Sodium in the structure of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked With Divalent Mercury (pdb 3kbc)

The binding sites of Sodium atom in the structure of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked With Divalent Mercury (pdb code 3kbc). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3kbc structure was solved by N.REYES, C.GINTER, O.BOUDKER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 12.0-3.5 Space group C2221 a (A) 113.142 b (A) 206.780 c (A) 205.971 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 26.7 Rfree (%) 27 Sodium Binding Sites: Sodium binding site 1 out of 6 in 3kbc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3kbc. 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: Ser278, A: Gly306, A: Ala307, A: Ile309, A: Asn310, A: Met311, A: Asn401, A: Val402, A: Asp405, conact list: Atom Atom Distance (A) Na OG A:Ser278 4.34 Na O A:Gly306 2.14 Na C A:Gly306 3.35 Na CA A:Gly306 4.18 Na O A:Ala307 4.70 Na N A:Ala307 4.33 Na C A:Ala307 4.57 Na CA A:Ala307 4.47 Na O A:Ile309 3.24 Na C A:Ile309 4.33 Na O A:Asn310 2.50 Na N A:Asn310 4.82 Na CB A:Asn310 4.28 Na C A:Asn310 3.43 Na OD1 A:Asn310 4.78 Na CG A:Asn310 4.51 Na CA A:Asn310 4.35 Na N A:Met311 4.13 Na CB A:Met311 4.63 Na CG A:Met311 4.00 Na CA A:Met311 4.12 Na O A:Asn401 3.00 Na CB A:Asn401 3.88 Na C A:Asn401 3.62 Na CG A:Asn401 4.87 Na CA A:Asn401 4.01 Na N A:Val402 4.53 Na CA A:Val402 4.98 Na CB A:Asp405 4.74 Na OD2 A:Asp405 3.12 Na OD1 A:Asp405 2.66 Na CG A:Asp405 3.26 interactive model: Sodium binding site 2 out of 6 in 3kbc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3kbc. 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: Thr308, A: Ile309, A: Met311, A: Ser349, A: Ile350, A: Gly351, A: Thr352, A: Ala353, conact list: Atom Atom Distance (A) Na O A:Thr308 2.66 Na C A:Thr308 3.75 Na CA A:Thr308 4.71 Na N A:Ile309 4.53 Na CA A:Ile309 4.47 Na CG A:Met311 4.33 Na SD A:Met311 3.61 Na O A:Ser349 2.26 Na C A:Ser349 3.18 Na CA A:Ser349 4.55 Na O A:Ile350 2.65 Na N A:Ile350 3.49 Na CB A:Ile350 4.36 Na CG2 A:Ile350 4.62 Na C A:Ile350 2.51 Na CA A:Ile350 2.97 Na O A:Gly351 3.85 Na N A:Gly351 2.95 Na C A:Gly351 3.23 Na CA A:Gly351 3.55 Na O A:Thr352 2.58 Na N A:Thr352 3.00 Na CB A:Thr352 3.96 Na OG1 A:Thr352 4.82 Na C A:Thr352 3.44 Na CA A:Thr352 3.59 Na N A:Ala353 4.71 interactive model: Sodium binding site 3 out of 6 in 3kbc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3kbc. 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: Ser278, B: Gly306, B: Ala307, B: Ile309, B: Asn310, B: Met311, B: Asn401, B: Val402, B: Asp405, conact list: Atom Atom Distance (A) Na OG B:Ser278 4.36 Na O B:Gly306 2.10 Na C B:Gly306 3.31 Na CA B:Gly306 4.14 Na O B:Ala307 4.67 Na N B:Ala307 4.30 Na C B:Ala307 4.54 Na CA B:Ala307 4.45 Na O B:Ile309 3.19 Na C B:Ile309 4.28 Na O B:Asn310 2.51 Na N B:Asn310 4.79 Na CB B:Asn310 4.24 Na ND2 B:Asn310 4.97 Na C B:Asn310 3.42 Na OD1 B:Asn310 4.76 Na CG B:Asn310 4.48 Na CA B:Asn310 4.33 Na N B:Met311 4.13 Na CB B:Met311 4.64 Na CG B:Met311 4.01 Na CA B:Met311 4.13 Na O B:Asn401 3.05 Na CB B:Asn401 3.92 Na C B:Asn401 3.67 Na CG B:Asn401 4.91 Na CA B:Asn401 4.06 Na N B:Val402 4.57 Na CB B:Asp405 4.76 Na OD2 B:Asp405 3.14 Na OD1 B:Asp405 2.67 Na CG B:Asp405 3.28 interactive model: Sodium binding site 4 out of 6 in 3kbc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3kbc. 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: Thr308, B: Ile309, B: Met311, B: Ser349, B: Ile350, B: Gly351, B: Thr352, B: Ala353, conact list: Atom Atom Distance (A) Na O B:Thr308 2.70 Na C B:Thr308 3.79 Na CA B:Thr308 4.76 Na N B:Ile309 4.56 Na CA B:Ile309 4.49 Na CG B:Met311 4.31 Na SD B:Met311 3.61 Na O B:Ser349 2.20 Na C B:Ser349 3.12 Na CA B:Ser349 4.49 Na O B:Ile350 2.63 Na N B:Ile350 3.43 Na CB B:Ile350 4.32 Na CG2 B:Ile350 4.60 Na C B:Ile350 2.46 Na CA B:Ile350 2.92 Na O B:Gly351 3.87 Na N B:Gly351 2.90 Na C B:Gly351 3.22 Na CA B:Gly351 3.52 Na O B:Thr352 2.62 Na N B:Thr352 2.98 Na CB B:Thr352 3.93 Na OG1 B:Thr352 4.77 Na C B:Thr352 3.46 Na CA B:Thr352 3.59 Na N B:Ala353 4.74 interactive model: Sodium binding site 5 out of 6 in 3kbc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3kbc. 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: C: Ser278, C: Gly306, C: Ala307, C: Ile309, C: Asn310, C: Met311, C: Asn401, C: Val402, C: Asp405, conact list: Atom Atom Distance (A) Na OG C:Ser278 4.33 Na O C:Gly306 2.09 Na C C:Gly306 3.30 Na CA C:Gly306 4.13 Na O C:Ala307 4.65 Na N C:Ala307 4.28 Na C C:Ala307 4.53 Na CA C:Ala307 4.43 Na O C:Ile309 3.23 Na C C:Ile309 4.32 Na O C:Asn310 2.55 Na N C:Asn310 4.83 Na CB C:Asn310 4.28 Na ND2 C:Asn310 5.00 Na C C:Asn310 3.46 Na OD1 C:Asn310 4.78 Na CG C:Asn310 4.51 Na CA C:Asn310 4.37 Na N C:Met311 4.17 Na CB C:Met311 4.68 Na CG C:Met311 4.03 Na CA C:Met311 4.17 Na O C:Asn401 3.04 Na CB C:Asn401 3.92 Na C C:Asn401 3.65 Na CG C:Asn401 4.92 Na CA C:Asn401 4.06 Na N C:Val402 4.55 Na CA C:Val402 4.98 Na CB C:Asp405 4.72 Na OD2 C:Asp405 3.08 Na OD1 C:Asp405 2.64 Na CG C:Asp405 3.23 interactive model: Sodium binding site 6 out of 6 in 3kbc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3kbc. 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: C: Thr308, C: Ile309, C: Met311, C: Ser349, C: Ile350, C: Gly351, C: Thr352, C: Ala353, conact list: Atom Atom Distance (A) Na O C:Thr308 2.70 Na C C:Thr308 3.79 Na CA C:Thr308 4.76 Na N C:Ile309 4.55 Na CA C:Ile309 4.47 Na CG C:Met311 4.31 Na SD C:Met311 3.63 Na O C:Ser349 2.17 Na C C:Ser349 3.09 Na CA C:Ser349 4.48 Na O C:Ile350 2.65 Na N C:Ile350 3.41 Na CB C:Ile350 4.30 Na CG2 C:Ile350 4.58 Na C C:Ile350 2.46 Na CA C:Ile350 2.90 Na O C:Gly351 3.90 Na N C:Gly351 2.90 Na C C:Gly351 3.25 Na CA C:Gly351 3.53 Na O C:Thr352 2.65 Na N C:Thr352 3.01 Na CB C:Thr352 3.96 Na OG1 C:Thr352 4.80 Na C C:Thr352 3.49 Na CA C:Thr352 3.62 Na N C:Ala353 4.77 interactive model: