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Magnesium in PDB 3k0j: Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module

Protein crystallography data

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module, PDB code: 3k0j was solved by N.Kulshina, 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) 29.50 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.250, 71.600, 128.350, 90.00, 94.62, 90.00
R / Rfree (%) 19.7 / 27.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module (pdb code 3k0j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module, PDB code: 3k0j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3k0j

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Magnesium binding site 1 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg701

b:22.2
occ:1.00
O2A E:TPP601 2.3 72.7 1.0
O3B E:TPP601 2.5 98.2 1.0
O3A E:TPP601 2.8 75.9 1.0
PA E:TPP601 3.0 66.7 1.0
PB E:TPP601 3.2 95.8 1.0
O7 E:TPP601 3.6 61.3 1.0
O2B E:TPP601 4.0 0.5 1.0
N7 E:A75 4.0 43.3 1.0
O2' E:G72 4.1 57.1 1.0
OP2 E:A75 4.2 36.9 1.0
O1A E:TPP601 4.3 70.2 1.0
C7 E:TPP601 4.4 61.0 1.0
C8 E:A75 4.5 46.5 1.0
O1B E:TPP601 4.5 96.0 1.0
N7 E:G76 4.7 34.4 1.0
C2' E:G72 4.9 48.8 1.0
O6 E:G76 4.9 42.0 1.0

Magnesium binding site 2 out of 8 in 3k0j

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Magnesium binding site 2 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:32.1
occ:1.00
O1B E:TPP601 1.8 96.0 1.0
O6 E:G78 2.0 56.0 1.0
O6 E:G60 2.1 35.0 1.0
C6 E:G78 2.9 61.8 1.0
O1A E:TPP601 3.0 70.2 1.0
N1 E:G78 3.2 60.3 1.0
C6 E:G60 3.2 31.6 1.0
PB E:TPP601 3.3 95.8 1.0
N1 E:G60 3.7 28.3 1.0
N1 E:A61 3.9 49.9 1.0
O3A E:TPP601 4.0 75.9 1.0
O4 E:U59 4.0 6.0 1.0
C2 E:A61 4.1 47.8 1.0
PA E:TPP601 4.1 66.7 1.0
O2B E:TPP601 4.1 0.5 1.0
O3B E:TPP601 4.3 98.2 1.0
C5 E:G78 4.3 64.7 1.0
C5 E:G60 4.5 30.1 1.0
C2 E:G78 4.5 55.5 1.0
N7 E:G72 4.8 56.6 1.0
C4 E:U59 4.8 12.4 1.0
N3 E:C77 4.9 43.3 1.0
O2A E:TPP601 4.9 72.7 1.0
C8 E:G72 5.0 53.8 1.0

Magnesium binding site 3 out of 8 in 3k0j

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Magnesium binding site 3 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg703

b:21.2
occ:1.00
O6 F:G178 1.8 63.5 1.0
O6 F:G160 2.1 30.5 1.0
C6 F:G178 2.8 63.6 1.0
MG F:MG708 3.0 11.4 1.0
N1 F:G178 3.2 64.3 1.0
C6 F:G160 3.2 29.3 1.0
O3A F:TPP602 3.2 78.0 1.0
O4 F:U159 3.6 23.3 1.0
N1 F:G160 3.7 24.6 1.0
O7 F:TPP602 3.9 64.1 1.0
C5 F:G178 4.2 59.5 1.0
PA F:TPP602 4.2 73.0 1.0
C2 F:A161 4.3 23.5 1.0
N1 F:A161 4.3 32.4 1.0
C4 F:U159 4.5 26.2 1.0
O2B F:TPP602 4.5 91.2 1.0
PB F:TPP602 4.5 87.5 1.0
C5 F:G160 4.5 28.1 1.0
C2 F:G178 4.6 59.3 1.0
N3 F:C177 4.6 30.5 1.0
N4 F:C177 4.8 17.7 1.0
C5 F:U159 4.9 27.2 1.0
N7 F:G178 4.9 54.7 1.0

Magnesium binding site 4 out of 8 in 3k0j

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Magnesium binding site 4 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg704

b:28.2
occ:1.00
O4' E:C74 3.7 47.6 1.0
C1' E:C74 4.0 47.9 1.0
O2' E:C74 4.3 50.9 1.0
C4' E:C74 4.3 49.9 1.0
C2' E:C74 4.8 49.0 1.0

Magnesium binding site 5 out of 8 in 3k0j

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Magnesium binding site 5 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg705

b:26.9
occ:1.00
N7 E:G36 2.7 39.0 1.0
O6 E:G36 2.8 34.2 1.0
C5 E:G36 3.2 34.0 1.0
C6 E:G36 3.2 33.2 1.0
C8 E:G36 3.8 33.3 1.0
N7 E:G37 4.2 31.1 1.0
O6 E:G37 4.2 33.5 1.0
N7 E:A35 4.4 14.4 1.0
C4 E:G36 4.4 29.6 1.0
N1 E:G36 4.5 33.5 1.0
OP2 E:A35 4.7 30.2 1.0
N9 E:G36 4.7 29.1 1.0
C8 E:A35 4.7 17.0 1.0
OP2 E:G36 4.9 33.6 1.0
C6 E:G37 4.9 34.9 1.0
C5 E:G37 4.9 34.7 1.0

Magnesium binding site 6 out of 8 in 3k0j

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Magnesium binding site 6 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg706

b:39.2
occ:1.00
O6 E:G81 3.4 20.0 1.0
N7 E:A80 3.6 41.0 1.0
N6 E:A80 3.7 46.9 1.0
C5 E:A80 4.0 40.5 1.0
C6 E:A80 4.1 45.8 1.0
OP2 E:A80 4.3 64.4 1.0
C6 E:G81 4.4 22.8 1.0
C8 E:A80 4.5 34.4 1.0
O6 E:G82 4.5 13.3 1.0
N7 E:G81 4.6 26.5 1.0
N3 E:G78 4.8 55.1 1.0
N4 E:C58 4.8 27.2 1.0
C5 E:G81 4.9 26.7 1.0

Magnesium binding site 7 out of 8 in 3k0j

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Magnesium binding site 7 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg707

b:43.2
occ:1.00
O6 E:G65 2.1 27.0 1.0
O4 E:U64 2.9 35.5 1.0
C6 E:G65 3.3 33.3 1.0
O6 E:G66 3.5 24.8 1.0
C4 E:U64 3.6 31.2 1.0
N4 E:C74 3.9 43.5 1.0
C5 E:G65 4.0 41.2 1.0
N7 E:G65 4.1 42.9 1.0
C5 E:U64 4.2 38.5 1.0
N6 E:A75 4.2 36.2 1.0
N1 E:G65 4.4 29.1 1.0
C6 E:G66 4.4 29.0 1.0
N4 E:C73 4.4 29.5 1.0
OP2 E:G72 4.5 22.9 1.0
N3 E:U64 4.5 30.8 1.0
C6 E:A75 4.8 39.4 1.0
N1 E:A75 4.9 39.5 1.0

Magnesium binding site 8 out of 8 in 3k0j

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Magnesium binding site 8 out of 8 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thiamine Pyrophosphate and the U1A Crystallization Module within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg708

b:11.4
occ:1.00
O3A F:TPP602 1.9 78.0 1.0
PA F:TPP602 2.5 73.0 1.0
N1 F:G178 2.7 64.3 1.0
O7 F:TPP602 2.7 64.1 1.0
O2A F:TPP602 2.9 68.3 1.0
MG F:MG703 3.0 21.2 1.0
PB F:TPP602 3.0 87.5 1.0
N2 F:G178 3.3 53.4 1.0
O3B F:TPP602 3.4 79.5 1.0
C2 F:G178 3.5 59.3 1.0
C6 F:G178 3.6 63.6 1.0
O6 F:G178 3.6 63.5 1.0
O2B F:TPP602 3.6 91.2 1.0
C7 F:TPP602 3.9 64.8 1.0
O1A F:TPP602 3.9 68.1 1.0
N4 F:C177 4.1 17.7 1.0
O1B F:TPP602 4.4 88.7 1.0
N3 F:G178 4.7 55.1 1.0
C6 F:TPP602 4.8 74.1 1.0
C5 F:G178 4.8 59.5 1.0

Reference:

N.Kulshina, T.E.Edwards, A.R.Ferre-D'amare. Thermodynamic Analysis of Ligand Binding and Ligand Binding-Induced Tertiary Structure Formation By the Thiamine Pyrophosphate Riboswitch. Rna V. 16 186 2010.
ISSN: ISSN 1355-8382
PubMed: 19948769
DOI: 10.1261/RNA.1847310
Page generated: Mon Dec 14 08:21:13 2020

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