Sodium in PDB, part 231 (files: 9201-9240),
PDB 6ydj-6yu2
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: 9201-9240 (PDB 6ydj-6yu2).
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6ydj (Na: 1) - P146A Variant of Beta-Phosphoglucomutase From Lactococcus Lactis in Complex with Glucose 6-Phosphate and Trifluoromagnesate
Other atoms:
F (3);
Mg (2);
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6yen (Na: 1) - Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133)
Other atoms:
Zn (2);
Cl (3);
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6yeo (Na: 1) - Crystal Structure of Ampc From E. Coli with Cyclic Boronate 2
Other atoms:
Cl (3);
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6yev (Na: 4) - Crystal Structure of Msra C206 and Trx C35S Complex From Escherichia Coli
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6yf2 (Na: 1) - FKBP12 in Complex with the Bmp Potentiator Compound 6 at 1.03A Resolution
Other atoms:
Cl (2);
Cd (1);
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6yf3 (Na: 1) - FKBP12 in Complex with the Bmp Potentiator Compound 10 at 1.00A Resolution
Other atoms:
Cl (2);
Cd (1);
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6yg1 (Na: 4) - Crystal Structure of MKK7 (MAP2K7) in An Active State, Allosterically Triggered By the N-Terminal Helix
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6ygg (Na: 1) - Nadase From Aspergillus Fumigatus Complexed with A Substrate Anologue
Other atoms:
Ca (2);
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6yhg (Na: 2) - Thrombin in Complex with D-Phe-Pro-M-Methoxybenzylamide Derivative (16A)
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6yhj (Na: 2) - Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)
Other atoms:
Cl (2);
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6yhn (Na: 2) - Crystal Structure of Domains 4-5 of Cnfy From Yersinia Pseudotuberculosis
Other atoms:
Mg (4);
Cl (1);
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6yia (Na: 1) - 14-3-3 Sigma in Complex with SMAD2 PS465 Peptide
Other atoms:
Cl (1);
Mg (5);
Ca (1);
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6yib (Na: 1) - 14-3-3 Sigma in Complex with SMAD3 PS423 Peptide
Other atoms:
Ca (1);
Cl (3);
Mg (3);
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6yic (Na: 2) - 14-3-3 Sigma in Complex with SMAD4 PS403 Peptide
Other atoms:
Mg (2);
Ca (1);
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6yig (Na: 1) - Crystal Structure of the N-Terminal Ef-Hand Domain of Arabidopsis Thaliana ATEH1/PAN1
Other atoms:
Ca (1);
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6yii (Na: 3) - Crystal Structure of A Class III Adenylyl Cyclase-Like Atp-Binding Protein From Pseudomonas Aeruginosa
Other atoms:
Mg (1);
Mn (1);
Ca (1);
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6yjx (Na: 1) - Structure of Hen Egg-White Lysozyme Crystallized with Pas Polypeptide
Other atoms:
Cl (4);
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6yl5 (Na: 14) - Crystal Structure of the Sam-Sah Riboswitch with Sah
Other atoms:
Mg (5);
Br (6);
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6yls (Na: 1) - MEOS4B - Directionality of Optical Properties of Fluorescent Proteins
Other atoms:
Cl (1);
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6ymd (Na: 2) - Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate
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6ymj (Na: 3) - Crystal Structure of the Sam-Sah Riboswitch with Adenosine
Other atoms:
Br (6);
Mg (1);
-
6ymk (Na: 2) - Crystal Structure of the Sam-Sah Riboswitch with Amp
Other atoms:
Br (6);
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6ymm (Na: 1) - Crystal Structure of the Sam-Sah Riboswitch with Sam From Space Group P312
Other atoms:
Br (2);
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6ymp (Na: 2) - Thrombin in Complex with 3-((5-(Tert-Butyl)Isoxazol-3-Yl)Methyl) Oxetan-3-Amine (J54)
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6ymz (Na: 8) - Structure of the Cheb Methylsterase From P. Atrosepticum SCRI1043
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6yn3 (Na: 2) - Thrombin in Complex with 4-Hydroxybenzamide (J89)
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6yob (Na: 1) - Structure of Lysozyme From Coc Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging
Other atoms:
Br (7);
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6yoc (Na: 1) - Structure of Lysozyme From Coc Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging
Other atoms:
Br (7);
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6yod (Na: 1) - Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging
Other atoms:
Br (7);
-
6yoe (Na: 1) - Structure of Lysozyme From Sin Imisx Setup Collected By Still Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase-Contrast Imaging
Other atoms:
Br (7);
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6yq1 (Na: 1) - Focal Adhesion Kinase Catalytic Domain in Complex with N-Methyl-N-(3- {[2-(2-Oxo-1,2,3,4-Tetrahydro-Quinolin-6-Ylamino)-5-Trifluoromethyl- Pyrimidin-4-Ylamino]-Methyl}-Pyridin-2-Yl)-Methanesulfonamide
Other atoms:
F (12);
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6yqq (Na: 1) - Fort-Prpp Complex
Other atoms:
Cl (1);
-
6yqv (Na: 2) - Thrombin in Complex with 5-Chlorothiophene-2-Sulfonamide (J94)
Other atoms:
Cl (1);
-
6yro (Na: 3) - Streptococcus Suis Sadp Mutant - N285D
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6ysj (Na: 2) - Thrombin in Complex with 2-Amino-1-(4-Bromophenyl)Ethan-1-One (J10)
Other atoms:
Br (2);
-
6ysx (Na: 2) - Thrombin in Complex with 4-Amino-N-(5-Methylisoxazol-3-Yl) Benzenesulfonamide (J80)
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6yt4 (Na: 5) - Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0
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6ytt (Na: 6) - Co-Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum at 3.0-A Resolution
Other atoms:
F (9);
Ni (6);
Fe (28);
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6ytz (Na: 1) - Crystal Structure of Malus Domestica Double Bond Reductase (Mddbr) in Complex with Nadph
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6yu2 (Na: 4) - Crystal Structure of Mhst in Complex with L-Isoleucine
Page generated: Mon Dec 15 11:15:57 2025
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