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Barium in PDB 1u9s: Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type

Protein crystallography data

The structure of Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type, PDB code: 1u9s was solved by A.S.Krasilnikov, Y.Xiao, T.Pan, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 76.470, 120.890, 133.620, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 27.5

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type (pdb code 1u9s). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 21 binding sites of Barium where determined in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type, PDB code: 1u9s:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 21 in 1u9s

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Barium binding site 1 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1

b:79.5
occ:1.00
OP2 A:G167 2.9 51.4 1.0
O2' A:A165 3.9 83.6 1.0
P A:G167 4.3 59.9 1.0
N7 A:G167 4.7 68.3 1.0
O6 A:G168 4.7 89.8 1.0
O5' A:G167 4.9 63.5 1.0
N7 A:G168 4.9 84.5 1.0
C2' A:A165 4.9 64.4 1.0
C5' A:A166 4.9 44.0 1.0
OP2 A:A166 5.0 46.6 1.0

Barium binding site 2 out of 21 in 1u9s

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Barium binding site 2 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba2

b:58.1
occ:1.00
N7 A:G218 2.6 58.9 1.0
OP2 A:A192 2.7 49.8 1.0
O6 A:G218 3.3 70.8 1.0
C5 A:G218 3.5 55.3 1.0
C8 A:G218 3.6 58.6 1.0
C6 A:G218 3.8 56.4 1.0
P A:A192 4.2 60.2 1.0
C4 A:G218 4.7 53.4 1.0
N9 A:G218 4.8 49.3 1.0
N7 A:G188 4.9 53.3 1.0
O5' A:A192 4.9 49.1 1.0
OP2 A:C191 5.0 48.4 1.0
C3' A:C191 5.0 44.1 1.0

Barium binding site 3 out of 21 in 1u9s

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Barium binding site 3 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba3

b:70.1
occ:1.00
N7 A:G130 2.9 60.7 1.0
C8 A:G130 3.6 64.4 1.0
C5 A:G130 3.8 66.2 1.0
O6 A:G130 4.1 83.0 1.0
C6 A:G130 4.2 69.6 1.0
N9 A:G130 4.7 61.0 1.0
C4 A:G130 4.8 62.1 1.0

Barium binding site 4 out of 21 in 1u9s

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Barium binding site 4 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba4

b:0.6
occ:1.00
O6 A:G162 2.7 70.3 1.0
N7 A:G162 2.7 64.1 1.0
OP2 A:G161 3.0 94.6 1.0
C6 A:G162 3.3 63.3 1.0
C5 A:G162 3.3 63.0 1.0
C8 A:G162 3.9 70.2 1.0
OP2 A:C160 4.3 0.2 1.0
P A:G161 4.5 93.0 1.0
C4 A:G162 4.6 66.1 1.0
N1 A:G162 4.7 59.0 1.0
O2' A:G159 4.9 0.8 1.0
N9 A:G162 4.9 67.5 1.0

Barium binding site 5 out of 21 in 1u9s

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Barium binding site 5 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba5

b:0.6
occ:1.00
O6 A:G100 2.7 88.1 1.0
N7 A:G100 3.0 73.2 1.0
C6 A:G100 3.4 75.7 1.0
C5 A:G100 3.5 70.9 1.0
C8 A:G100 4.2 70.9 1.0
N7 A:G99 4.4 66.0 1.0
BA A:BA11 4.6 0.2 1.0
N1 A:G100 4.7 65.9 1.0
C4 A:G100 4.8 63.6 1.0

Barium binding site 6 out of 21 in 1u9s

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Barium binding site 6 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba6

b:0.9
occ:1.00
O2 A:C175 2.7 79.5 1.0
O2' A:C175 3.3 78.8 1.0
C2' A:C175 3.5 62.7 1.0
C2 A:C175 3.9 72.5 1.0
C1' A:C175 4.4 60.8 1.0
C3' A:C175 4.6 56.8 1.0
N1 A:C175 4.6 66.0 1.0
N3 A:C175 4.7 76.4 1.0
O3' A:C175 4.8 56.7 1.0

Barium binding site 7 out of 21 in 1u9s

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Barium binding site 7 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


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 the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba7

b:86.9
occ:0.50
OP2 A:C219 3.0 61.9 1.0
OP1 A:A220 3.3 56.2 1.0
C5' A:A220 4.0 58.0 1.0
P A:C219 4.3 62.9 1.0
C5' A:C219 4.3 50.2 1.0
O5' A:C219 4.4 53.6 1.0
P A:A220 4.5 57.1 1.0
O5' A:A220 4.7 50.0 1.0
O3' A:C219 4.8 56.1 1.0
C4' A:A220 4.9 58.8 1.0

Barium binding site 8 out of 21 in 1u9s

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Barium binding site 8 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba8

b:0.6
occ:1.00
O6 A:G205 2.6 0.3 1.0
N7 A:G205 3.0 90.7 1.0
C6 A:G205 3.3 94.4 1.0
C5 A:G205 3.4 88.4 1.0
N7 A:G204 4.0 78.0 1.0
C8 A:G205 4.2 90.0 1.0
N1 A:G205 4.6 89.2 1.0
C8 A:G204 4.6 80.9 1.0
C4 A:G205 4.8 81.6 1.0
C5 A:G204 4.9 76.4 1.0
OP1 A:A207 4.9 81.7 1.0
O6 A:G204 4.9 77.7 1.0

Barium binding site 9 out of 21 in 1u9s

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Barium binding site 9 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba9

b:0.7
occ:1.00
OP2 A:A82 4.5 70.6 1.0
N7 A:G83 4.5 96.9 1.0
OP2 A:G83 4.8 93.8 1.0
O6 A:G83 4.8 93.8 1.0
N7 A:A82 4.8 83.9 1.0

Barium binding site 10 out of 21 in 1u9s

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Barium binding site 10 out of 21 in the Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of the Specificity Domain of Ribonuclease P of the A-Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba10

b:1.0
occ:1.00
N6 A:A137 3.3 90.2 1.0
OP2 A:G159 3.6 80.2 1.0
N7 A:G159 3.6 87.5 1.0
N7 A:A137 3.9 89.9 1.0
C6 A:A137 4.1 89.0 1.0
C5 A:A137 4.3 86.9 1.0
C8 A:G159 4.4 87.8 1.0
C5 A:G159 4.4 88.7 1.0
O6 A:G159 4.4 96.0 1.0
OP2 A:C136 4.7 65.1 1.0
OP2 A:A137 4.7 52.9 1.0
C6 A:G159 4.8 91.3 1.0
OP2 A:U158 4.9 84.0 1.0
C8 A:A137 5.0 87.9 1.0

Reference:

A.S.Krasilnikov, Y.Xiao, T.Pan, A.Mondragon. Basis For Structural Diversity in Homologous Rnas. Science V. 306 104 2004.
ISSN: ISSN 0036-8075
PubMed: 15459389
DOI: 10.1126/SCIENCE.1101489
Page generated: Tue Oct 27 17:00:09 2020

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