Calcium in the structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal) (pdb 2dw1)

The binding sites of Calcium atom in the structure of Crystal Structure of VAP2 From Crotalus Atrox Venom (Form 2-2 Crystal) (pdb code 2dw1). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 2dw1 structure was solved by S.TAKEDA, T.IGARASHI, S.ARAKI, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.5 Space group P212121 a (A) 57.670 b (A) 118.180 c (A) 138.460 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 22.7 Rfree (%) 28.6 Calcium Binding Sites: Calcium binding site 1 out of 6 in 2dw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 2dw1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Phe199, A: Glu201, A: Asp285, A: Cys388, A: Ile389, A: Asn391, A: Hoh814, A: Hoh886, A: Hoh915, conact list: Atom Atom Distance (A) Ca O A:Phe199 4.40 Ca N A:Glu201 4.76 Ca OE1 A:Glu201 2.51 Ca CB A:Glu201 4.20 Ca OE2 A:Glu201 4.45 Ca CD A:Glu201 3.33 Ca CG A:Glu201 3.54 Ca CB A:Asp285 4.30 Ca OD2 A:Asp285 2.52 Ca OD1 A:Asp285 2.47 Ca CG A:Asp285 2.82 Ca O A:Cys388 2.31 Ca CB A:Cys388 4.51 Ca SG A:Cys388 5.00 Ca C A:Cys388 3.53 Ca CA A:Cys388 4.41 Ca N A:Ile389 4.45 Ca CA A:Ile389 4.42 Ca O A:Asn391 4.22 Ca N A:Asn391 4.93 Ca CB A:Asn391 4.64 Ca ND2 A:Asn391 3.71 Ca OD1 A:Asn391 2.25 Ca CG A:Asn391 3.30 Ca O A:Hoh814 2.49 Ca O A:Hoh886 2.09 Ca O A:Hoh915 4.21 interactive model: Calcium binding site 2 out of 6 in 2dw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 2dw1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Val403, A: Cys404, A: Gly405, A: Asn406, A: Glu407, A: Leu408, A: Leu409, A: Glu410, A: Glu413, A: Asp416, conact list: Atom Atom Distance (A) Ca O A:Val403 2.40 Ca N A:Val403 4.12 Ca CB A:Val403 4.98 Ca C A:Val403 3.33 Ca CA A:Val403 4.32 Ca N A:Cys404 4.01 Ca C A:Cys404 4.58 Ca CA A:Cys404 3.94 Ca N A:Gly405 4.26 Ca N A:Asn406 4.36 Ca CB A:Asn406 4.60 Ca ND2 A:Asn406 3.54 Ca OD1 A:Asn406 2.65 Ca CG A:Asn406 3.33 Ca CA A:Asn406 4.92 Ca N A:Glu407 4.91 Ca O A:Leu408 2.35 Ca N A:Leu408 4.11 Ca CB A:Leu408 4.51 Ca C A:Leu408 3.51 Ca CA A:Leu408 4.25 Ca N A:Leu409 4.54 Ca C A:Leu409 4.86 Ca CA A:Leu409 4.74 Ca N A:Glu410 4.24 Ca OE1 A:Glu410 2.43 Ca CB A:Glu410 4.27 Ca OE2 A:Glu410 4.24 Ca CD A:Glu410 3.28 Ca CG A:Glu410 3.74 Ca CA A:Glu410 4.93 Ca OE1 A:Glu413 2.57 Ca OE2 A:Glu413 2.67 Ca CD A:Glu413 2.97 Ca CG A:Glu413 4.49 Ca CB A:Asp416 4.13 Ca OD2 A:Asp416 2.62 Ca OD1 A:Asp416 4.47 Ca CG A:Asp416 3.56 interactive model: Calcium binding site 3 out of 6 in 2dw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 2dw1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg460, A: Asp467, A: Pro468, A: Ala469, A: Glu470, A: Asp482, A: Val483, A: Phe484, A: Hoh815, A: Hoh882, conact list: Atom Atom Distance (A) Ca CD A:Arg460 4.65 Ca NH1 A:Arg460 5.00 Ca O A:Asp467 4.68 Ca CB A:Asp467 4.63 Ca OD2 A:Asp467 2.27 Ca C A:Asp467 4.36 Ca OD1 A:Asp467 4.01 Ca CG A:Asp467 3.45 Ca CA A:Asp467 4.75 Ca O A:Pro468 2.55 Ca N A:Pro468 4.27 Ca CD A:Pro468 4.54 Ca C A:Pro468 3.69 Ca CG A:Pro468 4.57 Ca CA A:Pro468 4.58 Ca N A:Ala469 4.53 Ca C A:Ala469 4.63 Ca CA A:Ala469 4.50 Ca N A:Glu470 4.82 Ca OE1 A:Glu470 2.22 Ca OE2 A:Glu470 2.87 Ca CD A:Glu470 2.87 Ca CG A:Glu470 4.34 Ca CB A:Asp482 4.39 Ca OD2 A:Asp482 2.17 Ca C A:Asp482 4.09 Ca OD1 A:Asp482 4.17 Ca CG A:Asp482 3.41 Ca CA A:Asp482 4.16 Ca O A:Val483 2.53 Ca N A:Val483 3.20 Ca CB A:Val483 4.50 Ca C A:Val483 3.46 Ca CA A:Val483 3.87 Ca N A:Phe484 4.60 Ca CE2 A:Phe484 4.31 Ca CD2 A:Phe484 4.22 Ca O A:Hoh815 4.08 Ca O A:Hoh882 2.46 interactive model: Calcium binding site 4 out of 6 in 2dw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 2dw1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Phe199, B: Glu201, B: Lys283, B: Asp285, B: Cys388, B: Ile389, B: Asn391, B: Hoh812, B: Hoh849, conact list: Atom Atom Distance (A) Ca O B:Phe199 4.16 Ca N B:Glu201 4.57 Ca OE1 B:Glu201 2.36 Ca CB B:Glu201 4.12 Ca OE2 B:Glu201 4.33 Ca CD B:Glu201 3.25 Ca CG B:Glu201 3.58 Ca CE B:Lys283 4.19 Ca CD B:Lys283 4.89 Ca N B:Asp285 4.95 Ca CB B:Asp285 4.39 Ca OD2 B:Asp285 2.58 Ca OD1 B:Asp285 2.51 Ca CG B:Asp285 2.88 Ca O B:Cys388 2.43 Ca CB B:Cys388 4.75 Ca C B:Cys388 3.66 Ca CA B:Cys388 4.60 Ca N B:Ile389 4.51 Ca CA B:Ile389 4.39 Ca O B:Asn391 4.22 Ca CB B:Asn391 4.71 Ca ND2 B:Asn391 2.94 Ca OD1 B:Asn391 2.85 Ca CG B:Asn391 3.24 Ca O B:Hoh812 2.34 Ca O B:Hoh849 2.14 interactive model: Calcium binding site 5 out of 6 in 2dw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 2dw1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Val403, B: Cys404, B: Gly405, B: Asn406, B: Glu407, B: Leu408, B: Leu409, B: Glu410, B: Glu413, B: Asp416, conact list: Atom Atom Distance (A) Ca O B:Val403 2.40 Ca N B:Val403 4.45 Ca C B:Val403 3.59 Ca CA B:Val403 4.62 Ca N B:Cys404 4.36 Ca C B:Cys404 4.81 Ca CA B:Cys404 4.21 Ca N B:Gly405 4.37 Ca N B:Asn406 4.37 Ca CB B:Asn406 4.60 Ca ND2 B:Asn406 3.81 Ca C B:Asn406 4.96 Ca OD1 B:Asn406 2.22 Ca CG B:Asn406 3.32 Ca CA B:Asn406 4.88 Ca N B:Glu407 4.77 Ca O B:Leu408 2.37 Ca N B:Leu408 4.01 Ca CB B:Leu408 4.52 Ca C B:Leu408 3.50 Ca CA B:Leu408 4.23 Ca N B:Leu409 4.51 Ca C B:Leu409 4.81 Ca CA B:Leu409 4.72 Ca N B:Glu410 4.18 Ca OE1 B:Glu410 2.67 Ca CB B:Glu410 4.17 Ca OE2 B:Glu410 4.44 Ca CD B:Glu410 3.41 Ca CG B:Glu410 3.65 Ca CA B:Glu410 4.85 Ca OE1 B:Glu413 2.49 Ca OE2 B:Glu413 2.63 Ca CD B:Glu413 2.92 Ca CG B:Glu413 4.45 Ca CB B:Asp416 4.02 Ca OD2 B:Asp416 2.72 Ca OD1 B:Asp416 4.59 Ca CG B:Asp416 3.61 interactive model: Calcium binding site 6 out of 6 in 2dw1 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 2dw1. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Calcium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Arg460, B: Asp467, B: Pro468, B: Ala469, B: Glu470, B: Asp482, B: Val483, B: Phe484, B: Hoh871, conact list: Atom Atom Distance (A) Ca O B:Arg460 4.94 Ca CD B:Arg460 4.66 Ca O B:Asp467 4.45 Ca CB B:Asp467 4.60 Ca OD2 B:Asp467 2.24 Ca C B:Asp467 4.19 Ca OD1 B:Asp467 3.90 Ca CG B:Asp467 3.39 Ca CA B:Asp467 4.65 Ca O B:Pro468 2.23 Ca N B:Pro468 4.11 Ca CD B:Pro468 4.52 Ca C B:Pro468 3.46 Ca CG B:Pro468 4.50 Ca CA B:Pro468 4.37 Ca N B:Ala469 4.37 Ca C B:Ala469 4.65 Ca CA B:Ala469 4.38 Ca N B:Glu470 4.59 Ca OE1 B:Glu470 2.69 Ca OE2 B:Glu470 2.42 Ca CD B:Glu470 2.91 Ca CG B:Glu470 4.43 Ca CB B:Asp482 4.65 Ca OD2 B:Asp482 4.47 Ca C B:Asp482 4.32 Ca OD1 B:Asp482 2.46 Ca CG B:Asp482 3.70 Ca CA B:Asp482 4.40 Ca O B:Val483 2.61 Ca N B:Val483 3.68 Ca C B:Val483 3.69 Ca CA B:Val483 4.29 Ca N B:Phe484 4.77 Ca CE2 B:Phe484 4.36 Ca CD2 B:Phe484 4.22 Ca O B:Hoh871 2.57 interactive model: