Sodium in PDB, part 245 (files: 9761-9800),
PDB 7kt4-7l2r
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: 9761-9800 (PDB 7kt4-7l2r).
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7kt4 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)
Other atoms:
Mn (4);
Cl (2);
-
7kt5 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)
Other atoms:
Mn (7);
Cl (1);
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7kt6 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (960MIN)
Other atoms:
Mn (6);
-
7kt7 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN)
Other atoms:
Mg (2);
Cl (1);
-
7kt8 (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (180MIN)
Other atoms:
Cl (1);
Mg (2);
-
7kt9 (Na: 2) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN)
Other atoms:
Cl (1);
Mg (1);
-
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);
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7ktb (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 10 Mm MN2+ (40MIN)
Other atoms:
Mn (9);
-
7ktc (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (120MIN)
Other atoms:
Mn (7);
-
7ktd (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)
Other atoms:
Mn (6);
-
7kte (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Reaction State Ternary Complex, 50 Mm MG2+ (90MIN)
Other atoms:
Cl (1);
Mg (2);
-
7ktf (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)
Other atoms:
Mg (2);
-
7ktg (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (960MIN)
Other atoms:
Cl (1);
Mg (2);
-
7kth (Na: 2) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)
Other atoms:
Cl (1);
Mg (1);
-
7kti (Na: 1) - Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 20 Um MN2+ (120MIN)
Other atoms:
Mn (3);
-
7ktj (Na: 1) - Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)
Other atoms:
Cl (1);
Ca (3);
-
7ktk (Na: 1) - Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)
Other atoms:
Mg (2);
-
7ktl (Na: 1) - Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MN2+ (90MIN)
Other atoms:
Mn (9);
-
7ktn (Na: 2) - Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MG2+ (2160MIN)
Other atoms:
Cl (1);
Mg (1);
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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);
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7kuq (Na: 1) - Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N8-Acetylspermidine
Other atoms:
K (2);
Zn (1);
-
7kur (Na: 1) - Crystal Structure of Danio Rerio Histone Deacetylase 10 Y307F Mutant in Complex with N-Acetylputrescine
Other atoms:
Zn (1);
K (2);
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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);
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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);
-
7kyl (Na: 1) - Powassan Virus Envelope Protein Diii in Complex with Neutralizing Fab Powv-80
Other atoms:
Cl (1);
-
7kyr (Na: 1) - Crystal Structure of I107E Cub Myoglobin (I107E L29H F43H Sperm Whale Myoglobin)
Other atoms:
Fe (1);
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7kz1 (Na: 1) - Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site
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7kz3 (Na: 2) - Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Internal Aldimine
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7kz5 (Na: 2) - Crystal Structure of Kaba From Bacillus Cereus UW85 in Complex with the Plp External Aldimine Adduct with Kanosamine-6-Phosphate
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7kza (Na: 1) - Potent Sars-Cov-2 Binding and Neutralization Through Maturation of Iconic Sars-Cov-1ANTIBODIES
Other atoms:
Cl (2);
-
7kzg (Na: 1) - Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose
Other atoms:
Cl (1);
-
7l00 (Na: 8) - Crystal Structure of C. Difficile Enoyl-Acyl Carrier Protein Reductase (Fabk) in Complex with An Inhibitor
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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);
-
7l0n (Na: 6) - Circulating Sars-Cov-2 Spike N439K Variants Maintain Fitness While Evading Antibody-Mediated Immunity
Other atoms:
Zn (2);
Cl (27);
-
7l0z (Na: 2) - Spinach Variant Bound to Dfhbi-1T
Other atoms:
K (2);
F (5);
Mg (1);
-
7l1a (Na: 7) - Human Methionine Adenosyltransferase 2A Bound to Methylthioadenosine and Inhibitor, Di-Imido Triphosphate (Pnpnp)
Other atoms:
K (1);
Mg (2);
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7l2h (Na: 1) - Cryo-Em Structure of Unliganded Full-Length TRPV1 at Neutral pH
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7l2m (Na: 3) - Cryo-Em Structure of Dktx/Rtx-Bound Full-Length TRPV1
-
7l2p (Na: 1) - Cryo-Em Structure of Unliganded Minimal TRPV1
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7l2r (Na: 1) - Cryo-Em Structure of Dktx-Bound Minimal TRPV1 at the Pre-Open State
Page generated: Thu Dec 28 11:30:05 2023
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