Cobalt in the structure of Crystal Structure of SEC4-Gdp (pdb 1g16)

The binding sites of Cobalt atom in the structure of Crystal Structure of SEC4-Gdp (pdb code 1g16). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1g16 structure was solved by C.STROUPE, A.T.BRUNGER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 28.9-1.8 Space group P1 a (A) 56.007 b (A) 56.379 c (A) 59.374 alpha (°) 95.25 beta (°) 101.68 gamma (°) 116.20 Rfactor (%) 27.6 Rfree (%) 29.6 Cobalt Binding Sites: Cobalt binding site 1 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys33, A: Ser34, A: Asp75, A: Thr76, A: Gly78, A: Glu80, A: Gdp201, A: Hoh401, A: Hoh402, A: Hoh403, A: Hoh404, A: Hoh450, A: Hoh479, A: Hoh497, conact list: Atom Atom Distance (A) Co CB A:Lys33 4.77 Co CE A:Lys33 4.83 Co C A:Lys33 4.83 Co NZ A:Lys33 4.82 Co N A:Ser34 3.75 Co CB A:Ser34 3.10 Co OG A:Ser34 1.86 Co CA A:Ser34 3.95 Co OD2 A:Asp75 4.23 Co OD1 A:Asp75 4.00 Co CG A:Asp75 4.52 Co OG1 A:Thr76 4.23 Co N A:Gly78 4.73 Co OE2 A:Glu80 4.43 Co O3B A:Gdp201 3.63 Co PA A:Gdp201 4.62 Co O2A A:Gdp201 4.11 Co O1B A:Gdp201 4.23 Co PB A:Gdp201 3.22 Co O2B A:Gdp201 1.92 Co O3A A:Gdp201 4.23 Co O1A A:Gdp201 4.76 Co O A:Hoh401 1.98 Co O A:Hoh402 1.78 Co O A:Hoh403 1.98 Co O A:Hoh404 1.91 Co O A:Hoh450 4.98 Co O A:Hoh479 4.33 Co O A:Hoh497 4.18 interactive model: Cobalt binding site 2 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Arg39, A: Asp43, A: Asp166, A: Hoh417, A: Hoh418, A: Hoh419, conact list: Atom Atom Distance (A) Co CD A:Arg39 4.49 Co CZ A:Arg39 4.96 Co NH1 A:Arg39 4.04 Co O A:Asp43 4.92 Co CB A:Asp43 4.04 Co OD2 A:Asp43 2.37 Co OD1 A:Asp43 2.08 Co CG A:Asp43 2.53 Co CA A:Asp43 4.72 Co CB A:Asp166 4.22 Co OD2 A:Asp166 2.03 Co OD1 A:Asp166 3.84 Co CG A:Asp166 3.17 Co O A:Hoh417 4.33 Co O A:Hoh418 2.17 Co O A:Hoh419 2.18 interactive model: Cobalt binding site 3 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Lys33, B: Ser34, B: Asp75, B: Thr76, B: Gly78, B: Glu80, B: Gdp202, B: Hoh413, B: Hoh414, B: Hoh415, B: Hoh416, B: Hoh678, conact list: Atom Atom Distance (A) Co CB B:Lys33 4.94 Co N B:Ser34 3.90 Co CB B:Ser34 3.19 Co OG B:Ser34 1.87 Co CA B:Ser34 4.12 Co OD2 B:Asp75 3.97 Co OD1 B:Asp75 4.31 Co CG B:Asp75 4.51 Co OG1 B:Thr76 4.60 Co N B:Gly78 4.52 Co CA B:Gly78 4.92 Co OE1 B:Glu80 4.98 Co O3B B:Gdp202 3.56 Co PA B:Gdp202 4.51 Co O2A B:Gdp202 3.97 Co O1B B:Gdp202 4.28 Co PB B:Gdp202 3.22 Co O2B B:Gdp202 2.03 Co O3A B:Gdp202 4.17 Co O1A B:Gdp202 4.69 Co O B:Hoh413 1.89 Co O B:Hoh414 2.20 Co O B:Hoh415 1.82 Co O B:Hoh416 2.74 Co O B:Hoh678 4.74 interactive model: Cobalt binding site 4 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Lys33, C: Ser34, C: Thr51, C: Asp75, C: Thr76, C: Ala77, C: Gdp203, C: Hoh405, C: Hoh406, C: Hoh407, C: Hoh408, C: Hoh529, C: Hoh530, conact list: Atom Atom Distance (A) Co CB C:Lys33 4.93 Co C C:Lys33 4.97 Co N C:Ser34 3.84 Co CB C:Ser34 3.06 Co OG C:Ser34 2.00 Co CA C:Ser34 4.02 Co OG1 C:Thr51 4.59 Co OD2 C:Asp75 3.96 Co OD1 C:Asp75 4.27 Co CG C:Asp75 4.53 Co O C:Thr76 3.97 Co C C:Thr76 4.90 Co CA C:Ala77 4.80 Co O3B C:Gdp203 3.60 Co PA C:Gdp203 4.49 Co O2A C:Gdp203 3.97 Co O1B C:Gdp203 4.28 Co PB C:Gdp203 3.20 Co O2B C:Gdp203 1.92 Co O3A C:Gdp203 4.14 Co O1A C:Gdp203 4.65 Co O C:Hoh405 2.04 Co O C:Hoh406 1.73 Co O C:Hoh407 1.69 Co O C:Hoh408 2.15 Co O C:Hoh529 4.49 Co O C:Hoh530 4.36 interactive model: Cobalt binding site 5 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Arg39, C: Asp43, C: Asp166, C: Asn170, C: Hoh420, C: Hoh421, C: Hoh422, C: Hoh429, C: Hoh430, C: Hoh431, C: Hoh464, C: Hoh585, conact list: Atom Atom Distance (A) Co O C:Arg39 4.87 Co CD C:Arg39 4.61 Co OD1 C:Asp43 3.85 Co CG C:Asp43 4.56 Co CB C:Asp166 4.56 Co OD2 C:Asp166 2.38 Co OD1 C:Asp166 3.05 Co CG C:Asp166 3.08 Co ND2 C:Asn170 3.53 Co OD1 C:Asn170 4.11 Co CG C:Asn170 4.24 Co O C:Hoh420 2.00 Co O C:Hoh421 1.92 Co O C:Hoh422 2.01 Co O C:Hoh429 2.46 Co O C:Hoh430 4.33 Co O C:Hoh431 3.92 Co O C:Hoh464 4.27 Co O C:Hoh585 3.98 interactive model: Cobalt binding site 6 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Ser34, D: Asp75, D: Thr76, D: Ala77, D: Gdp204, D: Hoh409, D: Hoh410, D: Hoh411, D: Hoh412, D: Hoh664, conact list: Atom Atom Distance (A) Co N D:Ser34 3.92 Co CB D:Ser34 3.08 Co OG D:Ser34 2.00 Co CA D:Ser34 4.08 Co OD2 D:Asp75 4.30 Co OD1 D:Asp75 3.93 Co CG D:Asp75 4.54 Co O D:Thr76 4.20 Co C D:Thr76 4.89 Co CA D:Ala77 4.67 Co O3B D:Gdp204 3.72 Co PA D:Gdp204 4.46 Co O2A D:Gdp204 3.86 Co O1B D:Gdp204 4.49 Co PB D:Gdp204 3.37 Co O2B D:Gdp204 2.15 Co O3A D:Gdp204 4.22 Co O1A D:Gdp204 4.64 Co O D:Hoh409 1.75 Co O D:Hoh410 2.07 Co O D:Hoh411 2.05 Co O D:Hoh412 1.54 Co O D:Hoh664 4.88 interactive model: Cobalt binding site 7 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Arg39, D: Asp43, D: Asp166, D: Asn170, D: Hoh423, D: Hoh424, D: Hoh425, D: Hoh428, D: Hoh679, conact list: Atom Atom Distance (A) Co O D:Arg39 4.76 Co CD D:Arg39 4.49 Co CB D:Asp43 4.38 Co OD2 D:Asp43 2.17 Co OD1 D:Asp43 3.70 Co CG D:Asp43 3.21 Co CB D:Asp166 4.41 Co OD2 D:Asp166 2.16 Co OD1 D:Asp166 3.01 Co CG D:Asp166 2.94 Co ND2 D:Asn170 3.75 Co OD1 D:Asn170 4.33 Co CG D:Asn170 4.48 Co O D:Hoh423 2.21 Co O D:Hoh424 2.14 Co O D:Hoh425 2.30 Co O D:Hoh428 4.17 Co O D:Hoh679 4.27 interactive model: Cobalt binding site 8 out of 8 in 1g16 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 1g16. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Cobalt atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Ile85, D: Thr87, D: His121, D: Hoh426, D: Hoh427, conact list: Atom Atom Distance (A) Co O D:Ile85 4.03 Co CG2 D:Thr87 4.95 Co NE2 D:His121 2.07 Co ND1 D:His121 4.01 Co CD2 D:His121 3.28 Co CE1 D:His121 2.78 Co CG D:His121 4.27 Co O D:Hoh426 2.35 Co O D:Hoh427 2.44 interactive model: