Chemical elements
  Magnesium
    Isotopes
    Energy
    Preparation
    Physical Properties
    Chemical Properties
    PDB 101d-1atr
    PDB 1ats-1bup
    PDB 1bvw-1cp8
    PDB 1cqi-1d9d
    PDB 1d9z-1dxe
    PDB 1dxf-1ed9
    PDB 1edr-1f2u
    PDB 1f3f-1fmw
    PDB 1fnm-1g8n
    PDB 1g8t-1gtv
    PDB 1gua-1hnz
    PDB 1hpm-1i95
    PDB 1i96-1iv2
    PDB 1iv3-1jgy
    PDB 1jgz-1k01
    PDB 1k02-1kil
    PDB 1kiz-1l3p
    PDB 1l3r-1lvh
    PDB 1lvk-1mn9
    PDB 1mnd-1n33
    PDB 1n52-1ngg
    PDB 1ngj-1ntb
    PDB 1nu4-1o93
    PDB 1o9t-1ouo
    PDB 1ouq-1pg4
    PDB 1php-1q54
    PDB 1q5h-1qgx
    PDB 1qh1-1r4a
    PDB 1r4x-1rqy
    PDB 1rrf-1s9j
    PDB 1sa0-1svm
    PDB 1svs-1te6
    PDB 1tez-1u0c
    PDB 1u0h-1uhx
    PDB 1uik-1vc9
    PDB 1vcl-1vsd
    PDB 1vst-1wax
    PDB 1wb1-1wzn
    PDB 1x06-1xg4
    PDB 1xhf-1xqa
    PDB 1xr1-1y84
    PDB 1y8a-1yns
    PDB 1yq2-1z0a
    PDB 1z0d-1zc4
    PDB 1zca-1zvq
    PDB 1zvw-2a5l
    PDB 2a5y-2anr
    PDB 2anv-2b8q
    PDB 2b8r-2bku
    PDB 2bm0-2c18
    PDB 2c19-2cic
    PDB 2cie-2d0q
    PDB 2d1k-2dw6
    PDB 2dw7-2egh
    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
    PDB 2q66-2qlx
    PDB 2qm1-2qwy
    PDB 2qx0-2rdr
    PDB 2rds-2uxq
    PDB 2uxr-2vbn
    PDB 2vbu-2vk8
    PDB 2vkf-2w7x
    PDB 2w83-2wi3
    PDB 2wia-2wzd
    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
      3du7
      3duf
      3duq
      3dur
      3dus
      3duu
      3dv0
      3dv3
      3dv4
      3dv6
      3dv9
      3dva
      3dvl
      3dxj
      3dy7
      3dy8
      3dyf
      3dyg
      3dyh
      3dyl
      3dym
      3dyn
      3dyo
      3dyp
      3dys
      3dze
      3dzo
      3e18
      3e1f
      3e22
      3e25
      3e27
      3e2d
      3e2j
      3e2v
      3e35
      3e3z
      3e48
      3e4c
      3e4d
      3e4g
      3e4o
      3e54
      3e5h
      3e5z
      3e70
      3e76
      3e7e
      3e81
      3e84
    PDB 3e8m-3eni
    PDB 3eno-3ezw
    PDB 3ezx-3fcs
    PDB 3fct-3fqr
    PDB 3fqt-3g3y
    PDB 3g45-3gj3
    PDB 3gj4-3gve
    PDB 3gvn-3hdz
    PDB 3hfw-3hrz
    PDB 3hs0-3hzt
    PDB 3hzv-3iaf
    PDB 3iak-3ilo
    PDB 3imd-3jvt
    PDB 3jvv-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 T. Brucei Farnesyl Diphosphate Synthase Complexed With Bisphosphonate Bph-461 and Isopentyl Diphosphate (pdb 3dyf)






The binding sites of Magnesium atom in the structure of T. Brucei Farnesyl Diphosphate Synthase Complexed With Bisphosphonate Bph-461 and Isopentyl Diphosphate (pdb code 3dyf). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom.
The 3dyf structure was solved by R.CAO, Y.GAO, H.ROBINSON, A.GODDARD, E.OLDFIELD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)29.5-2.6
Space groupC121
a (A)133.939
b (A)117.898
c (A)63.274
alpha (°)90.00
beta (°)111.27
gamma (°)90.00
Rfactor (%)20.1
Rfree (%)26.8


Magnesium Binding Sites:

Magnesium binding site 1 out of 6 in 3dyf


Magnesium binding site 1 out of 6 in 3dyf
Click to enlarge
stereopicture of Magnesium binding site 1 out of 6 in 3dyf
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3dyf. 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: A: Asp103, A: Asp104, A: Asp107, A: Ser109, A: Arg112, A: Thr272, A: Mg3003, A: Mg3004, A: Ni93001, A: Hoh5001, A: Hoh5002, A: Hoh5003, A: Hoh5014, A: Hoh5027, A: Hoh5048, A: Hoh5143, A: Hoh5225,

conact list:


AtomAtomDistance (A)
MgO A:Asp1034.21
MgCB A:Asp1034.41
MgOD2 A:Asp1032.22
MgC A:Asp1034.48
MgOD1 A:Asp1033.50
MgCG A:Asp1033.15
MgN A:Asp1044.82
MgOD1 A:Asp1043.94
MgCA A:Asp1044.91
MgCB A:Asp1073.62
MgOD2 A:Asp1072.15
MgOD1 A:Asp1074.30
MgCG A:Asp1073.20
MgCB A:Ser1094.98
MgOG A:Ser1093.76
MgNH2 A:Arg1124.03
MgOG1 A:Thr2724.99
MgMG A:Mg30034.91
MgMG A:Mg30044.03
MgO5 A:Ni930014.64
MgP2 A:Ni930013.29
MgP1 A:Ni930013.55
MgC1 A:Ni930013.86
MgO1 A:Ni930013.26
MgO3 A:Ni930012.43
MgC2 A:Ni930014.13
MgO7 A:Ni930012.39
MgO4 A:Ni930014.80
MgO6 A:Ni930014.17
MgO A:Hoh50014.06
MgO A:Hoh50024.95
MgO A:Hoh50034.19
MgO A:Hoh50144.61
MgO A:Hoh50274.95
MgO A:Hoh50484.74
MgO A:Hoh51433.49
MgO A:Hoh52252.03

interactive model:


Magnesium binding site 2 out of 6 in 3dyf


Magnesium binding site 2 out of 6 in 3dyf
Click to enlarge
stereopicture of Magnesium binding site 2 out of 6 in 3dyf
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3dyf. 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: A: Gln252, A: Asp255, A: Asp259, A: Lys269, A: Asp273, A: Mg3002, A: Ni93001, A: Hoh5001, A: Hoh5060, A: Hoh5143, A: Hoh5225,

conact list:


AtomAtomDistance (A)
MgOE1 A:Gln2524.95
MgO A:Asp2554.13
MgCB A:Asp2554.49
MgOD2 A:Asp2552.40
MgC A:Asp2554.51
MgOD1 A:Asp2553.49
MgCG A:Asp2553.22
MgCB A:Asp2594.14
MgOD2 A:Asp2594.91
MgOD1 A:Asp2593.77
MgCG A:Asp2594.10
MgCE A:Lys2694.83
MgNZ A:Lys2694.75
MgOD2 A:Asp2734.37
MgOD1 A:Asp2734.57
MgCG A:Asp2734.88
MgMG A:Mg30024.91
MgO5 A:Ni930012.75
MgP2 A:Ni930013.04
MgP1 A:Ni930013.60
MgC1 A:Ni930013.61
MgO1 A:Ni930014.53
MgO3 A:Ni930012.66
MgO2 A:Ni930013.61
MgO7 A:Ni930014.41
MgO4 A:Ni930014.83
MgO6 A:Ni930012.55
MgO A:Hoh50012.40
MgO A:Hoh50604.41
MgO A:Hoh51434.44
MgO A:Hoh52254.17

interactive model:


Magnesium binding site 3 out of 6 in 3dyf


Magnesium binding site 3 out of 6 in 3dyf
Click to enlarge
stereopicture of Magnesium binding site 3 out of 6 in 3dyf
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3dyf. 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: A: Asp103, A: Asp107, A: Gln172, A: Asp175, A: Lys212, A: Lys278, A: Mg3002, A: Ni93001, A: Hoh5002, A: Hoh5003, A: Hoh5060, A: Hoh5225,

conact list:


AtomAtomDistance (A)
MgCB A:Asp1034.68
MgOD2 A:Asp1033.63
MgOD1 A:Asp1032.42
MgCG A:Asp1033.36
MgOD2 A:Asp1073.00
MgOD1 A:Asp1073.59
MgCG A:Asp1073.69
MgNE2 A:Gln1724.01
MgOE1 A:Gln1723.92
MgCD A:Gln1724.40
MgCB A:Asp1754.90
MgOD2 A:Asp1753.47
MgOD1 A:Asp1754.08
MgCG A:Asp1753.91
MgNZ A:Lys2124.08
MgNZ A:Lys2784.40
MgMG A:Mg30024.03
MgN A:Ni930014.31
MgP1 A:Ni930012.85
MgC1 A:Ni930014.29
MgC2 A:Ni930014.42
MgC5 A:Ni930014.88
MgC7 A:Ni930014.84
MgC3 A:Ni930014.29
MgO7 A:Ni930012.10
MgO4 A:Ni930012.57
MgO6 A:Ni930013.84
MgO A:Hoh50021.76
MgO A:Hoh50032.13
MgO A:Hoh50604.14
MgO A:Hoh52254.35

interactive model:


Magnesium binding site 4 out of 6 in 3dyf


Magnesium binding site 4 out of 6 in 3dyf
Click to enlarge
stereopicture of Magnesium binding site 4 out of 6 in 3dyf
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3dyf. 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: B: Asp103, B: Asp104, B: Asp107, B: Ser109, B: Arg112, B: Mg4003, B: Mg4004, B: Ni94001, B: Hoh5015, B: Hoh5067, B: Hoh5116, B: Hoh5117, B: Hoh5122, B: Hoh5161,

conact list:


AtomAtomDistance (A)
MgO B:Asp1034.46
MgCB B:Asp1034.47
MgOD2 B:Asp1033.40
MgC B:Asp1034.67
MgOD1 B:Asp1032.09
MgCG B:Asp1033.09
MgN B:Asp1044.98
MgOD1 B:Asp1044.50
MgCB B:Asp1073.56
MgOD2 B:Asp1072.17
MgOD1 B:Asp1074.32
MgCG B:Asp1073.20
MgOG B:Ser1093.91
MgNH2 B:Arg1124.47
MgMG B:Mg40034.57
MgMG B:Mg40043.86
MgO5 B:Ni940014.36
MgP2 B:Ni940013.03
MgP1 B:Ni940013.37
MgC1 B:Ni940013.68
MgO1 B:Ni940013.10
MgO3 B:Ni940012.10
MgC2 B:Ni940014.06
MgO7 B:Ni940012.31
MgO4 B:Ni940014.68
MgO6 B:Ni940013.91
MgO B:Hoh50154.51
MgO B:Hoh50674.90
MgO B:Hoh51163.54
MgO B:Hoh51174.92
MgO B:Hoh51224.44
MgO B:Hoh51614.01

interactive model:


Magnesium binding site 5 out of 6 in 3dyf


Magnesium binding site 5 out of 6 in 3dyf
Click to enlarge
stereopicture of Magnesium binding site 5 out of 6 in 3dyf
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3dyf. 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: B: Gln252, B: Asp255, B: Asp256, B: Asp259, B: Lys269, B: Asp273, B: Mg4002, B: Ni94001, B: Hoh5116, B: Hoh5117, B: Hoh5161, B: Hoh5264,

conact list:


AtomAtomDistance (A)
MgNE2 B:Gln2524.48
MgO B:Asp2554.40
MgCB B:Asp2554.50
MgOD2 B:Asp2552.39
MgC B:Asp2554.72
MgOD1 B:Asp2553.11
MgCG B:Asp2553.08
MgOD1 B:Asp2564.73
MgCB B:Asp2594.69
MgOD1 B:Asp2594.03
MgCG B:Asp2594.62
MgCE B:Lys2694.83
MgNZ B:Lys2694.60
MgOD2 B:Asp2734.36
MgOD1 B:Asp2734.66
MgCG B:Asp2734.95
MgMG B:Mg40024.57
MgO5 B:Ni940012.75
MgP2 B:Ni940012.95
MgP1 B:Ni940013.23
MgC1 B:Ni940013.29
MgO1 B:Ni940014.47
MgO3 B:Ni940012.69
MgC2 B:Ni940014.83
MgO2 B:Ni940013.24
MgO7 B:Ni940014.16
MgO4 B:Ni940014.38
MgO6 B:Ni940012.16
MgO B:Hoh51164.46
MgO B:Hoh51174.27
MgO B:Hoh51612.40
MgO B:Hoh52642.19

interactive model:


Magnesium binding site 6 out of 6 in 3dyf


Magnesium binding site 6 out of 6 in 3dyf
Click to enlarge
stereopicture of Magnesium binding site 6 out of 6 in 3dyf
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3dyf. 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: B: Asp103, B: Asp107, B: Gln172, B: Asp175, B: Lys212, B: Lys278, B: Mg4002, B: Ni94001, B: Hoh5004, B: Hoh5117, B: Hoh5122,

conact list:


AtomAtomDistance (A)
MgCB B:Asp1034.84
MgOD2 B:Asp1032.46
MgOD1 B:Asp1033.96
MgCG B:Asp1033.56
MgCB B:Asp1074.50
MgOD2 B:Asp1072.40
MgOD1 B:Asp1072.95
MgCG B:Asp1073.02
MgNE2 B:Gln1724.78
MgOE1 B:Gln1724.77
MgCB B:Asp1754.92
MgOD2 B:Asp1753.79
MgOD1 B:Asp1753.23
MgCG B:Asp1753.74
MgNZ B:Lys2124.62
MgCE B:Lys2784.45
MgNZ B:Lys2784.44
MgMG B:Mg40023.86
MgP1 B:Ni940013.32
MgC1 B:Ni940014.80
MgO3 B:Ni940015.00
MgO7 B:Ni940012.25
MgO4 B:Ni940013.30
MgO6 B:Ni940014.13
MgO B:Hoh50042.27
MgO B:Hoh51173.72
MgO B:Hoh51224.80

interactive model:




© Copyright 2008-2012 by atomistry.com