Cobalt in the structure of Arginine Residues As Stabilizing Elements in Proteins (pdb 1xim)

The binding sites of Cobalt atom in the structure of Arginine Residues As Stabilizing Elements in Proteins (pdb code 1xim). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1xim structure was solved by N.T.MRABET, A.VAN DENBROEK, I.VAN DEN BRANDE, P.STANSSENS, Y.LAROCHE, A.-M.LAMBEIR, G.MATTHYSSENS, J.JENKINS, M.CHIADMI, H.VANTILBEURGH, F.REY, J.JANIN, W.J.QUAX, I.LASTERS, M.DEMAEYER, S.J.WODAK, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 2.2 Space group P3221 a (A) 143.450 b (A) 143.450 c (A) 231.500 alpha (°) 90.00 beta (°) 90.00 gamma (°) 120.00 Rfactor (%) n/a Rfree (%) n/a Cobalt Binding Sites: Cobalt binding site 1 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1xim. 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: Glu181, A: Asn215, A: Glu217, A: His220, A: Asp245, A: Asp292, A: Xyl397, A: Co396, A: Hoh456, A: Hoh541, conact list: Atom Atom Distance (A) Co OE1 A:Glu181 3.28 Co OE2 A:Glu181 2.21 Co CD A:Glu181 3.08 Co CG A:Glu181 4.41 Co ND2 A:Asn215 4.73 Co OE1 A:Glu217 2.22 Co CB A:Glu217 4.29 Co OE2 A:Glu217 4.20 Co CD A:Glu217 3.44 Co CG A:Glu217 4.22 Co NE2 A:His220 4.50 Co CE1 A:His220 4.17 Co CB A:Asp245 3.86 Co OD2 A:Asp245 2.21 Co OD1 A:Asp245 4.29 Co CG A:Asp245 3.34 Co CB A:Asp292 3.86 Co OD2 A:Asp292 2.15 Co OD1 A:Asp292 4.15 Co CG A:Asp292 3.20 Co C5 A:Xyl397 4.75 Co O2 A:Xyl397 2.20 Co C4 A:Xyl397 3.52 Co C1 A:Xyl397 4.49 Co O1 A:Xyl397 4.84 Co C3 A:Xyl397 3.67 Co O3 A:Xyl397 3.76 Co O4 A:Xyl397 2.47 Co C2 A:Xyl397 3.36 Co CO A:Co396 4.83 Co O A:Hoh456 3.95 Co O A:Hoh541 4.01 interactive model: Cobalt binding site 2 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1xim. 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: Lys183, A: Glu217, A: His220, A: Asn247, A: Asp255, A: Asp257, A: Xyl397, A: Co395, A: Hoh429, A: Hoh541, A: Hoh592, conact list: Atom Atom Distance (A) Co CE A:Lys183 4.51 Co NZ A:Lys183 4.35 Co OE1 A:Glu217 3.54 Co OE2 A:Glu217 2.19 Co CD A:Glu217 3.19 Co CG A:Glu217 4.55 Co NE2 A:His220 2.76 Co ND1 A:His220 4.87 Co CD2 A:His220 3.41 Co CE1 A:His220 3.90 Co CG A:His220 4.68 Co ND2 A:Asn247 4.29 Co CB A:Asp255 4.32 Co OD2 A:Asp255 2.52 Co OD1 A:Asp255 2.52 Co CG A:Asp255 2.85 Co OD2 A:Asp257 3.83 Co OD1 A:Asp257 2.90 Co CG A:Asp257 3.76 Co O2 A:Xyl397 3.46 Co C1 A:Xyl397 3.54 Co O1 A:Xyl397 2.73 Co C2 A:Xyl397 4.18 Co CO A:Co395 4.83 Co O A:Hoh429 4.83 Co O A:Hoh541 2.32 Co O A:Hoh592 4.42 interactive model: Cobalt binding site 3 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1xim. 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: Glu181, B: Asn215, B: Glu217, B: His220, B: Asp245, B: Asp292, B: Xyl397, B: Co396, B: Hoh456, B: Hoh537, conact list: Atom Atom Distance (A) Co OE1 B:Glu181 3.14 Co OE2 B:Glu181 2.34 Co CD B:Glu181 3.06 Co CG B:Glu181 4.46 Co ND2 B:Asn215 4.76 Co OE1 B:Glu217 2.11 Co CB B:Glu217 4.23 Co OE2 B:Glu217 4.06 Co CD B:Glu217 3.33 Co CG B:Glu217 4.14 Co NE2 B:His220 4.61 Co ND1 B:His220 4.99 Co CE1 B:His220 4.15 Co CB B:Asp245 3.98 Co OD2 B:Asp245 2.25 Co OD1 B:Asp245 4.30 Co CG B:Asp245 3.38 Co CB B:Asp292 3.95 Co OD2 B:Asp292 2.30 Co OD1 B:Asp292 4.38 Co CG B:Asp292 3.37 Co C5 B:Xyl397 4.71 Co O2 B:Xyl397 2.34 Co C4 B:Xyl397 3.46 Co C1 B:Xyl397 4.62 Co O1 B:Xyl397 4.76 Co C3 B:Xyl397 3.74 Co O3 B:Xyl397 3.78 Co O4 B:Xyl397 2.46 Co C2 B:Xyl397 3.45 Co CO B:Co396 4.92 Co O B:Hoh456 3.87 Co O B:Hoh537 4.06 interactive model: Cobalt binding site 4 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1xim. 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: Lys183, B: Glu217, B: His220, B: Asn247, B: Asp255, B: Asp257, B: Xyl397, B: Co395, B: Hoh429, B: Hoh537, B: Hoh589, conact list: Atom Atom Distance (A) Co CE B:Lys183 4.43 Co NZ B:Lys183 4.11 Co OE1 B:Glu217 3.78 Co OE2 B:Glu217 2.33 Co CD B:Glu217 3.36 Co CG B:Glu217 4.67 Co NE2 B:His220 2.72 Co ND1 B:His220 4.80 Co CD2 B:His220 3.43 Co CE1 B:His220 3.80 Co CG B:His220 4.66 Co ND2 B:Asn247 4.27 Co CB B:Asp255 4.29 Co OD2 B:Asp255 2.44 Co OD1 B:Asp255 2.56 Co CG B:Asp255 2.80 Co OD2 B:Asp257 3.81 Co OD1 B:Asp257 2.94 Co CG B:Asp257 3.81 Co O2 B:Xyl397 3.58 Co C1 B:Xyl397 3.86 Co O1 B:Xyl397 2.74 Co C2 B:Xyl397 4.42 Co CO B:Co395 4.92 Co O B:Hoh429 4.37 Co O B:Hoh537 2.30 Co O B:Hoh589 4.43 interactive model: Cobalt binding site 5 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 1xim. 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: Glu181, C: Asn215, C: Glu217, C: His220, C: Asp245, C: Asp292, C: Xyl397, C: Co396, C: Hoh467, C: Hoh552, conact list: Atom Atom Distance (A) Co OE1 C:Glu181 3.37 Co OE2 C:Glu181 2.27 Co CD C:Glu181 3.13 Co CG C:Glu181 4.47 Co ND2 C:Asn215 4.62 Co OE1 C:Glu217 2.27 Co CB C:Glu217 4.29 Co OE2 C:Glu217 4.28 Co CD C:Glu217 3.47 Co CG C:Glu217 4.25 Co NE2 C:His220 4.54 Co CE1 C:His220 4.18 Co CB C:Asp245 3.91 Co OD2 C:Asp245 2.23 Co OD1 C:Asp245 4.27 Co CG C:Asp245 3.36 Co CB C:Asp292 3.88 Co OD2 C:Asp292 2.25 Co OD1 C:Asp292 4.31 Co CG C:Asp292 3.30 Co C5 C:Xyl397 4.81 Co O2 C:Xyl397 2.26 Co C4 C:Xyl397 3.58 Co C1 C:Xyl397 4.57 Co O1 C:Xyl397 4.77 Co C3 C:Xyl397 3.83 Co O3 C:Xyl397 3.84 Co O4 C:Xyl397 2.52 Co C2 C:Xyl397 3.52 Co CO C:Co396 4.97 Co O C:Hoh467 4.00 Co O C:Hoh552 4.05 interactive model: Cobalt binding site 6 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 1xim. 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: Lys183, C: Glu217, C: His220, C: Asn247, C: Asp255, C: Asp257, C: Xyl397, C: Co395, C: Hoh438, C: Hoh552, C: Hoh610, conact list: Atom Atom Distance (A) Co CE C:Lys183 4.50 Co NZ C:Lys183 4.36 Co OE1 C:Glu217 3.62 Co OE2 C:Glu217 2.33 Co CD C:Glu217 3.27 Co CG C:Glu217 4.64 Co NE2 C:His220 2.74 Co ND1 C:His220 4.83 Co CD2 C:His220 3.29 Co CE1 C:His220 3.91 Co CG C:His220 4.57 Co ND2 C:Asn247 4.17 Co CB C:Asp255 4.17 Co OD2 C:Asp255 2.29 Co OD1 C:Asp255 2.44 Co CG C:Asp255 2.67 Co OD2 C:Asp257 3.74 Co OD1 C:Asp257 2.77 Co CG C:Asp257 3.71 Co O2 C:Xyl397 3.92 Co C1 C:Xyl397 3.98 Co O1 C:Xyl397 2.95 Co C2 C:Xyl397 4.65 Co CO C:Co395 4.97 Co O C:Hoh438 4.26 Co O C:Hoh552 2.26 Co O C:Hoh610 4.61 interactive model: Cobalt binding site 7 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 1xim. 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: Glu181, D: Asn215, D: Glu217, D: His220, D: Asp245, D: Asp292, D: Xyl397, D: Co396, D: Hoh467, D: Hoh548, conact list: Atom Atom Distance (A) Co OE1 D:Glu181 3.50 Co OE2 D:Glu181 2.21 Co CD D:Glu181 3.17 Co CG D:Glu181 4.47 Co ND2 D:Asn215 4.75 Co OE1 D:Glu217 2.21 Co CB D:Glu217 4.24 Co OE2 D:Glu217 4.21 Co CD D:Glu217 3.41 Co CG D:Glu217 4.15 Co NE2 D:His220 4.50 Co ND1 D:His220 4.99 Co CE1 D:His220 4.16 Co CB D:Asp245 3.89 Co OD2 D:Asp245 2.26 Co OD1 D:Asp245 4.37 Co CG D:Asp245 3.36 Co CB D:Asp292 3.86 Co OD2 D:Asp292 2.09 Co OD1 D:Asp292 4.21 Co CG D:Asp292 3.19 Co C5 D:Xyl397 4.71 Co O2 D:Xyl397 2.32 Co C4 D:Xyl397 3.48 Co C1 D:Xyl397 4.55 Co O1 D:Xyl397 4.78 Co C3 D:Xyl397 3.61 Co O3 D:Xyl397 3.59 Co O4 D:Xyl397 2.40 Co C2 D:Xyl397 3.39 Co CO D:Co396 4.66 Co O D:Hoh467 4.01 Co O D:Hoh548 3.89 interactive model: Cobalt binding site 8 out of 8 in 1xim Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 1xim. 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: Lys183, D: Glu217, D: His220, D: Asn247, D: Asp255, D: Asp257, D: Asp292, D: Xyl397, D: Co395, D: Hoh440, D: Hoh548, D: Hoh598, conact list: Atom Atom Distance (A) Co CE D:Lys183 4.65 Co NZ D:Lys183 4.46 Co OE1 D:Glu217 3.46 Co OE2 D:Glu217 2.30 Co CD D:Glu217 3.21 Co CG D:Glu217 4.62 Co NE2 D:His220 2.79 Co ND1 D:His220 4.88 Co CD2 D:His220 3.59 Co CE1 D:His220 3.85 Co CG D:His220 4.80 Co ND2 D:Asn247 4.19 Co CB D:Asp255 4.29 Co OD2 D:Asp255 2.28 Co OD1 D:Asp255 2.59 Co CG D:Asp255 2.85 Co OD2 D:Asp257 3.62 Co OD1 D:Asp257 2.66 Co CG D:Asp257 3.56 Co OD2 D:Asp292 4.81 Co O2 D:Xyl397 3.32 Co C1 D:Xyl397 3.74 Co O1 D:Xyl397 2.78 Co C2 D:Xyl397 4.25 Co CO D:Co395 4.66 Co O D:Hoh440 4.55 Co O D:Hoh548 2.23 Co O D:Hoh598 4.79 interactive model: