Sodium in PDB, part 253 (files: 10081-10120),
PDB 7m0d-7md0
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: 10081-10120 (PDB 7m0d-7md0).
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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);
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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);
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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);
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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);
-
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);
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7m6k (Na: 2) - Crystal Structure of the Arm Domain From Drosophila SARM1 in Complex with Vmn
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7m8q (Na: 1) - Complex Structure of Methane Monooxygenase Hydroxylase and Regulatory Subunit with Fluorosubstituted Tryptophans
Other atoms:
Fe (4);
F (4);
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7m8t (Na: 2) - Crystal Structure of Hla-A*11:01 in Complex with Nsasfstfk, An 9-Mer Epitope From Sars-Cov-2 Spike (S370-378)
Other atoms:
Ca (1);
Cl (2);
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7m8u (Na: 3) - Crystal Structure of Hla-B*35:01 in Complex with Ipfamqmay, An 9-Mer Epitope From Sars-Cov-2 Spike (S896-904)
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7m8w (Na: 1) - Xfel Crystal Structure of the Prostaglandin D2 Receptor CRTH2 in Complex with 15R-Methyl-PGD2
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7mcb (Na: 2) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme
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7mcl (Na: 1) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Plp Bound
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7mcn (Na: 2) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme with High Hepes
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7mcp (Na: 6) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma-Lyase, Holoenzyme Dimer
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7mcq (Na: 4) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Aoaa-Bound Enzyme in Dimeric Form
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7mct (Na: 2) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL1
Other atoms:
Br (5);
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7mcu (Na: 2) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL2
Other atoms:
Br (1);
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7mcy (Na: 3) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase, Holoenzyme with Bound NL3
Other atoms:
Cl (1);
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7md0 (Na: 3) - Crystal Structure of Staphylococcus Aureus Cystathionine Gamma Lyase Holoenzyme in the Presence of NL1F3
Page generated: Sat Aug 23 06:30:58 2025
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