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 |
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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 |
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