Atomistry » Barium » PDB 2y5y-4e60 » 3oxj
Atomistry »
  Barium »
    PDB 2y5y-4e60 »
      3oxj »

Barium in PDB 3oxj: Crystal Structure of Glycine Riboswitch, Soaked in BA2+

Protein crystallography data

The structure of Crystal Structure of Glycine Riboswitch, Soaked in BA2+, PDB code: 3oxj was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.215, 84.215, 201.382, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 22.4

Other elements in 3oxj:

The structure of Crystal Structure of Glycine Riboswitch, Soaked in BA2+ also contains other interesting chemical elements:

Magnesium (Mg) 21 atoms

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+ (pdb code 3oxj). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 24 binding sites of Barium where determined in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+, PDB code: 3oxj:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 1 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba201

b:0.8
occ:1.00
O6 A:GDP1 3.3 0.2 1.0
N7 A:GDP1 3.5 0.4 1.0
C5 A:GDP1 4.1 0.4 1.0
C6 A:GDP1 4.1 0.7 1.0
C8 A:GDP1 4.6 0.7 1.0

Barium binding site 2 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 2 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba202

b:0.8
occ:1.00
BA A:BA222 2.3 0.7 1.0
O6 A:G80 2.6 92.2 1.0
C6 A:G80 3.7 92.1 1.0
O6 A:G8 3.9 90.7 1.0
BA A:BA204 4.0 0.3 1.0
N7 A:G80 4.3 93.5 1.0
BA A:BA203 4.3 0.0 1.0
C5 A:G80 4.3 92.6 1.0
OP2 A:G79 4.4 89.5 1.0
N7 A:G79 4.4 93.7 1.0
C6 A:G8 4.6 89.2 1.0
N7 A:G8 4.7 87.6 1.0
OP2 A:A78 4.7 91.2 1.0
N1 A:G80 4.8 91.5 1.0
O6 A:G79 4.9 93.1 1.0
C5 A:G8 5.0 88.0 1.0

Barium binding site 3 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 3 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba203

b:0.0
occ:1.00
O6 A:G8 2.7 90.7 1.0
C6 A:G8 3.9 89.2 1.0
BA A:BA222 4.1 0.7 1.0
BA A:BA202 4.3 0.8 1.0
N1 A:G8 4.4 89.4 1.0
O4 A:U6 4.5 98.5 1.0
N7 A:G80 4.5 93.5 1.0

Barium binding site 4 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 4 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba204

b:0.3
occ:1.00
O6 A:G79 2.6 93.1 1.0
O6 A:G80 3.5 92.2 1.0
C6 A:G79 3.8 93.2 1.0
N1 A:G80 3.8 91.5 1.0
C6 A:G80 3.9 92.1 1.0
BA A:BA202 4.0 0.8 1.0
OP2 A:A78 4.2 91.2 1.0
N7 A:G79 4.4 93.7 1.0
C5 A:G79 4.5 93.8 1.0
OP2 A:A77 4.5 92.2 1.0
OP1 A:A77 4.8 91.6 1.0
C2 A:G80 4.8 91.6 1.0
N1 A:G79 4.9 93.1 1.0
C5 A:G80 5.0 92.6 1.0

Barium binding site 5 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 5 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba205

b:0.8
occ:1.00
OP2 A:A75 2.7 95.2 1.0
OP1 A:A22 2.9 90.6 1.0
P A:A22 4.0 91.1 1.0
O3' A:A21 4.1 89.6 1.0
P A:A75 4.1 93.7 1.0
O5' A:A75 4.7 93.8 1.0
N7 A:A75 4.7 96.1 1.0
OP2 A:C74 4.8 97.8 1.0
C3' A:C74 4.8 94.0 1.0
O3' A:C74 4.8 93.5 1.0
C8 A:A75 4.9 95.6 1.0
OP2 A:A22 4.9 92.4 1.0
OP1 A:A14 4.9 96.6 1.0
OP2 A:A14 5.0 94.8 1.0

Barium binding site 6 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 6 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba206

b:0.8
occ:1.00
OP1 A:A33 3.7 86.5 1.0
OP1 B:A33 3.9 80.5 1.0
OP1 B:C66 4.4 88.1 1.0
OP1 A:C66 4.4 88.5 1.0

Barium binding site 7 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 7 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba207

b:0.5
occ:1.00
O6 B:G80 2.9 82.6 1.0
BA B:BA208 3.0 0.5 1.0
BA B:BA223 3.2 0.7 1.0
N7 B:G79 3.4 86.0 1.0
OP2 B:A78 3.7 90.7 1.0
C6 B:G80 3.8 81.5 1.0
O6 B:G79 4.0 86.5 1.0
OP2 B:G79 4.2 86.0 1.0
N7 B:G80 4.2 81.9 1.0
C8 B:G79 4.3 86.2 1.0
C5 B:G79 4.3 86.0 1.0
C5 B:G80 4.3 81.4 1.0
O5' B:A78 4.5 90.5 1.0
P B:A78 4.5 91.4 1.0
C6 B:G79 4.6 85.8 1.0
O6 B:G8 4.8 79.0 1.0
N1 B:G80 4.9 81.3 1.0

Barium binding site 8 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 8 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba208

b:0.5
occ:1.00
O6 B:G79 2.8 86.5 1.0
BA B:BA207 3.0 0.5 1.0
O6 B:G80 3.3 82.6 1.0
C6 B:G80 3.8 81.5 1.0
C6 B:G79 3.9 85.8 1.0
N1 B:G80 4.0 81.3 1.0
OP2 B:A77 4.1 94.1 1.0
N7 B:G79 4.4 86.0 1.0
C5 B:G79 4.5 86.0 1.0
OP2 B:A78 4.6 90.7 1.0
OP1 B:A77 4.7 93.6 1.0
BA B:BA223 4.7 0.7 1.0
C5 B:G80 4.8 81.4 1.0
P B:A77 4.9 93.8 1.0

Barium binding site 9 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 9 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba209

b:0.2
occ:1.00
O6 B:G8 2.8 79.0 1.0
C6 B:G8 3.8 78.2 1.0
N1 B:G8 4.2 78.0 1.0
BA B:BA223 4.3 0.7 1.0
O4 B:U6 4.4 87.2 1.0
O6 B:G7 4.6 86.6 1.0
N7 B:G80 4.9 81.9 1.0
C4 B:U6 4.9 86.8 1.0

Barium binding site 10 out of 24 in 3oxj

Go back to Barium Binding Sites List in 3oxj
Barium binding site 10 out of 24 in the Crystal Structure of Glycine Riboswitch, Soaked in BA2+


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 Glycine Riboswitch, Soaked in BA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba210

b:0.9
occ:1.00
N7 B:G25 3.7 85.8 1.0
N7 B:G26 3.7 88.6 1.0
O6 B:G25 4.1 85.8 1.0
C5 B:G25 4.4 86.2 1.0
O6 B:G26 4.5 87.6 1.0
C6 B:G25 4.6 86.0 1.0
C8 B:G26 4.6 89.3 1.0
C8 B:G25 4.6 86.4 1.0
C5 B:G26 4.7 88.5 1.0
C6 B:G26 5.0 88.1 1.0

Reference:

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Tue Oct 27 17:00:46 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy