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Sodium in PDB, part 243 (files: 9681-9720), PDB 7km6-7l03

Experimental structures of coordination spheres of Sodium (Na) in bioorganic molecules from X-Ray and NMR experiments. Coordination spheres were calculated with 5.0 Angstroms radius around Sodium atoms. PDB files: 9681-9720 (PDB 7km6-7l03).
  1. 7km6 (Na: 2) - APOBEC3B Antibody 5G7 Fv-Clasp
    Other atoms: Cl (3);
  2. 7kme (Na: 2) - Crystal Structure of Human Alpha-Thrombin Inhibited with SEL2711.
  3. 7kn8 (Na: 2) - Crystal Structure of the GH74 Xyloglucanase From Xanthomonas Campestris (XCC1752)
    Other atoms: I (14);
  4. 7knf (Na: 4) - 1.80A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-1 Nhoh)
    Other atoms: Zn (4);
  5. 7kng (Na: 4) - 2.10A Resolution Structure of Independent Phosphoglycerate Mutase From C. Elegans in Complex with A Macrocyclic Peptide Inhibitor (Ce-2 Y7F)
    Other atoms: Zn (4); Cl (4);
  6. 7knk (Na: 1) - Structure of Hen Egg-White Lysozyme Grown with Kitchen Recipe
    Other atoms: Cl (1);
  7. 7kom (Na: 1) - High Resolution Crystal Structure of Putative Pterin Binding Protein Prur (VV2_1280) From Vibrio Vulnificus CMCP6
  8. 7kos (Na: 5) - 1.50 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58
  9. 7kou (Na: 10) - 1.83 Angstroms Resolution Crystal Structure of Putative Pterin Binding Protein Prur (ATU3496) From Agrobacterium Fabrum Str. C58
    Other atoms: Cl (2);
  10. 7kst (Na: 1) - Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (2MIN)
    Other atoms: Mn (6);
  11. 7ksv (Na: 1) - Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)
    Other atoms: Mn (6);
  12. 7ksw (Na: 1) - Dna Polymerase Mu, Dgtp:Ct Reaction State Ternary Complex, 10 Mm MG2+ (10MIN)
    Other atoms: Cl (1); Mg (3);
  13. 7ksx (Na: 2) - Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN)
    Other atoms: Mg (1);
  14. 7ksy (Na: 2) - Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)
    Other atoms: Mg (1);
  15. 7kt3 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)
    Other atoms: Cl (3); Ca (3);
  16. 7kt4 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
    Other atoms: Mn (4); Cl (2);
  17. 7kt5 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
    Other atoms: Mn (7); Cl (1);
  18. 7kt6 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)
    Other atoms: Mn (6);
  19. 7kt7 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN)
    Other atoms: Mg (2); Cl (1);
  20. 7kt8 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (180MIN)
    Other atoms: Cl (1); Mg (2);
  21. 7kt9 (Na: 2) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN)
    Other atoms: Cl (1); Mg (1);
  22. 7kta (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)
    Other atoms: Ca (2); Cl (1);
  23. 7kte (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MG2+ (90MIN)
    Other atoms: Cl (1); Mg (2);
  24. 7ktf (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)
    Other atoms: Mg (2);
  25. 7ktg (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (960MIN)
    Other atoms: Cl (1); Mg (2);
  26. 7ktn (Na: 2) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MG2+ (2160MIN)
    Other atoms: Cl (1); Mg (1);
  27. 7ku9 (Na: 1) - The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase with Sodium Ion at the Metal Coordination Site, Two Molecules of F6F Inhibitor at the Enzyme Alpha-Site and Another F6F Molecule at the Enzyme Beta-Site at 1.40 Angstrom Resolution
    Other atoms: Cl (3); F (9);
  28. 7kuq (Na: 1) - Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine
    Other atoms: K (2); Zn (1);
  29. 7kur (Na: 1) - Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine
    Other atoms: Zn (1); K (2);
  30. 7kut (Na: 1) - Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)
    Other atoms: K (2); Zn (1);
  31. 7kxc (Na: 1) - The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site, Sodium Ion at the Metal Coordination Site and Benzimidazole (Bzi) at the Enzyme Beta-Site at 1.30 Angstrom Resolution. One of the Beta-Q114 Rotamer Conformations Allows A Hydrogen Bond to Form with the Plp Oxygen at the Position 3 in the Ring
    Other atoms: Cl (1); F (3);
  32. 7kyl (Na: 1) - Powassan Virus Envelope Protein Diii in Complex with Neutralizing Fab Powv-80
    Other atoms: Cl (1);
  33. 7kyr (Na: 1) - Crystal Structure of I107E Cub Myoglobin (I107E L29H F43H Sperm Whale Myoglobin)
    Other atoms: Fe (1);
  34. 7kz1 (Na: 1) - Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site
  35. 7kz3 (Na: 2) - Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine
  36. 7kz5 (Na: 2) - Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate
  37. 7kza (Na: 1) - Potent Sars-Cov-2 Binding and Neutralization Through Maturation of Iconic Sars-Cov-1ANTIBODIES
    Other atoms: Cl (2);
  38. 7kzg (Na: 1) - Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose
    Other atoms: Cl (1);
  39. 7l00 (Na: 8) - Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor
  40. 7l03 (Na: 1) - The Aminoacrylate Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Inhibitor N-(4'- Trifluoromethoxybenzenesulfonyl)-2-Amino-1-Ethylphosphate (F9F) at the Enzyme Alpha-Site and Sodium Ion at the Metal Coordination Site at 1.60 Angstrom Resolution. Three Water Molecules Are Close to the Amynoacrylate at the Enzyme Beta-Site
    Other atoms: F (3);
Page generated: Fri Dec 24 09:55:51 2021

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