Sodium in the structure of Dna Polymerase Lambda in Complex With Dttp and A Dna Duplex Containing An Unpaired Dtmp (pdb 2bcv)

The binding sites of Sodium atom in the structure of Dna Polymerase Lambda in Complex With Dttp and A Dna Duplex Containing An Unpaired Dtmp (pdb code 2bcv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 2bcv structure was solved by M.GARCIA-DIAZ, K.BEBENEK, J.M.KRAHN, L.C.PEDERSEN, T.A.KUNKEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 31.2-2.0 Space group P212121 a (A) 55.140 b (A) 62.988 c (A) 141.936 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.4 Rfree (%) 23.2 Sodium Binding Sites: Sodium binding site 1 out of 3 in 2bcv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2bcv. 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: Dt4, P: Da5, A: Ser339, A: Asn340, A: Ile341, A: Trp342, A: Gly343, A: Ala344, A: Gly345, P: Hoh109, P: Hoh250, P: Hoh271, A: Hoh581, A: Hoh735, conact list: Atom Atom Distance (A) Na O3' P:Dt4 4.35 Na OP1 P:Da5 2.48 Na P P:Da5 3.51 Na OP2 P:Da5 3.68 Na O5' P:Da5 4.78 Na O A:Ser339 2.53 Na CB A:Ser339 4.90 Na C A:Ser339 3.45 Na CA A:Ser339 4.27 Na O A:Asn340 4.65 Na N A:Asn340 4.25 Na C A:Asn340 4.09 Na CA A:Asn340 4.28 Na O A:Ile341 2.58 Na N A:Ile341 3.92 Na C A:Ile341 3.44 Na CA A:Ile341 4.40 Na N A:Trp342 4.08 Na C A:Trp342 4.32 Na CA A:Trp342 4.02 Na N A:Gly343 3.94 Na C A:Gly343 4.69 Na CA A:Gly343 4.89 Na O A:Ala344 2.44 Na N A:Ala344 3.69 Na C A:Ala344 3.52 Na CB A:Ala344 4.60 Na CA A:Ala344 4.13 Na N A:Gly345 4.58 Na CA A:Gly345 4.82 Na O P:Hoh109 2.65 Na O P:Hoh250 4.72 Na O P:Hoh271 4.08 Na O A:Hoh581 2.66 Na O A:Hoh735 4.11 interactive model: Sodium binding site 2 out of 3 in 2bcv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 2bcv. 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: T: Dt11, A: Ser463, A: Gln464, A: Glu465, A: Glu466, T: Hoh28, T: Hoh42, T: Hoh45, T: Hoh46, T: Hoh61, A: Hoh721, A: Hoh754, conact list: Atom Atom Distance (A) Na OP1 T:Dt11 3.71 Na P T:Dt11 4.61 Na OP2 T:Dt11 4.51 Na O A:Ser463 2.48 Na N A:Ser463 4.54 Na CB A:Ser463 4.42 Na OG A:Ser463 4.98 Na C A:Ser463 3.52 Na CA A:Ser463 4.38 Na N A:Gln464 4.36 Na C A:Gln464 4.97 Na CA A:Gln464 4.40 Na N A:Glu465 4.37 Na OE2 A:Glu465 4.86 Na OE2 A:Glu466 4.31 Na O T:Hoh28 2.98 Na O T:Hoh42 3.82 Na O T:Hoh45 4.01 Na O T:Hoh46 2.58 Na O T:Hoh61 2.34 Na O A:Hoh721 2.53 Na O A:Hoh754 2.74 interactive model: Sodium binding site 3 out of 3 in 2bcv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 2bcv. 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: O2c6, A: Asp427, A: Asp429, A: Asp490, A: Phe506, A: Mg576, A: Ttp580, P: Hoh45, A: Hoh587, A: Hoh632, conact list: Atom Atom Distance (A) Na C3' P:O2c6 3.75 Na C5' P:O2c6 4.19 Na O1P P:O2c6 4.85 Na C2' P:O2c6 4.92 Na C4' P:O2c6 4.14 Na O5' P:O2c6 4.87 Na O2' P:O2c6 4.93 Na CB A:Asp427 4.70 Na OD2 A:Asp427 3.33 Na OD1 A:Asp427 2.42 Na CG A:Asp427 3.25 Na CB A:Asp429 4.73 Na OD2 A:Asp429 3.79 Na OD1 A:Asp429 2.38 Na CG A:Asp429 3.43 Na CB A:Asp490 3.31 Na OD2 A:Asp490 4.51 Na OD1 A:Asp490 2.51 Na CG A:Asp490 3.31 Na CA A:Asp490 4.82 Na CE2 A:Phe506 4.92 Na MG A:Mg576 3.62 Na PA A:Ttp580 3.49 Na O3G A:Ttp580 4.79 Na O2A A:Ttp580 3.95 Na O1B A:Ttp580 4.95 Na C5' A:Ttp580 3.82 Na O5' A:Ttp580 3.63 Na O3A A:Ttp580 4.87 Na O1A A:Ttp580 2.59 Na O P:Hoh45 2.70 Na O A:Hoh587 3.93 Na O A:Hoh632 4.07 interactive model: