Sodium in PDB, part 247 (files: 9841-9880),
PDB 7lpf-7m48
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: 9841-9880 (PDB 7lpf-7m48).
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7lpf (Na: 1) - The Internal Aldimine 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 1.10 Angstrom Resolution
Other atoms:
F (3);
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7lpl (Na: 2) - X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Dataset 3 (Merged)
Other atoms:
Cl (2);
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7lpm (Na: 2) - X-Ray Radiation Damage Series on Lysozyme at 277K, Multi-Conformer Model, Crystal 2
Other atoms:
Cl (2);
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7lqj (Na: 2) - Crystal Structure of Leut Bound to L-Alanine
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7lqk (Na: 2) - Crystal Structure of the R375A Mutant of Leut
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7lql (Na: 2) - Crystal Structure of the R375D Mutant of Leut
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7lqy (Na: 1) - Structure of Squirrel TRPV1 in Apo State
Other atoms:
Cl (1);
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7lqz (Na: 1) - Structure of Squirrel TRPV1 in Complex with Rtx
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7lr0 (Na: 1) - Structure of Squirrel TRPV1 in Complex with Capsaicin
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7lrf (Na: 1) - Netrin-1 in Complex with Sos
Other atoms:
Cl (1);
Ca (2);
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7lsf (Na: 2) - Crystal Structure of the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype)
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7lst (Na: 1) - Ruminococcus Bromii AMY12-D392A with 63-A-D-Glucosyl-Maltotriosyl- Maltotriose
Other atoms:
Ca (1);
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7lsu (Na: 1) - Ruminococcus Bromii AMY12-D392A with 63-A-D-Glucosyl-Maltotriose
Other atoms:
Ca (1);
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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);
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7m46 (Na: 4) - Dna Polymerase Lambda, Ttp:at MG2+ Product State Ternary Complex, 5 Min
Other atoms:
Mg (1);
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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);
Page generated: Thu Dec 28 11:30:15 2023
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