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  Praseodymium
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    PDB 1k0z-4flb
      1k0z
      2f1r
      2if5
      2isn
      2vsy
      2vxb
      2vxc
      2wvi
      2znr
      3fou
      3mvc
      4afi
      4flb

Praseodymium in the structure of High Resolution Crystal Structure Of the Heme Domain of Glb-6 From C. Elegans (pdb 3mvc)






The binding sites of Praseodymium atom in the structure of High Resolution Crystal Structure Of the Heme Domain of Glb-6 From C. Elegans (pdb code 3mvc). This binding sites where shown with 5.0 Angstroms radius around Praseodymium atom.
The 3mvc structure was solved by J.YOON, M.A.HERZIK JR, M.B.WINTER, R.TRAN, C.OLEA JR, M.A.MARLETTA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)33.7-1.4
Space groupP1211
a (A)37.582
b (A)76.347
c (A)62.696
alpha (°)90.00
beta (°)91.76
gamma (°)90.00
Rfactor (%)16.1
Rfree (%)20.5


Praseodymium Binding Sites:

Praseodymium binding site 1 out of 4 in 3mvc


Praseodymium binding site 1 out of 4 in 3mvc
Click to enlarge
stereopicture of Praseodymium binding site 1 out of 4 in 3mvc
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Praseodymium in the PDB 3mvc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Praseodymium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu284, A: Glu349, A: Pr3, A: Hoh38, A: Hoh41,

conact list:


AtomAtomDistance (A)
PrOE1 A:Glu2842.98
PrOE1 A:Glu2843.46
PrOE2 A:Glu2842.95
PrOE2 A:Glu2842.68
PrCD A:Glu2843.19
PrCD A:Glu2843.12
PrCG A:Glu2844.46
PrCG A:Glu2844.06
PrOE1 A:Glu3492.77
PrOE2 A:Glu3494.19
PrCD A:Glu3493.72
PrCG A:Glu3494.84
PrPR A:Pr33.62
PrO A:Hoh384.89
PrO A:Hoh412.89

interactive model:


Praseodymium binding site 2 out of 4 in 3mvc


Praseodymium binding site 2 out of 4 in 3mvc
Click to enlarge
stereopicture of Praseodymium binding site 2 out of 4 in 3mvc
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Praseodymium in the PDB 3mvc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Praseodymium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Pro289, A: Thr290, A: Arg291, A: Arg354, A: Arg355, A: No3141, A: Hoh23, A: Hoh26, A: Hoh29, A: Hoh39, A: Hoh105,

conact list:


AtomAtomDistance (A)
PrO A:Pro2892.42
PrC A:Pro2893.61
PrCA A:Pro2894.47
PrN A:Thr2904.51
PrCA A:Thr2904.56
PrN A:Arg2914.84
PrCG A:Arg2914.93
PrO A:Arg3544.78
PrO A:Arg3552.55
PrC A:Arg3553.69
PrCA A:Arg3554.48
PrO1 A:No31412.75
PrO2 A:No31412.68
PrN A:No31413.12
PrO3 A:No31414.51
PrO A:Hoh234.58
PrO A:Hoh262.57
PrO A:Hoh292.64
PrO A:Hoh392.71
PrO A:Hoh1052.64

interactive model:


Praseodymium binding site 3 out of 4 in 3mvc


Praseodymium binding site 3 out of 4 in 3mvc
Click to enlarge
stereopicture of Praseodymium binding site 3 out of 4 in 3mvc
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Praseodymium in the PDB 3mvc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Praseodymium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu281, A: Glu284, A: Pr1, A: Hoh41, A: Hoh113, A: Hoh120,

conact list:


AtomAtomDistance (A)
PrOE1 A:Glu2812.63
PrOE2 A:Glu2812.62
PrCD A:Glu2812.98
PrCG A:Glu2814.49
PrOE1 A:Glu2842.66
PrOE1 A:Glu2842.63
PrOE2 A:Glu2843.93
PrOE2 A:Glu2842.54
PrCD A:Glu2843.63
PrCD A:Glu2842.92
PrCG A:Glu2844.92
PrCG A:Glu2844.42
PrPR A:Pr13.62
PrO A:Hoh412.56
PrO A:Hoh1134.39
PrO A:Hoh1204.73

interactive model:


Praseodymium binding site 4 out of 4 in 3mvc


Praseodymium binding site 4 out of 4 in 3mvc
Click to enlarge
stereopicture of Praseodymium binding site 4 out of 4 in 3mvc
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Praseodymium in the PDB 3mvc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Praseodymium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Pro289, B: Thr290, B: Arg291, B: No3146, B: Hoh116, B: Hoh124,

conact list:


AtomAtomDistance (A)
PrO B:Pro2892.48
PrC B:Pro2893.67
PrCA B:Pro2894.53
PrN B:Thr2904.59
PrCA B:Thr2904.65
PrN B:Arg2914.86
PrCG B:Arg2914.81
PrO1 B:No31463.00
PrO2 B:No31462.81
PrN B:No31463.33
PrO3 B:No31464.72
PrO B:Hoh1164.69
PrO B:Hoh1242.61

interactive model:




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