Calcium in the structure of Crystal Structure Of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed With Binding Protein (pdb 1j34)

The binding sites of Calcium atom in the structure of Crystal Structure Of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed With Binding Protein (pdb code 1j34). This binding sites where shown with 5.0 Angstroms radius around Calcium atom. The 1j34 structure was solved by Y.SHIKAMOTO, T.MORITA, Z.FUJIMOTO, H.MIZUNO, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 19.6-1.6 Space group C121 a (A) 128.552 b (A) 37.204 c (A) 62.626 alpha (°) 90.00 beta (°) 103.56 gamma (°) 90.00 Rfactor (%) 18.3 Rfree (%) 21.2 Calcium Binding Sites: Calcium binding site 1 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Calcium in the PDB 1j34. 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: His12, A: Tyr14, A: Ser41, A: Ile42, A: Glu43, A: Glu47, A: Glu128, A: Hoh720, A: Hoh789, A: Hoh809, A: Hoh837, A: Hoh880, A: Hoh947, A: Hoh981, conact list: Atom Atom Distance (A) Ca CD2 A:His12 4.68 Ca CE2 A:Tyr14 4.85 Ca CZ A:Tyr14 4.98 Ca OH A:Tyr14 4.22 Ca O A:Ser41 2.38 Ca N A:Ser41 4.07 Ca CB A:Ser41 3.62 Ca OG A:Ser41 2.47 Ca C A:Ser41 3.44 Ca CA A:Ser41 3.92 Ca N A:Ile42 4.61 Ca N A:Glu43 4.75 Ca OE1 A:Glu43 4.53 Ca CB A:Glu43 4.82 Ca OE2 A:Glu43 2.40 Ca CD A:Glu43 3.52 Ca CG A:Glu43 4.10 Ca OE1 A:Glu47 3.31 Ca OE2 A:Glu47 2.41 Ca CD A:Glu47 3.22 Ca CG A:Glu47 4.65 Ca OE1 A:Glu128 2.60 Ca OE2 A:Glu128 2.37 Ca CD A:Glu128 2.83 Ca CG A:Glu128 4.34 Ca O A:Hoh720 4.52 Ca O A:Hoh789 4.57 Ca O A:Hoh809 2.44 Ca O A:Hoh837 2.51 Ca O A:Hoh880 4.85 Ca O A:Hoh947 4.74 Ca O A:Hoh981 4.93 interactive model: Calcium binding site 2 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Calcium in the PDB 1j34. 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: Asp85, B: His212, B: Tyr214, B: Ser241, B: Phe242, B: Gln243, B: Glu247, B: Glu320, A: Hoh735, B: Hoh818, B: Hoh820, B: Hoh903, B: Hoh951, conact list: Atom Atom Distance (A) Ca OD2 A:Asp85 4.64 Ca ND1 B:His212 4.18 Ca CE1 B:His212 4.53 Ca CE2 B:Tyr214 4.77 Ca CZ B:Tyr214 4.98 Ca OH B:Tyr214 4.25 Ca O B:Ser241 2.38 Ca N B:Ser241 3.95 Ca CB B:Ser241 3.74 Ca OG B:Ser241 2.61 Ca C B:Ser241 3.32 Ca CA B:Ser241 3.89 Ca N B:Phe242 4.36 Ca CA B:Phe242 4.68 Ca NE2 B:Gln243 3.80 Ca N B:Gln243 4.61 Ca OE1 B:Gln243 2.27 Ca CD B:Gln243 3.29 Ca CG B:Gln243 4.52 Ca OE1 B:Glu247 3.35 Ca OE2 B:Glu247 2.37 Ca CD B:Glu247 3.21 Ca CG B:Glu247 4.62 Ca OE1 B:Glu320 2.67 Ca OE2 B:Glu320 2.44 Ca CD B:Glu320 2.91 Ca CG B:Glu320 4.42 Ca O A:Hoh735 4.80 Ca O B:Hoh818 2.41 Ca O B:Hoh820 2.49 Ca O B:Hoh903 4.75 Ca O B:Hoh951 4.66 interactive model: Calcium binding site 3 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Calcium in the PDB 1j34. 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: Tyr298, C: Asn402, C: Cgu408, C: Cgu426, C: Cgu427, C: Cgu430, C: Mg501, C: Ca503, B: Hoh711, B: Hoh804, C: Hoh805, C: Hoh807, C: Hoh828, C: Hoh936, C: Hoh970, C: Hoh1006, conact list: Atom Atom Distance (A) Ca OH B:Tyr298 4.97 Ca ND2 C:Asn402 4.29 Ca OD1 C:Asn402 4.57 Ca CG C:Asn402 4.83 Ca OE12 C:Cgu408 4.18 Ca CB C:Cgu408 4.45 Ca OE21 C:Cgu408 4.46 Ca CD1 C:Cgu408 3.25 Ca CD2 C:Cgu408 3.36 Ca CG C:Cgu408 3.80 Ca OE11 C:Cgu408 2.37 Ca OE22 C:Cgu408 2.31 Ca OE12 C:Cgu426 4.42 Ca CD1 C:Cgu426 4.67 Ca CG C:Cgu426 4.88 Ca OE12 C:Cgu427 2.40 Ca CD1 C:Cgu427 3.38 Ca CG C:Cgu427 4.74 Ca OE11 C:Cgu427 3.67 Ca OE21 C:Cgu430 2.55 Ca CD1 C:Cgu430 4.79 Ca CD2 C:Cgu430 2.77 Ca CG C:Cgu430 4.26 Ca OE11 C:Cgu430 4.89 Ca OE22 C:Cgu430 2.36 Ca MG C:Mg501 4.30 Ca CA C:Ca503 3.89 Ca O B:Hoh711 4.07 Ca O B:Hoh804 2.42 Ca O C:Hoh805 4.53 Ca O C:Hoh807 2.33 Ca O C:Hoh828 4.28 Ca O C:Hoh936 4.26 Ca O C:Hoh970 4.51 Ca O C:Hoh1006 4.22 interactive model: Calcium binding site 4 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Calcium in the PDB 1j34. 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: C: Asn402, C: Cgu408, C: Gly412, C: Cgu417, C: Cgu427, C: Cgu430, C: Ca502, C: Ca504, B: Hoh682, B: Hoh804, C: Hoh803, C: Hoh805, C: Hoh810, C: Hoh936, C: Hoh953, conact list: Atom Atom Distance (A) Ca OD1 C:Asn402 4.90 Ca OE12 C:Cgu408 2.84 Ca CB C:Cgu408 4.94 Ca CD1 C:Cgu408 2.93 Ca CG C:Cgu408 4.43 Ca OE11 C:Cgu408 2.36 Ca OE22 C:Cgu408 4.97 Ca CA C:Cgu408 4.96 Ca CA C:Gly412 4.50 Ca OE21 C:Cgu417 3.74 Ca CD2 C:Cgu417 3.58 Ca OE22 C:Cgu417 2.68 Ca OE12 C:Cgu427 3.91 Ca O C:Cgu427 4.60 Ca CB C:Cgu427 4.76 Ca CD1 C:Cgu427 3.48 Ca CG C:Cgu427 4.70 Ca OE11 C:Cgu427 2.46 Ca CA C:Cgu427 4.66 Ca CB C:Cgu430 4.10 Ca OE21 C:Cgu430 2.55 Ca CD2 C:Cgu430 3.74 Ca CG C:Cgu430 4.54 Ca OE22 C:Cgu430 4.65 Ca CA C:Ca502 3.89 Ca CA C:Ca504 3.74 Ca O B:Hoh682 4.65 Ca O B:Hoh804 4.87 Ca O C:Hoh803 2.34 Ca O C:Hoh805 2.40 Ca O C:Hoh810 2.47 Ca O C:Hoh936 4.26 Ca O C:Hoh953 4.65 interactive model: Calcium binding site 5 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Calcium in the PDB 1j34. 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: C: Tyr401, C: Asn402, C: Cgu407, C: Cgu408, C: Cgu417, C: Cgu427, C: Ca503, C: Ca505, C: Hoh803, C: Hoh810, C: Hoh953, conact list: Atom Atom Distance (A) Ca O C:Tyr401 3.28 Ca N C:Tyr401 4.36 Ca C C:Tyr401 3.85 Ca CA C:Tyr401 4.71 Ca N C:Asn402 4.29 Ca CB C:Asn402 4.48 Ca ND2 C:Asn402 4.34 Ca OD1 C:Asn402 2.35 Ca CG C:Asn402 3.51 Ca CA C:Asn402 4.26 Ca OE21 C:Cgu407 2.52 Ca CD2 C:Cgu407 3.56 Ca CG C:Cgu407 4.38 Ca OE22 C:Cgu407 4.34 Ca OE12 C:Cgu408 2.34 Ca CD1 C:Cgu408 3.39 Ca CG C:Cgu408 4.39 Ca OE11 C:Cgu408 4.04 Ca OE12 C:Cgu417 4.05 Ca CB C:Cgu417 4.39 Ca OE21 C:Cgu417 4.59 Ca CD1 C:Cgu417 3.19 Ca CD2 C:Cgu417 3.48 Ca CG C:Cgu417 3.82 Ca OE11 C:Cgu417 2.35 Ca OE22 C:Cgu417 2.49 Ca OE12 C:Cgu427 4.04 Ca CB C:Cgu427 4.58 Ca OE21 C:Cgu427 4.49 Ca CD1 C:Cgu427 3.22 Ca CD2 C:Cgu427 3.40 Ca CG C:Cgu427 3.84 Ca OE11 C:Cgu427 2.43 Ca OE22 C:Cgu427 2.33 Ca CA C:Ca503 3.74 Ca CA C:Ca505 3.93 Ca O C:Hoh803 4.94 Ca O C:Hoh810 4.40 Ca O C:Hoh953 4.05 interactive model: Calcium binding site 6 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Calcium in the PDB 1j34. 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: C: Tyr401, C: Asn402, C: Ser403, C: Cgu407, C: Cgu417, C: Cgu421, C: Cgu427, C: Ca504, C: Ca506, C: Hoh603, C: Hoh762, C: Hoh808, C: Hoh813, C: Hoh816, C: Hoh847, C: Hoh953, conact list: Atom Atom Distance (A) Ca O C:Tyr401 2.32 Ca N C:Tyr401 4.05 Ca CB C:Tyr401 4.59 Ca C C:Tyr401 3.50 Ca CA C:Tyr401 4.25 Ca N C:Asn402 4.51 Ca CA C:Asn402 4.65 Ca N C:Ser403 4.81 Ca OG C:Ser403 4.79 Ca CB C:Cgu407 4.79 Ca OE21 C:Cgu407 2.50 Ca CD2 C:Cgu407 2.83 Ca CG C:Cgu407 4.31 Ca OE22 C:Cgu407 2.54 Ca OE12 C:Cgu417 2.59 Ca CB C:Cgu417 4.97 Ca CD1 C:Cgu417 2.87 Ca CG C:Cgu417 4.38 Ca OE11 C:Cgu417 2.48 Ca CA C:Cgu417 4.97 Ca OE21 C:Cgu421 2.91 Ca CD2 C:Cgu421 3.05 Ca CG C:Cgu421 4.54 Ca OE22 C:Cgu421 2.51 Ca OE22 C:Cgu427 4.83 Ca CA C:Ca504 3.93 Ca CA C:Ca506 4.98 Ca O C:Hoh603 4.57 Ca O C:Hoh762 4.59 Ca O C:Hoh808 2.43 Ca O C:Hoh813 4.48 Ca O C:Hoh816 2.35 Ca O C:Hoh847 4.49 Ca O C:Hoh953 4.62 interactive model: Calcium binding site 7 out of 7 in 1j34 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Calcium in the PDB 1j34. 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: C: Arg416, C: Cgu420, C: Cgu421, C: Ca505, C: Hoh646, C: Hoh808, C: Hoh813, C: Hoh816, C: Hoh817, C: Hoh847, C: Hoh1011, conact list: Atom Atom Distance (A) Ca O C:Arg416 4.49 Ca CG C:Arg416 4.75 Ca OE22 C:Cgu420 4.95 Ca OE12 C:Cgu421 2.37 Ca CB C:Cgu421 4.87 Ca OE21 C:Cgu421 2.38 Ca CD1 C:Cgu421 3.21 Ca CD2 C:Cgu421 3.23 Ca CG C:Cgu421 3.34 Ca OE11 C:Cgu421 4.38 Ca OE22 C:Cgu421 4.41 Ca CA C:Ca505 4.98 Ca O C:Hoh646 2.32 Ca O C:Hoh808 4.57 Ca O C:Hoh813 2.39 Ca O C:Hoh816 4.20 Ca O C:Hoh817 2.23 Ca O C:Hoh847 2.27 Ca O C:Hoh1011 3.08 interactive model: