Sodium in the structure of Methyl-Coenzyme M Reductase Enzyme Product Complex (pdb 1hbm)

The binding sites of Sodium atom in the structure of Methyl-Coenzyme M Reductase Enzyme Product Complex (pdb code 1hbm). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1hbm structure was solved by U.ERMLER, W.GRABARSE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 10.0-1.8 Space group P1211 a (A) 82.000 b (A) 118.300 c (A) 122.800 alpha (°) 90.00 beta (°) 92.00 gamma (°) 90.00 Rfactor (%) 16.4 Rfree (%) 19.3 Sodium Binding Sites: Sodium binding site 1 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1hbm. 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: A: Lys11, A: Lys12, A: Phe14, A: Glu15, A: Glu16, A: Hoh2024, A: Hoh2026, A: Hoh2027, A: Hoh2035, A: Hoh2036, A: Hoh2044, conact list: Atom Atom Distance (A) Na O A:Lys11 2.34 Na CB A:Lys11 4.44 Na C A:Lys11 3.44 Na CA A:Lys11 3.97 Na N A:Lys12 4.53 Na C A:Lys12 5.00 Na CA A:Lys12 4.86 Na O A:Phe14 2.35 Na N A:Phe14 4.54 Na C A:Phe14 3.50 Na CA A:Phe14 4.63 Na O A:Glu15 3.89 Na N A:Glu15 4.14 Na C A:Glu15 4.11 Na CA A:Glu15 3.93 Na O A:Glu16 4.57 Na N A:Glu16 5.00 Na O A:Hoh2024 4.52 Na O A:Hoh2026 4.35 Na O A:Hoh2027 2.33 Na O A:Hoh2035 2.35 Na O A:Hoh2036 2.35 Na O A:Hoh2044 2.35 interactive model: Sodium binding site 2 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 1hbm. 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: A: Val269, A: Arg270, A: Agm271, D: Arg225, D: Mhs257, D: Glu275, A: Sht1551, D: Gol1553, A: Hoh2261, A: Hoh2420, D: Hoh2273, D: Hoh2422, D: Hoh2423, D: Hoh2437, conact list: Atom Atom Distance (A) Na O A:Val269 4.24 Na C A:Val269 4.96 Na O A:Arg270 2.42 Na N A:Arg270 4.81 Na CB A:Arg270 4.37 Na C A:Arg270 3.40 Na CG A:Arg270 3.82 Na CA A:Arg270 3.63 Na N A:Agm271 4.62 Na NH1 D:Arg225 4.08 Na CE1 D:Mhs257 4.41 Na OE2 D:Glu275 4.41 Na O A:Sht1551 4.46 Na O1P A:Sht1551 4.62 Na C1 D:Gol1553 3.99 Na O1 D:Gol1553 3.86 Na C3 D:Gol1553 3.61 Na O3 D:Gol1553 2.44 Na C2 D:Gol1553 4.36 Na O A:Hoh2261 2.38 Na O A:Hoh2420 2.36 Na O D:Hoh2273 3.28 Na O D:Hoh2422 4.60 Na O D:Hoh2423 3.66 Na O D:Hoh2437 2.34 interactive model: Sodium binding site 3 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 1hbm. 