Chemical elements
  Nickel
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    Compounds
    PDB 1a5n-1g2a
    PDB 1g3v-1mn0
    PDB 1mro-1s9b
    PDB 1scr-1xmk
      1scr
      1sdw
      1sf8
      1sk3
      1slw
      1su6
      1su7
      1su8
      1suf
      1sum
      1t6u
      1tgg
      1twq
      1u5z
      1ubh
      1ubj
      1ubk
      1ubl
      1ubm
      1ubo
      1ubp
      1ubr
      1ubt
      1ubu
      1uiv
      1umh
      1uuo
      1uwv
      1vjr
      1vkl
      1vr3
      1w9h
      1wmo
      1wn7
      1ws0
      1ws1
      1wu4
      1wu5
      1wu6
      1wuh
      1wui
      1wuj
      1wuk
      1wul
      1wvc
      1xcv
      1xea
      1xi3
      1xm5
      1xmk
    PDB 1xu1-2cg5
    PDB 2cqz-2jih
    PDB 2jk8-2v4b
    PDB 2vbq-3c2q
    PDB 3c6c-3h85
    PDB 3hdp-3kvb
    PDB 3l1m-3o00
    PDB 3o01-4ubp
    PDB 8icl-9ant

Nickel in the structure of Crystal Structure Of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha (pdb 1sk3)






The binding sites of Nickel atom in the structure of Crystal Structure Of the C-Terminal Peptidoglycan-Binding Domain of Human Peptidoglycan Recognition Protein Ialpha (pdb code 1sk3). This binding sites where shown with 5.0 Angstroms radius around Nickel atom.
The 1sk3 structure was solved by R.GUAN, E.L.MALCHIODI, W.QIAN, P.SCHUCK, R.A.MARIUZZA, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)29.6-2.8
Space groupP3221
a (A)102.632
b (A)102.632
c (A)41.496
alpha (°)90.00
beta (°)90.00
gamma (°)120.00
Rfactor (%)21.9
Rfree (%)25.3


Nickel Binding Sites:

Nickel binding site 1 out of 2 in 1sk3


Nickel binding site 1 out of 2 in 1sk3
Click to enlarge
stereopicture of Nickel binding site 1 out of 2 in 1sk3
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Nickel in the PDB 1sk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Val177, A: Cys178, A: Asp296, A: Gln299, A: Cys300, A: Hoh1, A: Hoh4, A: Hoh9,

conact list:


AtomAtomDistance (A)
NiO A:Val1772.09
NiN A:Val1772.57
NiCB A:Val1774.49
NiCG2 A:Val1774.49
NiC A:Val1772.85
NiCA A:Val1773.25
NiN A:Cys1783.96
NiC A:Cys1784.82
NiCA A:Cys1784.48
NiO A:Asp2963.97
NiCB A:Asp2964.37
NiOD2 A:Asp2962.13
NiC A:Asp2964.63
NiOD1 A:Asp2963.32
NiCG A:Asp2963.03
NiCA A:Asp2964.62
NiOE1 A:Gln2994.26
NiCB A:Cys3004.81
NiO A:Hoh12.45
NiO A:Hoh44.10
NiO A:Hoh94.41

interactive model:


Nickel binding site 2 out of 2 in 1sk3


Nickel binding site 2 out of 2 in 1sk3
Click to enlarge
stereopicture of Nickel binding site 2 out of 2 in 1sk3
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Nickel in the PDB 1sk3. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Nickel atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Glu292,

conact list:


AtomAtomDistance (A)
NiOE1 A:Glu2922.80
NiCB A:Glu2924.82
NiOE2 A:Glu2922.88
NiCD A:Glu2922.94
NiCG A:Glu2924.08

interactive model:




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