Sodium in the structure of Crystal Structure of the Thrombin-Thrombomodulin Complex (pdb 1dx5)

The binding sites of Sodium atom in the structure of Crystal Structure of the Thrombin-Thrombomodulin Complex (pdb code 1dx5). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1dx5 structure was solved by P.FUENTES-PRIOR, Y.IWANAGA, R.HUBER, R.PAGILA, G.RUMENNIK, M.SETO, J.MORSER, D.R.LIGHT, W.BODE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-2.3 Space group H3 a (A) 214.400 b (A) 214.400 c (A) 131.410 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 20 Rfree (%) 24.1 Sodium Binding Sites: Sodium binding site 1 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: I: Glu357, I: Tyr358, I: Cys372, I: Ala373, I: Phe376, I: Cys386, I: Fmt501, conact list: Atom Atom Distance (A) Na OE2 I:Glu357 4.79 Na CB I:Tyr358 3.89 Na CE2 I:Tyr358 4.70 Na CD1 I:Tyr358 3.75 Na CD2 I:Tyr358 4.15 Na CZ I:Tyr358 4.78 Na CE1 I:Tyr358 4.35 Na CG I:Tyr358 3.64 Na CB I:Cys372 3.57 Na SG I:Cys372 4.43 Na C I:Cys372 4.09 Na CA I:Cys372 3.91 Na O I:Ala373 4.76 Na N I:Ala373 3.24 Na C I:Ala373 4.92 Na CB I:Ala373 3.78 Na CA I:Ala373 4.12 Na CB I:Phe376 3.78 Na CE2 I:Phe376 4.74 Na CD1 I:Phe376 4.20 Na CD2 I:Phe376 4.08 Na CE1 I:Phe376 4.84 Na CG I:Phe376 3.77 Na CB I:Cys386 3.66 Na SG I:Cys386 3.66 Na O1 I:Fmt501 2.87 Na O2 I:Fmt501 2.96 Na C I:Fmt501 3.47 interactive model: Sodium binding site 2 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: J: Glu357, J: Tyr358, J: Cys372, J: Ala373, J: Phe376, J: Cys386, J: Fmt501, conact list: Atom Atom Distance (A) Na OE2 J:Glu357 4.71 Na CB J:Tyr358 3.99 Na CE2 J:Tyr358 4.61 Na CD1 J:Tyr358 3.80 Na CD2 J:Tyr358 4.11 Na CZ J:Tyr358 4.71 Na CE1 J:Tyr358 4.34 Na CG J:Tyr358 3.68 Na CB J:Cys372 3.67 Na SG J:Cys372 4.56 Na C J:Cys372 3.98 Na CA J:Cys372 3.92 Na O J:Ala373 4.64 Na N J:Ala373 3.06 Na C J:Ala373 4.70 Na CB J:Ala373 3.45 Na CA J:Ala373 3.85 Na CB J:Phe376 3.72 Na CE2 J:Phe376 4.73 Na CD1 J:Phe376 4.10 Na CD2 J:Phe376 4.06 Na CE1 J:Phe376 4.76 Na CG J:Phe376 3.70 Na CB J:Cys386 3.79 Na SG J:Cys386 3.76 Na O1 J:Fmt501 3.04 Na O2 J:Fmt501 2.85 Na C J:Fmt501 3.51 interactive model: Sodium binding site 3 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: K: Glu357, K: Tyr358, K: Cys372, K: Ala373, K: Phe376, K: Cys386, K: Fmt501, conact list: Atom Atom Distance (A) Na OE2 K:Glu357 4.77 Na CB K:Tyr358 3.93 Na CE2 K:Tyr358 