Chemical elements
  Nickel
    History
    Occurrence
    Isotopes
    Energy
    Production
    Preparation
    Application
    Catalyst
    Physical Properties
    Compounds
    PDB 1a5n-1g2a
    PDB 1g3v-1mn0
    PDB 1mro-1s9b
    PDB 1scr-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
      3o01
      3o02
      3od2
      3oni
      3op0
      3opt
      3phm
      3pua
      3pus
      3qsi
      3rva
      3rvh
      3sai
      3tq0
      3ubp
      3uqy
      3usc
      3use
      3vj6
      3vj9
      3vja
      446d
      473d
      4a2c
      4al2
      4auu
      4auy
      4av0
      4avh
      4avi
      4avj
      4avk
      4b29
      4diq
      4dun
      4e2g
      4egb
      4eox
      4er8
      4evv
      4ew0
      4ew4
      4eyu
      4ez4
      4ezh
      4f9d
      4fca
      4gd4
      4gfs
      4ubp
    PDB 8icl-9ant

Nickel in PDB, part 12 (551-600), PDB files 3o01 - 4ubp






Experimental structures of coordination spheres of Nickel (Ni) in bioorganic molecules from X-Ray and NMR experiments. Coordination spheres were calculated with 5.0 Angstroms radius around Nickel atoms.
PDB files 551-600 (3o01 - 4ubp):
  1. 3o01 - The Crystal Structure of the Salmonella Type III Secretion System Tip Protein Sipd in Complex With Deoxycholate
  2. 3o02 - The Crystal Structure of the Salmonella Type III Secretion System Tip Protein Sipd in Complex With Chenodeoxycholate
  3. 3od2 - E. Coli Nikr Soaked With Excess Nickel Ions
  4. 3oni - Crystal Structure Of The Second Bromodomain of Humand BRD2 in Complex With the Inhibitor JQ1
  5. 3op0 - Crystal Structure of Cbl-C (Cbl-3) Tkb Domain in Complex With Egfr PY1069 Peptide
  6. 3opt - Crystal Structure of the RPH1 Catalytic Core With A-Ketoglutarate
  7. 3phm - Reduced (Cu+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm)
  8. 3pua - PHF2 Jumonji-Nog-Ni(II)
  9. 3pus - PHF2 Jumonji-Nog-Ni(II)
  10. 3qsi - Nickel Binding Domain of Nikr From Helicobacter Pylori Disclosing Partial Metal Occupancy
  11. 3rva - Crystal Structure of Organophosphorus Acid Anhydrolase From Alteromonas Macleodii
  12. 3rvh - Crystal Structure of JMJD2A Complexed With Inhibitor
  13. 3sai - Bacuills Anthracis Dihydrofolate Reductase Bound to Propargyl-Linked Tmp Analog, UCP1015
  14. 3tq0 - Crystal Structure of Leishmania Major Dihydroorotate Dehydrogenase in Complex With Fumarate
  15. 3ubp - Diamidophosphate Inhibited Bacillus Pasteurii Urease
  16. 3uqy - H2-Reduced Structure of E. Coli Hydrogenase-1
  17. 3usc - Crystal Structure of E. Coli Hydrogenase-1 in A Ferricyanide-Oxidized Form
  18. 3use - Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form
  19. 3vj6 - Structure of the Mhc Class Ib Molecule Qa-1B
  20. 3vj9 - Crystal Structure of the Human Squalene Synthase
  21. 3vja - Crystal Structure of the Human Squalene Synthase
  22. 446d - Structure of the Oligonucleotide D(Cgtatatacg) As A Site Specific Complex With Nickel Ions
  23. 473d - NI2+/Guanine Interactions and Netropsin/Guanine Stacking in D(Cgtatatacg)2
  24. 4a2c - Crystal Structure of Galactitol-1-Phosphate Dehydrogenase From Escherichia Coli
  25. 4al2 - Peptide Deformylase (Ni-Form) With Hydrosulfide
  26. 4auu - Crystal Structure of Apo Fimh Lectin Domain At 1.5 A Resolution
  27. 4auy - Structure of The Fimh Lectin Domain In the Trigonal Space Group, in Complex With An Hydroxyl Propynyl Phenyl Alpha-D- Mannoside At 2.1 A Resolution
  28. 4av0 - Structure of The Fimh Lectin Domain In the Trigonal Space Group, in Complex With A Methoxy Phenyl Propynyl Alpha-D- Mannoside At 2.1 A Resolution
  29. 4avh - Structure of The Fimh Lectin Domain In the Trigonal Space Group, in Complex With A Thioalkyl Alpha-D-Mannoside At 2.1 A Resolution
  30. 4avi - Structure of The Fimh Lectin Domain In the Trigonal Space Group, in Complex With A Methyl Ester Octyl Alpha-D- Mannoside At 2.4 A Resolution
  31. 4avj - Structure of The Fimh Lectin Domain In the Trigonal Space Group, in Complex With A Methanol Triazol Ethyl Phenyl Alpha-D-Mannoside At 2.1 A Resolution
  32. 4avk - Structure of Trigonal Fimh Lectin Domain Crystal Soaked With An Alpha-D-Mannoside O-Linked to Propynyl Pyridine At 2.4 A Resolution
  33. 4b29 - Crystal Structures of Dmsp Lyases Rddddp and Rndddqii
  34. 4diq - Crystal Structure of Human NO66
  35. 4dun - 1.76A X-Ray Crystal Structure of A Putative Phenazine Biosynthesis Phzc/Phzf Protein From Clostridium Difficile (Strain 630)
  36. 4e2g - Crystal Structure of Cupin Fold Protein STHE2323 From Sphaerobacter Thermophilus
  37. 4egb - 3.0 Angstrom Resolution Crystal Structure of Dtdp-Glucose 4,6- Dehydratase (Rfbb) From Bacillus Anthracis Str. Ames in Complex With Nad
  38. 4eox - X-Ray Structure of Polypeptide Deformylase Bound to A Acylprolinamide Inhibitor
  39. 4er8 - Structure of the Rep Associates Tyrosine Transposase Bound to A Rep Hairpin
  40. 4evv - Mouse MBD4 Glycosylase Domain in Complex With A G:T Mismatch
  41. 4ew0 - Mouse MBD4 Glycosylase Domain in Complex With A G:5HMU (5- Hydroxymethyluracil) Mismatch
  42. 4ew4 - Mouse MBD4 Glycosylase Domain in Complex With Dna Containing A Ribose Sugar
  43. 4eyu - The Free Structure Of the Mouse C-Terminal Domain of KDM6B
  44. 4ez4 - Free KDM6B Structure
  45. 4ezh - The Crystal Structure of KDM6B Bound With H3K27ME3 Peptide
  46. 4f9d - Structure of Escherichia Coli Pgab 42-655 in Complex With Nickel
  47. 4fca - The Crystal Structure of A Functionally Unknown Conserved Protein From Bacillus Anthracis Str. Ames.
  48. 4gd4 - Crystal Structure of JMJD2A Complexed With Inhibitor
  49. 4gfs - 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (Arod) From Salmonella Typhimurium LT2 With Nickel Bound At Active Site
  50. 4ubp - Structure of Bacillus Pasteurii Urease Inhibited With Acetohydroxamic Acid At 1.55 A Resolution


Acknowledgement

We would like to acknowledge that these pictures of PDB structures of Nickel coordination spheres were produced with valuable advice from our colleagues from http://3dpdb.com.
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