Sodium in the structure of Ternary Crystal Structure of A Polymerase Lambda Variant With A Gt Mispair At the Primer Terminus and Sodium At Catalytic Metal Site (pdb 3pnc)

The binding sites of Sodium atom in the structure of Ternary Crystal Structure of A Polymerase Lambda Variant With A Gt Mispair At the Primer Terminus and Sodium At Catalytic Metal Site (pdb code 3pnc). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3pnc structure was solved by K.BEBENEK, L.C.PEDERSEN, T.A.KUNKEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 22.4-2.0 Space group P212121 a (A) 56.161 b (A) 62.254 c (A) 139.834 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.8 Rfree (%) 23.6 Sodium Binding Sites: Sodium binding site 1 out of 3 in 3pnc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3pnc. 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: Asp427, A: Val428, A: Asp429, A: Arg488, A: Asp490, B: Dg6, A: 1gc1, A: Mg576, A: Trs577, conact list: Atom Atom Distance (A) Na CB A:Asp427 4.34 Na OD2 A:Asp427 3.03 Na OD1 A:Asp427 2.17 Na CG A:Asp427 2.93 Na O A:Val428 4.98 Na CB A:Asp429 4.51 Na OD2 A:Asp429 2.16 Na OD1 A:Asp429 3.49 Na CG A:Asp429 3.16 Na NH2 A:Arg488 4.71 Na CB A:Asp490 3.90 Na OD2 A:Asp490 2.37 Na OD1 A:Asp490 4.16 Na CG A:Asp490 3.28 Na OP1 B:Dg6 4.96 Na C3' B:Dg6 3.63 Na O3' B:Dg6 3.39 Na C5' B:Dg6 4.78 Na C2' B:Dg6 4.75 Na C4' B:Dg6 4.65 Na O5' B:Dg6 4.85 Na PA A:1gc1 3.27 Na C3A A:1gc1 4.83 Na O5' A:1gc1 3.83 Na O2B A:1gc1 4.75 Na O2A A:1gc1 2.22 Na C5' A:1gc1 3.93 Na O1G A:1gc1 4.66 Na O1A A:1gc1 3.56 Na MG A:Mg576 3.35 Na N A:Trs577 3.69 Na O1 A:Trs577 4.57 interactive model: Sodium binding site 2 out of 3 in 3pnc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3pnc. 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: Ser339, A: Asn340, A: Ile341, A: Trp342, A: Gly343, A: Ala344, A: Gly345, B: Dt4, B: Da5, A: Hoh3, A: Hoh121, A: Hoh603, B: Hoh8, B: Hoh9, B: Hoh211, conact list: Atom Atom Distance (A) Na O A:Ser339 2.44 Na CB A:Ser339 4.70 Na C A:Ser339 3.43 Na CA A:Ser339 4.16 Na O A:Asn340 4.82 Na N A:Asn340 4.36 Na C A:Asn340 4.26 Na CA A:Asn340 4.49 Na O A:Ile341 2.47 Na N A:Ile341 4.03 Na C A:Ile341 3.41 Na CA A:Ile341 4.42 Na N A:Trp342 4.04 Na C A:Trp342 4.25 Na CA A:Trp342 3.93 Na N A:Gly343 3.89 Na C A:Gly343 4.63 Na CA A:Gly343 4.85 Na O A:Ala344 2.34 Na N A:Ala344 3.66 Na C A:Ala344 3.43 Na CB A:Ala344 4.56 Na CA A:Ala344 4.09 Na N A:Gly345 4.47 Na CA A:Gly345 4.73 Na O3' B:Dt4 4.37 Na OP1 B:Da5 2.38 Na P B:Da5 3.47 Na OP2 B:Da5 3.71 Na O5' B:Da5 4.68 Na O A:Hoh3 2.34 Na O A:Hoh121 3.44 Na O A:Hoh603 4.94 Na O B:Hoh8 2.65 Na O B:Hoh9 3.99 Na O B:Hoh211 4.85 interactive model: Sodium binding site 3 out of 3 in 3pnc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3pnc. 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: Da5, B: Dg6, C: Dc5, A: 1gc1, A: Hoh44, A: Hoh64, B: Hoh42, B: Hoh54, B: Hoh92, B: Hoh110, B: Hoh160, B: Hoh212, C: Hoh37, conact list: Atom Atom Distance (A) Na N9 B:Da5 4.69 Na C8 B:Da5 4.37 Na C6 B:Da5 4.95 Na C5 B:Da5 4.42 Na N7 B:Da5 4.21 Na C4 B:Da5 4.73 Na C2' B:Da5 4.90 Na N9 B:Dg6 4.69 Na C8 B:Dg6 3.46 Na C6 B:Dg6 4.17 Na C5 B:Dg6 3.68 Na N7 B:Dg6 2.62 Na C4 B:Dg6 4.80 Na O6 B:Dg6 3.91 Na N4 C:Dc5 4.36 Na C6 A:1gc1 3.81 Na C5 A:1gc1 4.30 Na N1 A:1gc1 5.00 Na N7 A:1gc1 4.09 Na O6 A:1gc1 2.85 Na O A:Hoh44 2.87 Na O A:Hoh64 2.57 Na O B:Hoh42 2.39 Na O B:Hoh54 2.43 Na O B:Hoh92 4.68 Na O B:Hoh110 4.56 Na O B:Hoh160 4.42 Na O B:Hoh212 4.78 Na O C:Hoh37 4.74 interactive model: