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Calcium 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
Barium (Ba) 9 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Thiamine Pyrophosphate, Barium Ions, PDB code: 2hol:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2hol

Go back to Calcium Binding Sites List in 2hol
Calcium binding site 1 out of 4 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 Calcium with other atoms in the Ca 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:Ca115

b:73.6
occ:1.00
OP1 A:A69 2.2 31.3 1.0
P A:A69 3.7 30.2 1.0
O5' A:A69 4.2 31.9 1.0
C5' A:A69 4.5 29.4 1.0
OP2 A:A69 4.5 32.5 1.0
O3' A:U68 4.7 31.7 1.0

Calcium binding site 2 out of 4 in 2hol

Go back to Calcium Binding Sites List in 2hol
Calcium binding site 2 out of 4 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 Calcium with other atoms in the Ca 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:Ca116

b:49.7
occ:1.00
OP2 A:A91 2.2 32.5 1.0
P A:A91 3.7 32.4 1.0
C3' A:A91 4.3 39.6 1.0
O3' A:C90 4.3 30.9 1.0
O3' A:A91 4.4 44.0 1.0
OP1 A:A91 4.5 32.5 1.0
O5' A:A91 4.7 32.5 1.0
C2' A:A91 5.0 40.5 1.0

Calcium binding site 3 out of 4 in 2hol

Go back to Calcium Binding Sites List in 2hol
Calcium binding site 3 out of 4 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 Calcium with other atoms in the Ca 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:Ca117

b:99.8
occ:1.00
OP1 A:G60 4.3 28.7 1.0
OP1 A:U59 4.6 28.2 1.0
OP2 A:G60 4.7 26.7 1.0
P A:G60 4.9 26.0 1.0

Calcium binding site 4 out of 4 in 2hol

Go back to Calcium Binding Sites List in 2hol
Calcium binding site 4 out of 4 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 Calcium with other atoms in the Ca 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:Ca118

b:85.1
occ:1.00
OP2 A:A67 4.8 40.1 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 03:39:26 2020

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