Atomistry » Barium » PDB 1djh-2x6b » 2hol
Atomistry »
  Barium »
    PDB 1djh-2x6b »
      2hol »

Barium in PDB 2hol: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions

Protein crystallography data

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions, PDB code: 2hol was solved by T.E.Edwards, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.90
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 65.500, 65.500, 101.700, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 24.4

Other elements in 2hol:

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Calcium (Ca) 4 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions (pdb code 2hol). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions, PDB code: 2hol:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 1 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba106

b:78.5
occ:1.00
 O1B A:TPP105 1.9 55.6 1.0
O2A A:TPP105 2.2 58.8 1.0
O A:HOH102 2.6 42.6 1.0
O A:HOH104 3.2 25.8 1.0
O A:HOH98 3.2 33.1 1.0
PB A:TPP105 3.4 49.4 1.0
PA A:TPP105 3.5 55.4 1.0
O1A A:TPP105 3.8 59.0 1.0
N4 A:C77 3.9 39.9 1.0
N7 A:A75 4.0 32.0 1.0
O3A A:TPP105 4.1 57.2 1.0
O2B A:TPP105 4.2 51.6 1.0
O3B A:TPP105 4.3 54.8 1.0
N6 A:A75 4.6 36.7 1.0
C5 A:A75 4.7 33.5 1.0
C8 A:A75 4.7 31.8 1.0
N7 A:G76 4.8 39.0 1.0
O7 A:TPP105 4.8 56.6 1.0
O6 A:G76 4.9 41.9 1.0
OP2 A:A75 4.9 34.5 1.0
C6 A:A75 4.9 33.6 1.0
O A:HOH96 4.9 17.6 1.0

Barium binding site 2 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 2 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba107

b:67.8
occ:1.00
 O6 A:G60 2.2 26.2 1.0
O A:HOH96 2.4 17.6 1.0
O6 A:G78 2.5 30.4 1.0
O A:HOH97 2.5 30.1 1.0
O2B A:TPP105 2.6 51.6 1.0
O A:HOH99 2.6 18.9 1.0
C6 A:G60 3.2 23.1 1.0
C6 A:G78 3.4 26.9 1.0
O3A A:TPP105 3.5 57.2 1.0
PB A:TPP105 3.6 49.4 1.0
N1 A:G60 3.7 22.8 1.0
O4 A:U59 3.7 29.2 1.0
N1 A:G78 3.7 23.2 1.0
N1 A:A61 4.2 21.4 1.0
N3 A:C77 4.3 39.1 1.0
O A:HOH102 4.4 42.6 1.0
C2 A:A61 4.4 20.5 1.0
C4 A:U59 4.5 29.1 1.0
N4 A:C77 4.5 39.9 1.0
C5 A:G60 4.5 20.9 1.0
O1B A:TPP105 4.5 55.6 1.0
O1A A:TPP105 4.6 59.0 1.0
PA A:TPP105 4.7 55.4 1.0
C5 A:G78 4.7 30.2 1.0
O3B A:TPP105 4.8 54.8 1.0
C4 A:C77 4.8 39.3 1.0
N6 A:A80 4.9 37.4 1.0

Barium binding site 3 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 3 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba108

b:70.7
occ:1.00
 OP1 A:C63 2.2 22.8 1.0
OP2 A:U64 2.4 20.9 1.0
O A:HOH101 2.5 34.4 1.0
P A:C63 3.6 21.5 1.0
P A:U64 3.7 15.4 1.0
OP1 A:U64 4.2 15.5 1.0
O3' A:U62 4.2 21.9 1.0
OP2 A:C63 4.2 20.1 1.0
O3' A:C63 4.4 17.8 1.0
C3' A:C63 4.6 20.3 1.0
O5' A:C63 4.6 22.1 1.0
O5' A:U64 4.8 16.2 1.0
C5' A:C63 4.9 23.9 1.0

Barium binding site 4 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 4 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba109

b:1.0
occ:1.00
 N7 A:A41 2.5 24.8 1.0
C8 A:A41 3.4 25.1 1.0
C5 A:A41 3.6 22.6 1.0
N6 A:A41 3.9 26.5 1.0
C6 A:A41 4.2 22.8 1.0
O2' A:G40 4.3 18.0 1.0
O6 A:G42 4.3 25.3 1.0
N9 A:A41 4.6 23.4 1.0
C4 A:A41 4.8 24.5 1.0

Barium binding site 5 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 5 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba110

b:93.0
occ:1.00
 N7 A:G40 2.5 27.1 1.0
C8 A:G40 3.5 26.2 1.0
C5 A:G40 3.5 27.3 1.0
O6 A:G40 3.6 32.9 1.0
O A:HOH93 3.8 29.1 1.0
C6 A:G40 3.9 29.1 1.0
OP2 A:G40 4.2 18.4 1.0
OP2 A:U39 4.5 16.9 1.0
N9 A:G40 4.7 23.6 1.0
C4 A:G40 4.7 26.6 1.0
C5 A:U39 4.7 18.3 1.0
OP2 A:G42 5.0 21.5 1.0

Barium binding site 6 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 6 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba111

b:0.0
occ:1.00
 OP2 A:A80 3.2 60.4 1.0
N7 A:G81 3.9 43.5 1.0
OP1 A:A80 4.1 59.8 1.0
P A:A80 4.2 59.7 1.0
N7 A:G82 4.3 36.5 1.0
O6 A:G83 4.3 37.9 1.0
OP2 A:G81 4.6 50.6 1.0
C8 A:G81 4.7 44.2 1.0
O6 A:G81 4.7 42.0 1.0
C5 A:G81 4.8 43.9 1.0
O6 A:G82 4.8 37.2 1.0
C6 A:G83 4.9 37.4 1.0

Barium binding site 7 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 7 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba112

b:0.0
occ:1.00
 N7 A:G36 2.7 33.5 1.0
O A:HOH95 3.0 12.5 1.0
C8 A:G36 3.7 31.8 1.0
O6 A:G36 3.7 36.9 1.0
C5 A:G36 3.7 31.9 1.0
OP2 A:A35 3.9 69.6 1.0
C6 A:G36 4.1 32.7 1.0
N7 A:A35 4.1 40.0 1.0
OP2 A:A34 4.3 77.0 1.0
C8 A:A35 4.5 40.7 1.0
OP2 A:G36 4.6 43.3 1.0
N9 A:G36 4.9 31.0 1.0
C4 A:G36 4.9 31.8 1.0
C5 A:A35 4.9 39.9 1.0

Barium binding site 8 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 8 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba113

b:0.0
occ:1.00
 N7 A:G66 3.7 40.9 1.0
O6 A:G66 4.0 43.0 1.0
N6 A:A67 4.3 41.1 1.0
C5 A:G66 4.5 42.0 1.0
C6 A:G66 4.6 42.8 1.0
C8 A:G66 4.7 39.8 1.0
N7 A:A67 4.8 43.7 1.0

Barium binding site 9 out of 9 in 2hol

Go back to Barium Binding Sites List in 2hol
Barium binding site 9 out of 9 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions


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 An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba114

b:85.4
occ:1.00
 O6 A:G40 2.9 32.9 1.0
OP2 A:A43 3.0 24.4 1.0
C6 A:G40 3.8 29.1 1.0
N1 A:G40 3.8 27.3 1.0
P A:A43 4.2 21.2 1.0
OP1 A:A43 4.5 23.8 1.0
O4 A:U39 4.9 19.5 1.0
O5' A:A43 4.9 25.4 1.0

Reference:

T.E.Edwards, A.R.Ferre-D'amare. Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive Rna-Small Molecule Recognition Structure V. 14 1459 2006.
ISSN: ISSN 0969-2126
PubMed: 16962976
DOI: 10.1016/J.STR.2006.07.008
Page generated: Sat Dec 12 01:55:23 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy