Chemical elements
  Manganese
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    PDB 2dvd-2g38
    PDB 2g4i-2ify
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    PDB 2pal-2r21
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    PDB 2vs3-2z87
    PDB 2zad-3bso
      2zad
      2zav
      2zbj
      2zmk
      2zml
      2zmn
      2zof
      2zti
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      300d
      3a0b
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      3a4k
      3a62
      3a6d
      3a6e
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      3a6h
      3a6k
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      3a7j
      3a9r
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      3a9t
      3aam
      3ac9
      3aca
      3afa
      3ak2
      3ax4
      3b59
      3b6f
      3b6g
      3bam
      3bce
      3bdk
      3bfr
      3bg3
      3bg5
      3bg9
      3bi3
      3bie
      3bkz
      3bsn
      3bso
    PDB 3bu0-3e7b
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    PDB 3n37-3pvb
    PDB 3py5-3tmy
    PDB 3twz-4e5f
    PDB 4e5g-8icv
    PDB 8icw-9xim

Manganese in the structure of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna (pdb 3bso)






The binding sites of Manganese atom in the structure of Norwalk Virus Polymerase Bound to Cytidine 5'-Triphosphate and Primer- Template Rna (pdb code 3bso). This binding sites where shown with 5.0 Angstroms radius around Manganese atom.
The 3bso structure was solved by D.F.ZAMYATKIN, K.K.S.NG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)60.0-1.7
Space groupP212121
a (A)75.100
b (A)93.473
c (A)96.538
alpha (°)90.00
beta (°)90.00
gamma (°)90.00
Rfactor (%)20.1
Rfree (%)23.2


Manganese Binding Sites:

Manganese binding site 1 out of 3 in 3bso


Manganese binding site 1 out of 3 in 3bso
Click to enlarge
stereopicture of Manganese binding site 1 out of 3 in 3bso
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 3bso. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp242, A: Asp343, A: Asp344, P: G8, A: Mn512, A: Ctp514, A: Hoh561, A: Hoh582, A: Hoh658, A: Hoh722,

conact list:


AtomAtomDistance (A)
MnCB A:Asp2424.48
MnOD2 A:Asp2423.49
MnOD1 A:Asp2422.14
MnCG A:Asp2423.15
MnO A:Asp3434.83
MnN A:Asp3434.89
MnCB A:Asp3434.38
MnOD2 A:Asp3433.17
MnC A:Asp3434.33
MnOD1 A:Asp3432.15
MnCG A:Asp3432.98
MnCA A:Asp3434.76
MnN A:Asp3443.93
MnCB A:Asp3444.29
MnOD2 A:Asp3444.22
MnOD1 A:Asp3442.13
MnCG A:Asp3443.39
MnCA A:Asp3444.27
MnOP1 P:G84.88
MnC3' P:G83.58
MnO3' P:G82.23
MnC5' P:G84.37
MnC2' P:G84.76
MnC4' P:G84.25
MnO5' P:G84.98
MnO2' P:G84.88
MnMN A:Mn5123.71
MnPA A:Ctp5143.42
MnO2A A:Ctp5143.92
MnC5' A:Ctp5144.18
MnO5' A:Ctp5144.05
MnO3A A:Ctp5144.74
MnO1A A:Ctp5142.18
MnO A:Hoh5614.82
MnO A:Hoh5824.88
MnO A:Hoh6582.36
MnO A:Hoh7224.46

interactive model:


Manganese binding site 2 out of 3 in 3bso


Manganese binding site 2 out of 3 in 3bso
Click to enlarge
stereopicture of Manganese binding site 2 out of 3 in 3bso
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 3bso. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Asp242, A: Tyr243, A: Ser244, A: Arg245, A: Trp246, A: Asp343, A: Mn511, A: Ctp514, A: Hoh658, A: Hoh722,

conact list:


AtomAtomDistance (A)
MnCB A:Asp2424.37
MnOD2 A:Asp2422.15
MnC A:Asp2424.69
MnOD1 A:Asp2423.56
MnCG A:Asp2423.13
MnCA A:Asp2424.90
MnO A:Tyr2432.20
MnN A:Tyr2433.74
MnCB A:Tyr2434.84
MnC A:Tyr2433.39
MnCA A:Tyr2434.17
MnN A:Ser2444.40
MnC A:Ser2444.88
MnCA A:Ser2444.59
MnN A:Arg2454.73
MnN A:Trp2464.85
MnCB A:Trp2464.81
MnCB A:Asp3434.39
MnOD2 A:Asp3432.13
MnOD1 A:Asp3433.73
MnCG A:Asp3433.21
MnMN A:Mn5113.71
MnPG A:Ctp5143.37
MnO3B A:Ctp5143.55
MnO2G A:Ctp5144.41
MnPA A:Ctp5143.39
MnO3G A:Ctp5142.16
MnO2A A:Ctp5144.65
MnO1B A:Ctp5144.45
MnPB A:Ctp5143.06
MnC5' A:Ctp5144.16
MnO5' A:Ctp5144.27
MnO2B A:Ctp5142.08
MnO3A A:Ctp5143.28
MnO1G A:Ctp5144.29
MnO1A A:Ctp5142.41
MnO A:Hoh6584.59
MnO A:Hoh7223.96

interactive model:


Manganese binding site 3 out of 3 in 3bso


Manganese binding site 3 out of 3 in 3bso
Click to enlarge
stereopicture of Manganese binding site 3 out of 3 in 3bso
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 3bso. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Thr97, A: Ile98, A: Asp99, A: Glu205, A: Thr208, A: His209,

conact list:


AtomAtomDistance (A)
MnO A:Thr974.63
MnC A:Ile984.47
MnCA A:Ile984.44
MnN A:Asp993.77
MnCB A:Asp993.58
MnOD2 A:Asp992.13
MnOD1 A:Asp994.24
MnCG A:Asp993.15
MnCA A:Asp994.34
MnO A:Glu2054.92
MnOE1 A:Glu2053.18
MnOE2 A:Glu2052.06
MnCD A:Glu2052.94
MnCG A:Glu2054.31
MnCB A:Thr2084.89
MnCG2 A:Thr2084.48
MnNE2 A:His2092.09
MnND1 A:His2094.19
MnCD2 A:His2093.01
MnCE1 A:His2093.11
MnCG A:His2094.18

interactive model:




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