Sodium in the structure of Structure Of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex With A Blunt-Ended Dna and Ddatp (pdb 3lwm)

The binding sites of Sodium atom in the structure of Structure Of the Large Fragment of Thermus Aquaticus Dna Polymerase I in Complex With A Blunt-Ended Dna and Ddatp (pdb code 3lwm). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3lwm structure was solved by A.MARX, K.DIEDERICHS, S.OBEID, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 47.5-2.2 Space group P3121 a (A) 109.592 b (A) 109.592 c (A) 91.037 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 18.3 Rfree (%) 22.8 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3lwm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3lwm. 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: Arg573, A: Glu615, A: Leu670, A: Tyr671, A: Asn750, A: Gln754, C: Dt205, A: Hoh162, conact list: Atom Atom Distance (A) Na NH2 A:Arg573 4.46 Na OE1 A:Glu615 3.52 Na OE2 A:Glu615 3.33 Na CD A:Glu615 3.66 Na CG A:Glu615 4.87 Na CD2 A:Leu670 4.18 Na CG A:Leu670 4.71 Na CD1 A:Tyr671 4.17 Na CZ A:Tyr671 4.49 Na CE1 A:Tyr671 3.48 Na OH A:Tyr671 4.55 Na ND2 A:Asn750 3.86 Na OD1 A:Asn750 3.07 Na CG A:Asn750 3.87 Na N A:Gln754 4.71 Na OE1 A:Gln754 3.20 Na CB A:Gln754 3.62 Na CD A:Gln754 3.96 Na CG A:Gln754 3.98 Na CA A:Gln754 4.33 Na C2 C:Dt205 4.44 Na N1 C:Dt205 4.83 Na C1' C:Dt205 4.47 Na O2 C:Dt205 3.72 Na O A:Hoh162 3.16 interactive model: Sodium binding site 2 out of 4 in 3lwm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3lwm. 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: Arg715, A: Arg741, A: Glu745, A: Hoh14, A: Hoh26, A: Hoh84, A: Hoh86, conact list: Atom Atom Distance (A) Na NH1 A:Arg715 4.76 Na CD A:Arg741 3.95 Na CZ A:Arg741 4.24 Na CG A:Arg741 4.53 Na NE A:Arg741 3.30 Na NH2 A:Arg741 4.29 Na OE1 A:Glu745 3.82 Na OE2 A:Glu745 2.88 Na CD A:Glu745 3.71 Na O A:Hoh14 4.41 Na O A:Hoh26 3.85 Na O A:Hoh84 3.18 Na O A:Hoh86 3.63 interactive model: Sodium binding site 3 out of 4 in 3lwm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3lwm. 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: Glu774, conact list: Atom Atom Distance (A) Na OE1 A:Glu774 3.52 Na CD A:Glu774 4.71 interactive model: Sodium binding site 4 out of 4 in 3lwm Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3lwm. 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: Leu352, A: Ala353, A: Lys354, A: Asp355, A: Asp372, A: Hoh10, A: Hoh31, A: Hoh38, A: Hoh75, A: Hoh77, A: Hoh112, A: Hoh842, conact list: Atom Atom Distance (A) Na O A:Leu352 3.91 Na N A:Leu352 4.97 Na CB A:Leu352 4.09 Na CD2 A:Leu352 3.92 Na C A:Leu352 3.89 Na CG A:Leu352 4.65 Na CA A:Leu352 3.73 Na N A:Ala353 4.61 Na C A:Ala353 4.95 Na N A:Lys354 4.11 Na CB A:Lys354 3.75 Na CE A:Lys354 4.03 Na CD A:Lys354 4.82 Na C A:Lys354 4.39 Na CG A:Lys354 4.31 Na CA A:Lys354 4.27 Na NZ A:Lys354 3.57 Na N A:Asp355 3.62 Na CB A:Asp355 4.17 Na OD2 A:Asp355 3.96 Na OD1 A:Asp355 3.29 Na CG A:Asp355 3.55 Na CA A:Asp355 4.42 Na OD2 A:Asp372 4.88 Na O A:Hoh10 4.33 Na O A:Hoh31 3.24 Na O A:Hoh38 4.28 Na O A:Hoh75 4.66 Na O A:Hoh77 3.77 Na O A:Hoh112 2.98 Na O A:Hoh842 3.71 interactive model: