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Strontium in PDB 4lck: Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna

Protein crystallography data

The structure of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna, PDB code: 4lck was solved by J.Zhang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.42 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 100.382, 108.474, 266.886, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 25.1

Other elements in 4lck:

The structure of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Strontium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 79;

Binding sites:

The binding sites of Strontium atom in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna (pdb code 4lck). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 79 binding sites of Strontium where determined in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna, PDB code: 4lck:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 79 in 4lck

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Strontium binding site 1 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr101

b:0.7
occ:1.00
N7 B:G72 3.9 66.3 1.0
OP1 B:A74 4.3 60.9 1.0
C5 B:G72 4.5 60.2 1.0
C8 B:G72 4.5 60.0 1.0
O6 B:G72 4.7 96.4 1.0
C6 B:G72 4.8 78.5 1.0
OP2 B:A74 4.8 75.9 1.0
OP2 B:A73 4.8 72.0 1.0

Strontium binding site 2 out of 79 in 4lck

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Strontium binding site 2 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr102

b:0.7
occ:1.00
O B:HOH204 2.9 55.5 1.0
O B:HOH201 2.9 55.6 1.0
O B:HOH207 3.1 42.5 1.0
N7 B:G51 4.3 79.2 1.0
OP2 B:G51 4.9 70.5 1.0
OP2 B:G50 5.0 88.1 1.0

Strontium binding site 3 out of 79 in 4lck

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Strontium binding site 3 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr103

b:0.2
occ:1.00
O4 B:U54 2.8 84.9 1.0
C4 B:U54 3.8 77.7 1.0
O B:HOH202 4.1 40.5 1.0
OP2 B:U53 4.3 78.5 1.0
C5 B:U54 4.4 89.3 1.0
OP2 B:G52 4.7 83.4 1.0
OP1 B:G56 4.7 75.8 1.0
C5 B:U53 5.0 72.8 1.0
N3 B:U54 5.0 65.9 1.0

Strontium binding site 4 out of 79 in 4lck

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Strontium binding site 4 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr104

b:0.2
occ:1.00
O6 B:G69 3.4 74.9 1.0
SR B:SR114 3.6 0.1 1.0
N7 B:G69 3.8 69.8 1.0
C6 B:G69 4.1 69.7 1.0
C5 B:G69 4.3 61.2 1.0
O6 B:G70 4.3 81.8 1.0
C8 B:G69 4.9 70.9 1.0

Strontium binding site 5 out of 79 in 4lck

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Strontium binding site 5 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr105

b:0.4
occ:1.00
O3' B:U19 3.4 86.2 1.0
O2' B:U19 3.8 0.2 1.0
C3' B:U19 4.0 0.4 1.0
OP1 C:C64 4.4 85.5 1.0
OP1 B:A20 4.4 0.1 1.0
OP1 B:G21 4.4 0.1 1.0
C2' B:U19 4.4 1.0 1.0
OP2 B:G21 4.5 0.8 1.0
P B:A20 4.7 0.8 1.0
OP2 B:U19 4.9 95.0 1.0
C3' B:A20 4.9 0.6 1.0
OP1 C:U65 4.9 97.3 1.0
P B:G21 4.9 0.6 1.0

Strontium binding site 6 out of 79 in 4lck

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Strontium binding site 6 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr106

b:0.1
occ:1.00
N7 B:A6 4.2 88.8 1.0
N6 B:A6 4.6 70.0 1.0
OP2 B:G5 4.7 0.4 1.0
N7 B:G5 4.7 72.5 1.0
OP2 B:A6 4.9 98.5 1.0

Strontium binding site 7 out of 79 in 4lck

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Strontium binding site 7 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr107

b:0.4
occ:1.00
OP2 B:A14 4.2 0.3 1.0
OP2 B:G15 4.6 0.2 1.0
OP1 B:A6 4.7 0.6 1.0

Strontium binding site 8 out of 79 in 4lck

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Strontium binding site 8 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr108

b:0.9
occ:1.00
SR B:SR110 4.1 0.5 1.0
OP2 B:G5 4.3 0.4 1.0
OP1 B:C61 4.4 0.5 1.0
OP2 B:C79 4.9 76.7 1.0
OP2 B:C61 5.0 66.9 1.0

Strontium binding site 9 out of 79 in 4lck

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Strontium binding site 9 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr109

b:0.4
occ:1.00
O6 B:G48 3.4 88.5 1.0
O6 B:G7 3.7 80.9 1.0
N7 B:G48 3.9 69.4 1.0
N4 B:C49 4.0 86.6 1.0
C6 B:G48 4.2 83.1 1.0
C6 B:G7 4.3 80.8 1.0
SR B:SR115 4.3 0.8 1.0
C5 B:G48 4.4 75.8 1.0
O6 B:G63 4.5 95.3 1.0
O4 B:U64 4.6 76.8 1.0
N4 B:C65 4.7 69.1 1.0
C5 B:G7 4.7 78.6 1.0
N7 B:G7 4.7 76.9 1.0

Strontium binding site 10 out of 79 in 4lck

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Strontium binding site 10 out of 79 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr110

b:0.5
occ:1.00
OP1 B:G5 3.7 99.8 1.0
SR B:SR108 4.1 0.9 1.0
OP2 B:G5 4.2 0.4 1.0
P B:G5 4.5 97.1 1.0
OP2 B:C60 4.5 51.9 1.0
OP1 B:C60 4.8 66.3 1.0

Reference:

J.Zhang, A.R.Ferre-D'amare. Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna. Nature V. 500 363 2013.
ISSN: ISSN 0028-0836
PubMed: 23892783
DOI: 10.1038/NATURE12440
Page generated: Wed Dec 16 02:24:04 2020

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