Sodium in the structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed With 8-Quinolinol (pdb 3vh9)

The binding sites of Sodium atom in the structure of Crystal Structure of Aeromonas Proteolytica Aminopeptidase Complexed With 8-Quinolinol (pdb code 3vh9). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3vh9 structure was solved by S.SAIJO, K.HANAYA, M.SUETSUGU, K.KOBAYASHI, I.YAMATO, S.AOKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 13.6-1.3 Space group P6122 a (A) 108.463 b (A) 108.463 c (A) 90.737 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) 13.1 Rfree (%) 15.3 Sodium Binding Sites: Sodium binding site 1 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3vh9. 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: Thr194, A: Asp195, A: Tyr196, A: Thr197, A: Asp198, A: Ser199, A: Scn322, A: Hoh458, A: Hoh468, A: Hoh597, A: Hoh600, A: Hoh625, A: Hoh673, A: Hoh705, conact list: Atom Atom Distance (A) Na O A:Thr194 2.42 Na CB A:Thr194 4.61 Na C A:Thr194 3.52 Na CA A:Thr194 4.21 Na N A:Asp195 4.54 Na C A:Asp195 4.99 Na CA A:Asp195 4.68 Na N A:Tyr196 4.99 Na O A:Thr197 2.47 Na N A:Thr197 4.12 Na CB A:Thr197 4.43 Na OG1 A:Thr197 3.47 Na C A:Thr197 3.40 Na CA A:Thr197 4.19 Na N A:Asp198 4.28 Na C A:Asp198 4.46 Na CA A:Asp198 4.48 Na N A:Ser199 4.17 Na CB A:Ser199 4.60 Na CA A:Ser199 4.70 Na N A:Scn322 4.45 Na O A:Hoh458 3.49 Na O A:Hoh468 2.42 Na O A:Hoh597 4.55 Na O A:Hoh600 2.83 Na O A:Hoh625 2.41 Na O A:Hoh673 3.62 Na O A:Hoh705 4.82 interactive model: Sodium binding site 2 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3vh9. 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: Asn74, A: Na312, A: Hoh431, A: Hoh466, A: Hoh469, A: Hoh496, A: Hoh498, A: Hoh501, A: Hoh565, A: Hoh616, A: Hoh623, A: Hoh624, conact list: Atom Atom Distance (A) Na CB A:Asn74 4.12 Na ND2 A:Asn74 4.20 Na OD1 A:Asn74 2.44 Na CG A:Asn74 3.35 Na CA A:Asn74 4.29 Na NA A:Na312 3.58 Na O A:Hoh431 4.01 Na O A:Hoh466 4.54 Na O A:Hoh469 4.03 Na O A:Hoh496 2.42 Na O A:Hoh498 2.54 Na O A:Hoh501 2.43 Na O A:Hoh565 4.21 Na O A:Hoh616 4.67 Na O A:Hoh623 2.41 Na O A:Hoh624 4.44 interactive model: Sodium binding site 3 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3vh9. 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: Gln203, A: Thr206, A: Asp210, A: Tyr218, A: Hoh441, A: Hoh455, A: Hoh462, A: Hoh471, A: Hoh510, A: Hoh620, A: Hoh621, conact list: Atom Atom Distance (A) Na OE1 A:Gln203 4.77 Na CB A:Thr206 4.24 Na CG2 A:Thr206 5.00 Na OG1 A:Thr206 3.93 Na OD2 A:Asp210 4.05 Na OD1 A:Asp210 4.33 Na CG A:Asp210 4.62 Na CE2 A:Tyr218 4.61 Na CD1 A:Tyr218 4.90 Na CZ A:Tyr218 3.35 Na CE1 A:Tyr218 3.55 Na OH A:Tyr218 2.36 Na O A:Hoh441 2.39 Na O A:Hoh455 2.45 Na O A:Hoh462 4.90 Na O A:Hoh471 2.36 Na O A:Hoh510 2.50 Na O A:Hoh620 2.47 Na O A:Hoh621 4.37 interactive model: Sodium binding site 4 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3vh9. 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: Asn249, A: Hoh357, A: Hoh442, A: Hoh515, A: Hoh525, A: Hoh561, A: Hoh611, A: Hoh626, A: Hoh631, A: Hoh684, conact list: Atom Atom Distance (A) Na O A:Asn249 4.39 Na CB A:Asn249 4.60 Na ND2 A:Asn249 3.77 Na OD1 A:Asn249 2.28 Na CG A:Asn249 3.32 Na CA A:Asn249 4.84 Na O A:Hoh357 2.61 Na O A:Hoh442 2.40 Na O A:Hoh515 2.82 Na O A:Hoh525 2.49 Na O A:Hoh561 2.71 Na O A:Hoh611 3.40 Na O A:Hoh626 3.74 Na O A:Hoh631 4.42 Na O A:Hoh684 4.72 interactive model: Sodium binding site 5 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3vh9. 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: Asp266, A: Thr268, A: Ser270, A: Hoh355, A: Hoh500, A: Hoh567, A: Hoh609, A: Hoh618, A: Hoh627, A: Hoh652, A: Hoh740, conact list: Atom Atom Distance (A) Na OD2 A:Asp266 4.46 Na OD1 A:Asp266 4.54 Na CG A:Asp266 4.94 Na CB A:Thr268 3.38 Na CG2 A:Thr268 3.67 Na OG1 A:Thr268 2.59 Na CA A:Thr268 4.81 Na N A:Ser270 4.55 Na CB A:Ser270 3.28 Na CB A:Ser270 3.28 Na OG A:Ser270 2.42 Na OG A:Ser270 3.06 Na CA A:Ser270 4.51 Na O A:Hoh355 2.78 Na O A:Hoh500 4.26 Na O A:Hoh567 2.76 Na O A:Hoh609 2.48 Na O A:Hoh618 4.15 Na O A:Hoh627 2.57 Na O A:Hoh652 4.64 Na O A:Hoh740 3.57 interactive model: Sodium binding site 6 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3vh9. 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: Ala8, A: Thr11, A: Ala12, A: Hoh352, A: Hoh353, A: Hoh414, A: Hoh473, A: Hoh604, A: Hoh619, conact list: Atom Atom Distance (A) Na O A:Ala8 4.73 Na O A:Thr11 4.36 Na CB A:Thr11 3.35 Na CG2 A:Thr11 4.37 Na OG1 A:Thr11 2.56 Na C A:Thr11 4.21 Na CA A:Thr11 4.41 Na N A:Ala12 4.50 Na O A:Hoh352 2.56 Na O A:Hoh353 3.34 Na O A:Hoh414 4.81 Na O A:Hoh473 2.74 Na O A:Hoh604 4.71 Na O A:Hoh619 2.94 interactive model: Sodium binding site 7 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3vh9. 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: Glu151, A: Glu152, A: Tyr225, A: Cys227, A: His256, A: Zn301, A: Hqy303, A: Hoh451, A: Hoh479, A: Hoh534, A: Hoh535, A: Hoh563, A: Hoh572, A: Hoh662, conact list: Atom Atom Distance (A) Na O A:Glu151 4.56 Na OE1 A:Glu151 4.00 Na OE2 A:Glu151 4.09 Na CD A:Glu151 4.43 Na O A:Glu152 4.08 Na N A:Glu152 4.99 Na OE1 A:Glu152 2.33 Na CB A:Glu152 4.43 Na OE2 A:Glu152 4.29 Na CD A:Glu152 3.52 Na C A:Glu152 4.39 Na CG A:Glu152 4.49 Na CA A:Glu152 3.95 Na OH A:Tyr225 4.79 Na O A:Cys227 4.67 Na NE2 A:His256 4.38 Na CE1 A:His256 3.98 Na ZN A:Zn301 3.92 Na NAH A:Hqy303 3.94 Na OAA A:Hqy303 4.28 Na CAJ A:Hqy303 4.73 Na CAM A:Hqy303 4.57 Na CAE A:Hqy303 4.38 Na O A:Hoh451 2.31 Na O A:Hoh479 2.34 Na O A:Hoh534 2.48 Na O A:Hoh535 2.44 Na O A:Hoh563 3.75 Na O A:Hoh572 3.97 Na O A:Hoh662 4.15 interactive model: Sodium binding site 8 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Sodium in the PDB 3vh9. 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: Gln138, A: Hoh327, A: Hoh329, A: Hoh333, A: Hoh359, A: Hoh376, A: Hoh378, A: Hoh416, A: Hoh453, A: Hoh516, A: Hoh579, A: Hoh607, A: Hoh688, A: Hoh720, conact list: Atom Atom Distance (A) Na OE1 A:Gln138 4.24 Na CD A:Gln138 4.86 Na O A:Hoh327 4.55 Na O A:Hoh329 2.76 Na O A:Hoh333 2.75 Na O A:Hoh359 2.88 Na O A:Hoh376 4.67 Na O A:Hoh378 2.90 Na O A:Hoh416 2.75 Na O A:Hoh453 3.25 Na O A:Hoh516 4.48 Na O A:Hoh579 2.66 Na O A:Hoh607 4.47 Na O A:Hoh688 4.13 Na O A:Hoh720 3.62 interactive model: Sodium binding site 9 out of 9 in 3vh9 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Sodium in the PDB 3vh9. 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: Asn74, A: Na305, A: Cl316, A: Hoh466, A: Hoh498, A: Hoh501, A: Hoh549, A: Hoh565, A: Hoh616, A: Hoh623, A: Hoh691, conact list: Atom Atom Distance (A) Na N A:Asn74 4.95 Na CB A:Asn74 4.74 Na ND2 A:Asn74 3.57 Na OD1 A:Asn74 2.51 Na CG A:Asn74 3.37 Na NA A:Na305 3.58 Na CL A:Cl316 4.84 Na O A:Hoh466 4.66 Na O A:Hoh498 4.45 Na O A:Hoh501 2.42 Na O A:Hoh549 2.63 Na O A:Hoh565 2.55 Na O A:Hoh616 2.75 Na O A:Hoh623 4.61 Na O A:Hoh691 2.79 interactive model: