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    PDB 1ouq-1pg4
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    PDB 1xr1-1y84
    PDB 1y8a-1yns
    PDB 1yq2-1z0a
    PDB 1z0d-1zc4
    PDB 1zca-1zvq
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    PDB 2a5y-2anr
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    PDB 2b8r-2bku
    PDB 2bm0-2c18
    PDB 2c19-2cic
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    PDB 2eh3-2f6t
    PDB 2f6v-2fmh
    PDB 2fmk-2g3h
    PDB 2g3s-2gl5
    PDB 2gl6-2h7v
    PDB 2h7x-2hne
    PDB 2hny-2i34
    PDB 2i3d-2io7
    PDB 2io8-2j3e
    PDB 2j3q-2jg1
    PDB 2jg2-2nvu
    PDB 2nvx-2oem
    PDB 2ofw-2our
    PDB 2ous-2pcl
    PDB 2pda-2px3
    PDB 2pxi-2q5z
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    PDB 2w83-2wi3
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    PDB 2wzg-2xcp
    PDB 2xdg-2y0s
    PDB 2y3p-2z4r
    PDB 2z4s-2zjy
    PDB 2zkj-301d
    PDB 302d-3a5k
    PDB 3a5l-3ak8
    PDB 3ak9-3bb3
    PDB 3bb4-3bsu
    PDB 3btx-3c95
    PDB 3c9h-3ckg
    PDB 3clc-3cxc
    PDB 3cxo-3der
    PDB 3des-3du3
    PDB 3du7-3e84
    PDB 3e8m-3eni
    PDB 3eno-3ezw
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    PDB 3fqt-3g3y
    PDB 3g45-3gj3
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    PDB 3iak-3ilo
    PDB 3imd-3jvt
    PDB 3jvv-3ka6
      3jvv
      3jw7
      3jwg
      3jwq
      3jwr
      3jxq
      3jxu
      3jys
      3jyt
      3jyy
      3jz0
      3jzm
      3jzu
      3k09
      3k0a
      3k0c
      3k0e
      3k0f
      3k0j
      3k1e
      3k1g
      3k1s
      3k1u
      3k2g
      3k3b
      3k3e
      3k3h
      3k4i
      3k4s
      3k4z
      3k57
      3k58
      3k59
      3k5e
      3k5h
      3k5i
      3k5l
      3k6q
      3k6s
      3k71
      3k8d
      3k8k
      3k8t
      3k8y
      3k9f
      3k9l
      3k9n
      3ka3
      3ka4
      3ka6
    PDB 3ka8-3kkp
    PDB 3kkq-3kxi
    PDB 3kxo-3ldw
    PDB 3lee-3lwm
    PDB 3lwn-3mey
    PDB 3mf4-3n23
    PDB 3n2a-3nkv
    PDB 3nl3-3ocm
    PDB 3ocu-3oiu
    PDB 3oiv-3oye
    PDB 3oyf-3pu9
    PDB 3pwx-3rmj
    PDB 3ro8-3t3p
    PDB 3t5t-3ukd
    PDB 3umm-3v9w
    PDB 3v9x-412d
    PDB 421p-4aov
    PDB 4ap5-4dg1
    PDB 4dh1-4dug
    PDB 4dwd-4en4
    PDB 4en5-4fk1
    PDB 4fkx-8ici
    PDB 8ruc-9rub

Magnesium in the structure of Crystal Structure of The E. Coli Thim Riboswitch in Complex With Thiamine Pyrophosphate and the U1A Crystallization Module (pdb 3k0j)






The binding sites of Magnesium atom in the structure of 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 with 5.0 Angstroms radius around Magnesium atom.
The 3k0j structure was solved by N.KULSHINA, T.E.EDWARDS, A.R.FERRE-D'AMARE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)29.5-3.1
Space groupP1211
a (A)52.250
b (A)71.600
c (A)128.350
alpha (°)90.00
beta (°)94.62
gamma (°)90.00
Rfactor (%)19.7
Rfree (%)27.9


Magnesium Binding Sites:

Magnesium binding site 1 out of 8 in 3k0j


Magnesium binding site 1 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 1 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: G72, E: A75, E: G76, E: Tpp601,

conact list:


AtomAtomDistance (A)
MgC2' E:G724.94
MgO2' E:G724.11
MgC8 E:A754.52
MgN7 E:A754.04
MgOP2 E:A754.25
MgN7 E:G764.69
MgO6 E:G764.94
MgO3B E:Tpp6012.54
MgPA E:Tpp6013.00
MgO2A E:Tpp6012.34
MgO1B E:Tpp6014.53
MgPB E:Tpp6013.20
MgC7 E:Tpp6014.44
MgO2B E:Tpp6013.96
MgO7 E:Tpp6013.58
MgO3A E:Tpp6012.82
MgO1A E:Tpp6014.34

interactive model:


Magnesium binding site 2 out of 8 in 3k0j


Magnesium binding site 2 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 2 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: U59, E: G60, E: A61, E: G72, E: C77, E: G78, E: Tpp601,

conact list:


AtomAtomDistance (A)
MgC4 E:U594.82
MgO4 E:U594.01
MgC6 E:G603.20
MgN1 E:G603.71
MgC5 E:G604.46
MgO6 E:G602.10
MgC2 E:A614.06
MgN1 E:A613.88
MgC8 E:G724.96
MgN7 E:G724.80
MgN3 E:C774.91
MgC2 E:G784.51
MgC6 E:G782.94
MgN1 E:G783.16
MgC5 E:G784.31
MgO6 E:G782.04
MgO3B E:Tpp6014.28
MgPA E:Tpp6014.07
MgO2A E:Tpp6014.93
MgO1B E:Tpp6011.82
MgPB E:Tpp6013.33
MgO2B E:Tpp6014.12
MgO3A E:Tpp6013.98
MgO1A E:Tpp6013.02

interactive model:


Magnesium binding site 3 out of 8 in 3k0j


Magnesium binding site 3 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 3 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: F: U159, F: G160, F: A161, F: C177, F: G178, F: Tpp602, F: Mg708,

conact list:


AtomAtomDistance (A)
MgC5 F:U1594.90
MgC4 F:U1594.46
MgO4 F:U1593.62
MgC6 F:G1603.24
MgN1 F:G1603.71
MgC5 F:G1604.53
MgO6 F:G1602.14
MgC2 F:A1614.34
MgN1 F:A1614.35
MgN3 F:C1774.60
MgN4 F:C1774.78
MgC2 F:G1784.57
MgC6 F:G1782.83
MgN1 F:G1783.20
MgC5 F:G1784.17
MgN7 F:G1784.91
MgO6 F:G1781.82
MgPA F:Tpp6024.22
MgPB F:Tpp6024.53
MgO2B F:Tpp6024.50
MgO7 F:Tpp6023.86
MgO3A F:Tpp6023.25
MgMG F:Mg7082.96

interactive model:


Magnesium binding site 4 out of 8 in 3k0j


Magnesium binding site 4 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 4 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: C74,

conact list:


AtomAtomDistance (A)
MgC1' E:C744.03
MgO4' E:C743.70
MgC2' E:C744.77
MgC4' E:C744.32
MgO2' E:C744.27

interactive model:


Magnesium binding site 5 out of 8 in 3k0j


Magnesium binding site 5 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 5 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: A35, E: G36, E: G37,

conact list:


AtomAtomDistance (A)
MgC8 E:A354.72
MgN7 E:A354.40
MgOP2 E:A354.65
MgN9 E:G364.70
MgC8 E:G363.77
MgC6 E:G363.24
MgN1 E:G364.54
MgC5 E:G363.18
MgN7 E:G362.66
MgC4 E:G364.42
MgOP2 E:G364.90
MgO6 E:G362.82
MgC6 E:G374.92
MgC5 E:G374.93
MgN7 E:G374.23
MgO6 E:G374.24

interactive model:


Magnesium binding site 6 out of 8 in 3k0j


Magnesium binding site 6 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 6 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: C58, E: G78, E: A80, E: G81, E: G82,

conact list:


AtomAtomDistance (A)
MgN4 E:C584.80
MgN3 E:G784.80
MgC8 E:A804.51
MgC6 E:A804.11
MgC5 E:A804.02
MgN6 E:A803.74
MgN7 E:A803.65
MgOP2 E:A804.34
MgC6 E:G814.41
MgC5 E:G814.89
MgN7 E:G814.57
MgO6 E:G813.36
MgO6 E:G824.52

interactive model:


Magnesium binding site 7 out of 8 in 3k0j


Magnesium binding site 7 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 7 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: E: U64, E: G65, E: G66, E: G72, E: C73, E: C74, E: A75,

conact list:


AtomAtomDistance (A)
MgN3 E:U644.53
MgC5 E:U644.18
MgC4 E:U643.62
MgO4 E:U642.90
MgC6 E:G653.27
MgN1 E:G654.39
MgC5 E:G654.04
MgN7 E:G654.08
MgO6 E:G652.11
MgC6 E:G664.40
MgO6 E:G663.51
MgOP2 E:G724.48
MgN4 E:C734.41
MgN4 E:C743.94
MgC6 E:A754.83
MgN1 E:A754.91
MgN6 E:A754.19

interactive model:


Magnesium binding site 8 out of 8 in 3k0j


Magnesium binding site 8 out of 8 in 3k0j
Click to enlarge
stereopicture of Magnesium binding site 8 out of 8 in 3k0j
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3k0j. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: F: C177, F: G178, F: Tpp602, F: Mg703,

conact list:


AtomAtomDistance (A)
MgN4 F:C1774.15
MgN3 F:G1784.73
MgN2 F:G1783.31
MgC2 F:G1783.45
MgC6 F:G1783.56
MgN1 F:G1782.67
MgC5 F:G1784.83
MgO6 F:G1783.58
MgO3B F:Tpp6023.35
MgPA F:Tpp6022.53
MgO2A F:Tpp6022.91
MgO1B F:Tpp6024.35
MgC6 F:Tpp6024.79
MgPB F:Tpp6023.05
MgC7 F:Tpp6023.93
MgO2B F:Tpp6023.64
MgO7 F:Tpp6022.73
MgO3A F:Tpp6021.87
MgO1A F:Tpp6023.95
MgMG F:Mg7032.96

interactive model:




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