Sodium in the structure of Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1.70 A Resolution (pdb 3ihv)

The binding sites of Sodium atom in the structure of Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 At 1.70 A Resolution (pdb code 3ihv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3ihv structure was solved by JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 29.8-1.7 Space group P1211 a (A) 62.908 b (A) 72.318 c (A) 131.629 alpha (°) 90.00 beta (°) 97.31 gamma (°) 90.00 Rfactor (%) 16.2 Rfree (%) 19.3 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3ihv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3ihv. 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: Gly513, A: Tyr514, A: Trp515, A: Trp516, A: Glu517, A: Hoh572, A: Hoh901, conact list: Atom Atom Distance (A) Na O A:Gly513 2.44 Na C A:Gly513 3.58 Na CA A:Gly513 4.80 Na O A:Tyr514 2.93 Na N A:Tyr514 4.13 Na C A:Tyr514 3.44 Na CA A:Tyr514 3.72 Na N A:Trp515 4.39 Na C A:Trp515 4.34 Na CA A:Trp515 4.91 Na O A:Trp515 4.72 Na N A:Trp516 4.00 Na CB A:Trp516 4.58 Na C A:Trp516 3.49 Na CA A:Trp516 4.21 Na O A:Trp516 2.34 Na N A:Glu517 4.49 Na CA A:Glu517 4.68 Na O A:Hoh572 2.12 Na O A:Hoh901 2.53 interactive model: Sodium binding site 2 out of 4 in 3ihv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3ihv. 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: Thr271, A: Gly274, A: Ser286, A: Phe287, A: Tyr288, A: Asn411, A: Val412, A: Asn413, A: Hoh685, A: Hoh726, A: Hoh811, A: Hoh904, A: Hoh1057, A: Hoh1121, conact list: Atom Atom Distance (A) Na O A:Thr271 4.92 Na N A:Gly274 4.30 Na CA A:Gly274 3.96 Na OG A:Ser286 4.33 Na C A:Ser286 4.85 Na O A:Phe287 2.24 Na N A:Phe287 3.89 Na CB A:Phe287 4.67 Na C A:Phe287 3.40 Na CA A:Phe287 4.20 Na N A:Tyr288 4.36 Na CB A:Tyr288 4.17 Na CD1 A:Tyr288 4.98 Na CA A:Tyr288 4.48 Na O A:Asn411 2.30 Na CB A:Asn411 4.04 Na C A:Asn411 3.45 Na CA A:Asn411 4.13 Na N A:Val412 4.47 Na C A:Val412 4.53 Na CA A:Val412 4.68 Na N A:Asn413 4.38 Na CB A:Asn413 4.57 Na ND2 A:Asn413 3.52 Na OD1 A:Asn413 2.47 Na CG A:Asn413 3.28 Na CA A:Asn413 4.84 Na O A:Hoh685 2.82 Na O A:Hoh726 2.39 Na O A:Hoh811 2.33 Na O A:Hoh904 4.63 Na O A:Hoh1057 4.45 Na O A:Hoh1121 4.70 interactive model: Sodium binding site 3 out of 4 in 3ihv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3ihv. 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: Thr271, B: Gly274, B: Ser286, B: Phe287, B: Tyr288, B: Asn411, B: Val412, B: Asn413, B: Hoh605, B: Hoh662, B: Hoh714, B: Hoh880, B: Hoh905, conact list: Atom Atom Distance (A) Na O B:Thr271 4.93 Na N B:Gly274 4.35 Na CA B:Gly274 4.00 Na OG B:Ser286 4.37 Na C B:Ser286 4.80 Na CA B:Ser286 4.96 Na O B:Phe287 2.22 Na N B:Phe287 3.86 Na CB B:Phe287 4.62 Na C B:Phe287 3.42 Na CA B:Phe287 4.19 Na N B:Tyr288 4.40 Na CB B:Tyr288 4.33 Na CA B:Tyr288 4.55 Na O B:Asn411 2.29 Na CB B:Asn411 4.05 Na C B:Asn411 3.44 Na CA B:Asn411 4.13 Na O B:Val412 5.00 Na N B:Val412 4.45 Na C B:Val412 4.47 Na CA B:Val412 4.63 Na N B:Asn413 4.31 Na CB B:Asn413 4.52 Na ND2 B:Asn413 3.55 Na OD1 B:Asn413 2.39 Na CG B:Asn413 3.24 Na CA B:Asn413 4.76 Na O B:Hoh605 4.82 Na O B:Hoh662 2.48 Na O B:Hoh714 2.77 Na O B:Hoh880 4.81 Na O B:Hoh905 2.50 interactive model: Sodium binding site 4 out of 4 in 3ihv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3ihv. 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: Gly513, B: Tyr514, B: Trp515, B: Trp516, B: Glu517, B: Hoh636, B: Hoh892, B: Hoh916, conact list: Atom Atom Distance (A) Na O B:Gly513 2.44 Na C B:Gly513 3.59 Na CA B:Gly513 4.83 Na O B:Tyr514 2.88 Na N B:Tyr514 4.12 Na C B:Tyr514 3.41 Na CA B:Tyr514 3.70 Na N B:Trp515 4.35 Na C B:Trp515 4.35 Na CA B:Trp515 4.90 Na O B:Trp515 4.70 Na N B:Trp516 4.02 Na CB B:Trp516 4.66 Na C B:Trp516 3.56 Na CA B:Trp516 4.27 Na O B:Trp516 2.40 Na N B:Glu517 4.58 Na CA B:Glu517 4.78 Na O B:Hoh636 4.56 Na O B:Hoh892 2.23 Na O B:Hoh916 2.45 interactive model: