8 1.0
O A:HOH64 4.9 13.9 1.0

Barium binding site 10 out of 11 in 284d

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Barium binding site 10 out of 11 in the The Bi-Loop, A New General Four-Stranded Dna Motif


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of The Bi-Loop, A New General Four-Stranded Dna Motif within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba26

b:14.5
occ:0.34
 O B:HOH106 1.5 19.2 1.0
O B:HOH104 1.7 15.5 1.0
O B:HOH53 1.9 19.9 1.0
BA B:BA25 2.3 13.6 0.4
O B:HOH74 2.8 19.6 1.0
O B:HOH71 3.0 17.3 1.0
O B:HOH105 3.0 22.2 1.0
BA B:BA27 3.1 15.8 0.2
O B:HOH123 4.2 28.9 1.0
OP2 B:DT13 4.3 8.5 1.0
OP1 B:DT13 4.3 9.9 1.0
O B:HOH121 4.4 15.1 1.0
O B:HOH70 4.5 12.4 1.0
H3' B:DT12 4.6 11.7 1.0
H2' B:DT12 4.7 11.8 1.0
O B:HOH115 4.8 26.4 1.0
O A:HOH107 4.8 17.1 1.0
P B:DT13 4.9 7.8 1.0
O B:HOH43 5.0 11.2 1.0

Reference:

S.A.Salisbury, S.E.Wilson, H.R.Powell, O.Kennard, P.Lubini, G.M.Sheldrick, N.Escaja, E.Alazzouzi, A.Grandas, E.Pedroso. The Bi-Loop, A New General Four-Stranded Dna Motif. Proc.Natl.Acad.Sci.Usa V. 94 5515 1997.
ISSN: ISSN 0027-8424
PubMed: 9159103
DOI: 10.1073/PNAS.94.11.5515
Page generated: Wed Jul 10 15:00:47 2024

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