Sodium in PDB, part 248 (files: 9881-9920),
PDB 7lsv-7m4l
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: 9881-9920 (PDB 7lsv-7m4l).
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7lsv (Na: 2) - Non-Kinase Domain of Legionella Effector Protein Kinase LEGK2
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7ltw (Na: 2) - Crystal Structure of the Mouse KIRREL2 D1 Homodimer
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7lu6 (Na: 8) - Crystal Structure of the Mouse KIRREL3 D1 Homodimer
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7lul (Na: 1) - Structure of the MM2 Erbin Pdz Variant in Complex with A High-Affinity Peptide
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7lw9 (Na: 1) - Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na
Other atoms:
Fe (4);
Sm (2);
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7ly8 (Na: 1) - The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with Two Molecules of N-(4'- Trifluoromethoxybenzoyl)-2-Amino-1-Ethylphosphate (F6F) Inhibitor at the Enzyme Alpha-Site, A Single F6F Molecule at the Enzyme Beta-Site, and Sodium Ion at the Metal Coordination Site at 1.55 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:
F (9);
Cl (5);
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7lyi (Na: 1) - Crystal Structure of the Sars-Cov-2 (Covid-19) Main Protease in Complex with Inhibitor UAWJ9-36-3
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7lz2 (Na: 2) - Structure of Glutamate Receptor-Like Channel GLR3.4 Ligand-Binding Domain in Complex with Methionine
Other atoms:
Cl (4);
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7m07 (Na: 5) - Pre-Catalytic Ternary Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Other atoms:
Cl (2);
Mg (2);
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7m08 (Na: 3) - Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound 1-Nt Gapped Ssb Substrate and Incoming Dumpnpp
Other atoms:
Mg (1);
Cl (2);
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7m09 (Na: 3) - Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Blunt- Ended Dsb Substrate and Incoming Dumpnpp
Other atoms:
Ca (1);
Mg (2);
Cl (2);
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7m0a (Na: 3) - Incomplete in Crystallo Incorporation By Dna Polymerase Lambda Bound to Blunt-Ended Dsb Substrate and Incoming Dttp
Other atoms:
Cl (3);
Ca (1);
Mg (2);
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7m0b (Na: 2) - Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Mismatched Dsb and Incoming Dumpnpp
Other atoms:
Cl (4);
Mg (2);
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7m0c (Na: 2) - Post-Catalytic Nicked Complex of Dna Polymerase Lambda with Bound Mismatched Dsb Substrate
Other atoms:
Mg (2);
Cl (2);
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7m0d (Na: 5) - Pre-Catalytic Quaternary Complex of Dna Polymerase Lambda with Bound Complementary Dsb Substrate and Incoming Dumpnpp
Other atoms:
Mg (2);
K (6);
Cl (1);
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7m0e (Na: 4) - Pre-Catalytic Synaptic Complex of Dna Polymerase Lambda with Gapped Dsb Substrate and Incoming Dumpnpp
Other atoms:
Mg (6);
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7m14 (Na: 1) - X-Ray Structure of CJ1430 in the Presence of Gdp, A Gdp-D-Glycero-4- Keto-D-Lyxo-Heptose-3,5-Epimerase From Campylobacter Jejuni
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7m1y (Na: 2) - The Crystal Structure of Papain-Like Protease of Sars Cov-2, C111S Mutant, in Complex with Ebselen
Other atoms:
Cl (2);
Zn (2);
I (13);
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7m2l (Na: 2) - The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.60 Angstrom Resolution. Two 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 (6);
F (6);
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7m3q (Na: 2) - Structure of the SMURF2 Hect Domain with A High Affinity Ubiquitin Variant (Ubv)
Other atoms:
Cl (6);
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7m3s (Na: 2) - The Internal Aldimine Form of the Wild-Type Salmonella Typhimurium Tryptophan Synthase in Complex with N-(4'-Trifluoromethoxybenzoyl)-2- Amino-1-Ethylphosphate (F6F) Inhibitor at the Alpha-and Beta-Site, Sodium Ion at the Metal Coordination Site, and Another F6F Molecule at the Enzyme Beta-Site at 1.55 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:
F (6);
Cl (2);
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7m43 (Na: 5) - Dna Polymerase Lambda, Ttp:at CA2+ Ground State Ternary Complex
Other atoms:
Ca (1);
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7m44 (Na: 3) - Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 90 Sec
Other atoms:
Mg (2);
-
7m45 (Na: 4) - Dna Polymerase Lambda, Ttp:at MG2+ Reaction State Ternary Complex, 120 Sec
Other atoms:
Mg (1);
-
7m46 (Na: 4) - Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 Min
Other atoms:
Mg (1);
-
7m47 (Na: 4) - Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 60 Min
Other atoms:
Mg (1);
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7m48 (Na: 4) - Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 960 Min
Other atoms:
Mg (1);
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7m49 (Na: 3) - Dna Polymerase Lambda, Ttp:at MN2+ Reaction State Ternary Complex, 5 Min
Other atoms:
Mn (4);
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7m4a (Na: 3) - Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 20 Min
Other atoms:
Mn (4);
-
7m4b (Na: 3) - Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 60 Min
Other atoms:
Mn (4);
-
7m4c (Na: 3) - Dna Polymerase Lambda, Ttp:at MN2+ Product State Ternary Complex, 960 Min
Other atoms:
Mn (3);
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7m4d (Na: 2) - Dna Polymerase Lambda, Dctp:at CA2+ Ground State Ternary Complex
Other atoms:
Ca (1);
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7m4e (Na: 2) - Dna Polymerase Lambda, Dctp:at MG2+ Reaction State Ternary Complex, 120 Min
Other atoms:
Mg (2);
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7m4f (Na: 3) - Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 300 Min
Other atoms:
Cl (1);
Mg (1);
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7m4g (Na: 3) - Dna Polymerase Lambda, Dctp:at MG2+ Product State Ternary Complex, 960 Min
Other atoms:
Mg (1);
-
7m4h (Na: 2) - Dna Polymerase Lambda, Dctp:at MN2+ Reaction State Ternary Complex, 225 Min
Other atoms:
Mn (3);
-
7m4i (Na: 3) - Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 420 Min
Other atoms:
Mn (3);
-
7m4j (Na: 3) - Dna Polymerase Lambda, Dctp:at MN2+ Product State Ternary Complex, 960 Min
Other atoms:
Mn (2);
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7m4k (Na: 4) - Dna Polymerase Lambda, Ttpas:at CA2+ Ground State Ternary Complex
Other atoms:
Ca (1);
-
7m4l (Na: 2) - Dna Polymerase Lambda, Ttpas:at MN2+ Product State Ternary Complex, 60 Min
Other atoms:
Mn (3);
Page generated: Wed Nov 13 13:06:42 2024
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