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: A: Arg543, A: Ala544, A: Leu545, A: Thr547, A: Pro548, A: Ala549, A: Hoh2205, A: Hoh2407, A: Hoh2410, D: Hoh2208, D: Hoh2413, D: Hoh2419, conact list: Atom Atom Distance (A) Na O A:Arg543 4.90 Na O A:Ala544 2.41 Na N A:Ala544 4.99 Na C A:Ala544 3.40 Na CB A:Ala544 4.20 Na CA A:Ala544 3.68 Na N A:Leu545 4.64 Na O A:Thr547 2.39 Na N A:Thr547 3.94 Na CB A:Thr547 3.55 Na CG2 A:Thr547 4.74 Na OG1 A:Thr547 2.39 Na C A:Thr547 3.17 Na CA A:Thr547 3.77 Na O A:Pro548 2.41 Na N A:Pro548 3.86 Na C A:Pro548 3.34 Na CA A:Pro548 4.13 Na N A:Ala549 4.04 Na CA A:Ala549 4.34 Na O A:Hoh2205 4.56 Na O A:Hoh2407 2.34 Na O A:Hoh2410 2.34 Na O D:Hoh2208 4.95 Na O D:Hoh2413 4.12 Na O D:Hoh2419 4.55 interactive model: Sodium binding site 4 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 1hbm. 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: A: Asn57, A: Pro58, A: Asp59, A: Ile60, A: Gly61, A: Thr62, A: Pro63, A: Leu64, D: Ala144, A: Hoh2104, A: Hoh2110, A: Hoh2112, A: Hoh2113, D: Hoh2172, D: Hoh2173, D: Hoh2174, conact list: Atom Atom Distance (A) Na O A:Asn57 4.73 Na O A:Pro58 3.06 Na C A:Pro58 3.91 Na CA A:Pro58 4.44 Na N A:Asp59 4.76 Na C A:Asp59 4.70 Na CA A:Asp59 4.98 Na O A:Ile60 2.35 Na N A:Ile60 4.34 Na C A:Ile60 3.59 Na CA A:Ile60 4.56 Na O A:Gly61 4.08 Na N A:Gly61 4.44 Na C A:Gly61 3.91 Na CA A:Gly61 4.43 Na O A:Thr62 2.35 Na N A:Thr62 3.83 Na C A:Thr62 3.38 Na CA A:Thr62 4.17 Na N A:Pro63 4.23 Na C A:Pro63 4.95 Na CA A:Pro63 4.29 Na N A:Leu64 4.54 Na O D:Ala144 4.38 Na O A:Hoh2104 4.55 Na O A:Hoh2110 2.34 Na O A:Hoh2112 3.12 Na O A:Hoh2113 3.03 Na O D:Hoh2172 2.37 Na O D:Hoh2173 4.47 Na O D:Hoh2174 4.05 interactive model: Sodium binding site 5 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 1hbm. 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: B: Asn441, B: Glu442, B: Hoh2195, B: Hoh2366, B: Hoh2368, conact list: Atom Atom Distance (A) Na O B:Asn441 2.37 Na CB B:Asn441 3.81 Na ND2 B:Asn441 4.50 Na C B:Asn441 3.48 Na CG B:Asn441 4.69 Na CA B:Asn441 3.98 Na N B:Glu442 4.62 Na CA B:Glu442 4.97 Na O B:Hoh2195 4.31 Na O B:Hoh2366 4.52 Na O B:Hoh2368 2.37 interactive model: Sodium binding site 6 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 1hbm. 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: B: Lys90, B: Asp98, B: Asp99, B: Asp100, B: Thr101, B: Asn102, B: Hoh2122, B: Hoh2130, B: Hoh2140, B: Hoh2145, B: Hoh2147, conact list: Atom Atom Distance (A) Na CE B:Lys90 4.66 Na NZ B:Lys90 4.29 Na O B:Asp98 4.94 Na OD2 B:Asp98 4.34 Na C B:Asp98 4.52 Na CA B:Asp98 4.77 Na O B:Asp99 2.38 Na N B:Asp99 4.45 Na OD2 B:Asp99 4.64 Na C B:Asp99 3.58 Na CA B:Asp99 4.70 Na O B:Asp100 4.48 Na N B:Asp100 4.25 Na C B:Asp100 3.86 Na CA B:Asp100 3.98 Na O B:Thr101 2.38 Na N B:Thr101 3.66 Na CB B:Thr101 4.63 Na C B:Thr101 3.50 Na CA B:Thr101 4.11 Na N B:Asn102 4.58 Na OD1 B:Asn102 3.89 Na CG B:Asn102 4.76 Na CA B:Asn102 4.92 Na O B:Hoh2122 2.35 Na O B:Hoh2130 4.01 Na O B:Hoh2140 2.36 Na O B:Hoh2145 2.35 Na O B:Hoh2147 2.35 interactive model: Sodium binding site 7 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 1hbm. 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: D: Lys11, D: Lys12, D: Phe14, D: Glu15, D: Glu16, D: Hoh2004, D: Hoh2008, D: Hoh2012, D: Hoh2016, D: Hoh2017, D: Hoh2022, D: Hoh2028, conact list: Atom Atom Distance (A) Na O D:Lys11 2.36 Na CB D:Lys11 4.32 Na C D:Lys11 3.45 Na CA D:Lys11 3.90 Na N D:Lys12 4.60 Na CA D:Lys12 4.97 Na O D:Phe14 2.37 Na N D:Phe14 4.59 Na C D:Phe14 3.49 Na CA D:Phe14 4.65 Na O D:Glu15 3.88 Na N D:Glu15 4.17 Na C D:Glu15 4.08 Na CA D:Glu15 3.93 Na O D:Glu16 4.49 Na N D:Glu16 4.98 Na O D:Hoh2004 4.78 Na O D:Hoh2008 4.88 Na O D:Hoh2012 4.86 Na O D:Hoh2016 2.35 Na O D:Hoh2017 2.34 Na O D:Hoh2022 2.36 Na O D:Hoh2028 2.34 interactive model: Sodium binding site 8 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 1hbm. 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: A: Arg225, A: Mhs257, A: Glu275, D: Val269, D: Arg270, D: Agm271, A: Gol1552, D: Sht1551, A: Hoh2424, D: Hoh2139, D: Hoh2266, D: Hoh2432, E: Hoh2076, E: Hoh2087, conact list: Atom Atom Distance (A) Na NH1 A:Arg225 4.10 Na CE1 A:Mhs257 4.42 Na OE2 A:Glu275 4.48 Na O D:Val269 4.11 Na C D:Val269 4.81 Na O D:Arg270 2.41 Na N D:Arg270 4.67 Na CB D:Arg270 4.27 Na C D:Arg270 3.33 Na CG D:Arg270 3.70 Na CA D:Arg270 3.51 Na N D:Agm271 4.56 Na O2 A:Gol1552 3.96 Na C1 A:Gol1552 3.28 Na O1 A:Gol1552 2.43 Na C2 A:Gol1552 4.15 Na O D:Sht1551 4.48 Na O1P D:Sht1551 4.60 Na O A:Hoh2424 3.24 Na O D:Hoh2139 2.33 Na O D:Hoh2266 2.38 Na O D:Hoh2432 2.35 Na O E:Hoh2076 3.48 Na O E:Hoh2087 4.50 interactive model: Sodium binding site 9 out of 9 in 1hbm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 1hbm. 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: A: Ala144, D: Asn57, D: Pro58, D: Asp59, D: Ile60, D: Gly61, D: Thr62, D: Pro63, D: Leu64, A: Hoh2174, A: Hoh2177, D: Hoh2093, D: Hoh2098, D: Hoh2099, D: Hoh2103, D: Hoh2104, conact list: Atom Atom Distance (A) Na O A:Ala144 4.48 Na O D:Asn57 4.76 Na O D:Pro58 2.41 Na C D:Pro58 3.55 Na CA D:Pro58 4.39 Na O D:Asp59 4.85 Na N D:Asp59 4.41 Na C D:Asp59 4.28 Na CA D:Asp59 4.49 Na O D:Ile60 2.36 Na N D:Ile60 4.10 Na C D:Ile60 3.53 Na CA D:Ile60 4.41 Na O D:Gly61 4.08 Na N D:Gly61 4.40 Na C D:Gly61 3.88 Na CA D:Gly61 4.42 Na O D:Thr62 2.38 Na N D:Thr62 3.83 Na C D:Thr62 3.42 Na CA D:Thr62 4.22 Na N D:Pro63 4.25 Na CA D:Pro63 4.26 Na N D:Leu64 4.67 Na O A:Hoh2174 2.35 Na O A:Hoh2177 4.06 Na O D:Hoh2093 4.72 Na O D:Hoh2098 2.36 Na O D:Hoh2099 3.33 Na O D:Hoh2103 2.83 Na O D:Hoh2104 4.54 interactive model: