Atomistry » Calcium » PDB 2hih-2i52 » 2hoo
Atomistry »
  Calcium »
    PDB 2hih-2i52 »
      2hoo »

Calcium in PDB 2hoo: Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine

Protein crystallography data

The structure of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine, PDB code: 2hoo 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 / 3.00
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 61.400, 61.400, 102.900, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 27.5

Calcium Binding Sites:

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

Calcium binding site 1 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 1 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


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 Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca96

b:70.9
occ:1.00
O6 A:G78 2.0 65.4 1.0
O3 A:BFT95 2.3 99.3 1.0
O6 A:G60 2.5 82.9 1.0
O A:HOH93 2.7 31.3 1.0
C6 A:G78 3.0 71.8 1.0
O4 A:U59 3.2 64.5 1.0
N1 A:G78 3.4 72.8 1.0
C6 A:G60 3.4 80.1 1.0
P1 A:BFT95 3.4 89.7 1.0
N1 A:G60 3.6 77.6 1.0
O1 A:BFT95 3.8 90.0 1.0
O2 A:BFT95 4.0 92.6 1.0
N1 A:G72 4.0 0.0 1.0
N2 A:G72 4.1 0.0 1.0
C4 A:U59 4.2 67.9 1.0
C5 A:G78 4.3 77.7 1.0
C2 A:G72 4.4 0.0 1.0
N1 A:A61 4.6 90.1 1.0
C2 A:A61 4.6 88.7 1.0
O7 A:BFT95 4.7 97.5 1.0
N3 A:C77 4.7 88.3 1.0
C2 A:G78 4.7 75.7 1.0
C5 A:G60 4.7 81.4 1.0
C6 A:G72 4.8 0.4 1.0
C5 A:U59 4.9 68.9 1.0
N4 A:C77 4.9 83.8 1.0
C2 A:G60 4.9 75.3 1.0
O6 A:G72 5.0 0.0 1.0
N7 A:G78 5.0 75.7 1.0

Calcium binding site 2 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 2 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


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 Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca97

b:0.9
occ:1.00
N4 A:C77 3.2 83.8 1.0
N2 A:G72 3.2 0.0 1.0
O A:HOH92 3.3 42.5 1.0
O1 A:BFT95 3.4 90.0 1.0
N7 A:G76 3.6 0.6 1.0
O6 A:G76 3.8 0.8 1.0
O2 A:BFT95 4.1 92.6 1.0
N7 A:A75 4.1 93.3 1.0
C2 A:G72 4.2 0.0 1.0
C4 A:C77 4.2 86.1 1.0
N3 A:G72 4.2 0.2 1.0
P1 A:BFT95 4.3 89.7 1.0
C5 A:G76 4.4 0.1 1.0
C6 A:G76 4.4 0.4 1.0
OP2 A:A75 4.6 92.7 1.0
N3 A:C77 4.7 88.3 1.0
C8 A:G76 4.7 0.5 1.0
N6 A:A75 4.7 88.4 1.0
C5 A:A75 4.8 93.0 1.0
C8 A:A75 4.9 96.4 1.0

Calcium binding site 3 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 3 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


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 Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca98

b:80.8
occ:1.00
OP1 A:A80 2.9 0.1 1.0
OP2 A:G81 3.2 88.4 1.0
N7 A:G81 3.8 59.4 1.0
O5' A:A80 3.9 0.6 1.0
O6 A:G83 4.0 66.1 1.0
P A:A80 4.1 0.4 1.0
N7 A:G82 4.1 41.6 1.0
C8 A:G81 4.3 67.7 1.0
OP2 A:U54 4.3 0.4 1.0
P A:G81 4.5 85.7 1.0
C5 A:G81 4.6 64.4 1.0
O5' A:G81 4.7 81.6 1.0
C6 A:G83 4.9 61.4 1.0
O6 A:G82 4.9 57.4 1.0
C8 A:G82 4.9 44.1 1.0
OP2 A:G82 4.9 73.5 1.0
O6 A:G81 5.0 68.4 1.0
C3' A:A80 5.0 84.3 1.0

Calcium binding site 4 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 4 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


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 Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca99

b:0.0
occ:1.00
O6 A:G40 3.6 65.1 1.0
N7 A:G40 4.2 57.7 1.0
C6 A:G40 4.5 63.0 1.0
C5 A:G40 4.7 57.5 1.0
OP2 A:U39 4.8 62.0 1.0

Calcium binding site 5 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 5 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca100

b:0.6
occ:1.00
O2' A:U20 2.8 76.2 1.0
C2 A:A44 3.2 99.7 1.0
C2' A:U20 3.6 72.1 1.0
N1 A:A44 3.7 0.6 1.0
O3' A:U20 3.7 77.0 1.0
OP2 A:A44 3.9 92.9 1.0
OP2 A:G21 3.9 78.5 1.0
OP1 A:G21 4.0 76.8 1.0
P A:G21 4.0 78.7 1.0
C3' A:U20 4.1 72.1 1.0
N3 A:A44 4.1 98.2 1.0
O3' A:A43 4.2 85.1 1.0
O2' A:A43 4.3 78.9 1.0
P A:A44 4.7 91.4 1.0
C6 A:A44 4.9 1.0 1.0
C1' A:U20 5.0 69.6 1.0

Calcium binding site 6 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 6 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca101

b:97.6
occ:1.00
OP2 A:G36 2.6 0.4 1.0
OP2 A:A35 3.0 0.0 1.0
O5' A:A35 3.2 0.5 1.0
OP2 A:A34 3.4 0.0 1.0
N7 A:G36 3.5 80.6 1.0
P A:A35 3.7 0.1 1.0
C8 A:G36 3.8 79.7 1.0
C8 A:A35 3.9 0.8 1.0
P A:G36 4.0 0.6 1.0
C3' A:A35 4.0 0.4 1.0
N7 A:A35 4.1 0.5 1.0
C5' A:A35 4.5 0.6 1.0
OP1 A:A35 4.5 0.5 1.0
P A:A34 4.5 0.0 1.0
O3' A:A35 4.5 0.9 1.0
N9 A:A35 4.6 0.3 1.0
O5' A:G36 4.6 0.1 1.0
C4' A:A35 4.8 0.8 1.0
C5 A:G36 4.8 77.2 1.0
O5' A:A34 4.8 0.0 1.0
C5 A:A35 4.8 98.7 1.0
OP1 A:A34 4.9 0.9 1.0
C2' A:A35 5.0 0.4 1.0
O3' A:A34 5.0 0.1 1.0

Calcium binding site 7 out of 7 in 2hoo

Go back to Calcium Binding Sites List in 2hoo
Calcium binding site 7 out of 7 in the Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An E. Coli Thi-Box Riboswitch Bound to Benfotiamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:0.9
occ:1.00
OP1 A:C55 2.7 0.9 1.0
P A:C55 3.7 0.3 1.0
O5' A:C55 3.7 0.5 1.0
OP2 A:C55 4.3 0.6 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 03:39:28 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