4.64 Na CD1 K:Tyr358 3.74 Na CD2 K:Tyr358 4.13 Na CZ K:Tyr358 4.71 Na CE1 K:Tyr358 4.29 Na CG K:Tyr358 3.65 Na CB K:Cys372 3.63 Na SG K:Cys372 4.50 Na C K:Cys372 4.12 Na CA K:Cys372 3.94 Na O K:Ala373 4.77 Na N K:Ala373 3.26 Na C K:Ala373 4.91 Na CB K:Ala373 3.71 Na CA K:Ala373 4.10 Na CB K:Phe376 3.78 Na CE2 K:Phe376 4.74 Na CD1 K:Phe376 4.12 Na CD2 K:Phe376 4.08 Na CE1 K:Phe376 4.78 Na CG K:Phe376 3.73 Na CB K:Cys386 3.73 Na SG K:Cys386 3.70 Na O1 K:Fmt501 2.80 Na O2 K:Fmt501 2.79 Na C K:Fmt501 3.32 interactive model: Sodium binding site 4 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: L: Glu357, L: Tyr358, L: Cys372, L: Ala373, L: Phe376, L: Cys386, L: Fmt501, conact list: Atom Atom Distance (A) Na OE2 L:Glu357 4.83 Na CB L:Tyr358 3.96 Na CE2 L:Tyr358 4.69 Na CD1 L:Tyr358 3.67 Na CD2 L:Tyr358 4.20 Na CZ L:Tyr358 4.70 Na CE1 L:Tyr358 4.22 Na CG L:Tyr358 3.67 Na CB L:Cys372 3.60 Na SG L:Cys372 4.51 Na C L:Cys372 4.01 Na CA L:Cys372 3.89 Na O L:Ala373 4.63 Na N L:Ala373 3.14 Na C L:Ala373 4.79 Na CB L:Ala373 3.66 Na CA L:Ala373 4.00 Na CB L:Phe376 3.67 Na CE2 L:Phe376 4.76 Na CD1 L:Phe376 4.14 Na CD2 L:Phe376 4.05 Na CE1 L:Phe376 4.84 Na CG L:Phe376 3.69 Na CB L:Cys386 3.77 Na SG L:Cys386 3.74 Na O1 L:Fmt501 2.78 Na O2 L:Fmt501 2.90 Na C L:Fmt501 3.35 interactive model: Sodium binding site 5 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: M: Tyr184A, M: Arg187, M: Gly188, M: Asp221, M: Arg221A, M: Asp222, M: Lys224, M: Hoh2085, M: Hoh2086, M: Hoh2091, M: Hoh2092, M: Hoh2109, M: Hoh2110, M: Hoh2111, conact list: Atom Atom Distance (A) Na O M:Tyr184A 4.23 Na CB M:Arg187 4.04 Na CZ M:Arg187 4.13 Na NE M:Arg187 4.39 Na NH2 M:Arg187 3.72 Na NH1 M:Arg187 4.80 Na CA M:Arg187 4.62 Na O M:Gly188 4.39 Na N M:Gly188 4.52 Na O M:Asp221 3.71 Na CB M:Asp221 4.45 Na OD2 M:Asp221 4.39 Na C M:Asp221 3.79 Na OD1 M:Asp221 2.67 Na CG M:Asp221 3.63 Na CA M:Asp221 4.02 Na O M:Arg221A 3.47 Na N M:Arg221A 4.35 Na C M:Arg221A 4.16 Na CA M:Arg221A 4.86 Na N M:Asp222 4.83 Na OD1 M:Asp222 4.84 Na CA M:Asp222 4.95 Na O M:Lys224 4.75 Na O M:Hoh2085 3.42 Na O M:Hoh2086 4.64 Na O M:Hoh2091 3.14 Na O M:Hoh2092 4.54 Na O M:Hoh2109 2.83 Na O M:Hoh2110 3.33 Na O M:Hoh2111 3.52 interactive model: Sodium binding site 6 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: N: Tyr184A, N: Asp221, N: Arg221A, N: Asp222, N: Gly223, N: Lys224, N: Tyr225, N: Hoh2094, N: Hoh2095, N: Hoh2103, N: Hoh2104, N: Hoh2105, N: Hoh2116, conact list: Atom Atom Distance (A) Na O N:Tyr184A 4.16 Na O N:Asp221 4.31 Na C N:Asp221 3.88 Na OD1 N:Asp221 4.37 Na CA N:Asp221 4.19 Na O N:Arg221A 2.25 Na N N:Arg221A 3.79 Na C N:Arg221A 3.37 Na CA N:Arg221A 4.23 Na N N:Asp222 4.28 Na C N:Asp222 4.72 Na CA N:Asp222 4.37 Na N N:Gly223 4.55 Na O N:Lys224 2.62 Na N N:Lys224 4.09 Na CB N:Lys224 4.62 Na C N:Lys224 3.71 Na CA N:Lys224 4.37 Na N N:Tyr225 4.76 Na O N:Hoh2094 2.54 Na O N:Hoh2095 2.71 Na O N:Hoh2103 4.21 Na O N:Hoh2104 3.89 Na O N:Hoh2105 4.63 Na O N:Hoh2116 2.38 interactive model: Sodium binding site 7 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: O: Tyr184A, O: Arg187, O: Asp221, O: Arg221A, O: Asp222, O: Gly223, O: Lys224, O: Tyr225, O: Hoh2087, O: Hoh2094, O: Hoh2095, O: Hoh2096, O: Hoh2109, O: Hoh2111, O: Hoh2112, O: Hoh2113, conact list: Atom Atom Distance (A) Na O O:Tyr184A 4.09 Na NH2 O:Arg187 4.94 Na O O:Asp221 4.33 Na C O:Asp221 3.96 Na OD1 O:Asp221 4.54 Na CA O:Asp221 4.33 Na O O:Arg221A 2.25 Na N O:Arg221A 3.88 Na C O:Arg221A 3.35 Na CA O:Arg221A 4.25 Na N O:Asp222 4.21 Na C O:Asp222 4.58 Na CA O:Asp222 4.25 Na N O:Gly223 4.34 Na C O:Gly223 4.98 Na O O:Lys224 2.56 Na N O:Lys224 3.94 Na CB O:Lys224 4.57 Na C O:Lys224 3.64 Na CA O:Lys224 4.26 Na N O:Tyr225 4.70 Na CA O:Tyr225 4.98 Na O O:Hoh2087 2.68 Na O O:Hoh2094 3.99 Na O O:Hoh2095 4.21 Na O O:Hoh2096 4.82 Na O O:Hoh2109 2.49 Na O O:Hoh2111 3.84 Na O O:Hoh2112 2.44 Na O O:Hoh2113 2.55 interactive model: Sodium binding site 8 out of 8 in 1dx5 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1dx5. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: Tyr184A, P: Asp221, P: Arg221A, P: Asp222, P: Gly223, P: Lys224, P: Tyr225, P: Hoh2089, P: Hoh2090, P: Hoh2097, P: Hoh2098, P: Hoh2099, P: Hoh2114, P: Hoh2115, conact list: Atom Atom Distance (A) Na O P:Tyr184A 4.05 Na O P:Asp221 4.33 Na C P:Asp221 3.94 Na OD1 P:Asp221 4.45 Na CA P:Asp221 4.27 Na O P:Arg221A 2.33 Na N P:Arg221A 3.87 Na C P:Arg221A 3.42 Na CA P:Arg221A 4.30 Na N P:Asp222 4.31 Na C P:Asp222 4.70 Na CA P:Asp222 4.37 Na N P:Gly223 4.51 Na O P:Lys224 2.69 Na N P:Lys224 4.12 Na CB P:Lys224 4.77 Na C P:Lys224 3.76 Na CA P:Lys224 4.44 Na N P:Tyr225 4.75 Na CA P:Tyr225 4.96 Na O P:Hoh2089 2.55 Na O P:Hoh2090 2.71 Na O P:Hoh2097 3.96 Na O P:Hoh2098 4.10 Na O P:Hoh2099 4.83 Na O P:Hoh2114 3.79 Na O P:Hoh2115 2.37 interactive model: