Cobalt in the structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed With Glucuronic Acid and Xylotriose (pdb 1gql)

The binding sites of Cobalt atom in the structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed With Glucuronic Acid and Xylotriose (pdb code 1gql). This binding sites where shown with 5.0 Angstroms radius around Cobalt atom. The 1gql structure was solved by D.NURIZZO, T.NAGY, H.J.GILBERT, G.J.DAVIES, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.0-1.7 Space group P1 a (A) 69.256 b (A) 74.323 c (A) 87.273 alpha (°) 115.15 beta (°) 92.94 gamma (°) 109.24 Rfactor (%) 14.6 Rfree (%) 17.2 Cobalt Binding Sites: Cobalt binding site 1 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Cobalt in the PDB 1gql. 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: Met502, A: Val505, A: Ala625, A: Met626, A: Thr629, A: Hoh2225, A: Hoh2272, A: Hoh2514, A: Hoh2624, A: Hoh2625, A: Hoh2631, A: Hoh2704, conact list: Atom Atom Distance (A) Co N A:Met502 4.35 Co CB A:Met502 3.73 Co CG A:Met502 3.83 Co CA A:Met502 3.76 Co CG1 A:Val505 4.68 Co O A:Ala625 3.70 Co C A:Ala625 3.86 Co CB A:Ala625 4.46 Co CA A:Ala625 4.80 Co N A:Met626 3.87 Co CB A:Met626 4.51 Co C A:Met626 4.93 Co CG A:Met626 4.06 Co CA A:Met626 3.80 Co CB A:Thr629 3.74 Co CG2 A:Thr629 4.21 Co OG1 A:Thr629 3.04 Co O A:Hoh2225 4.80 Co O A:Hoh2272 4.96 Co O A:Hoh2514 3.49 Co O A:Hoh2624 3.13 Co O A:Hoh2625 4.32 Co O A:Hoh2631 4.77 Co O A:Hoh2704 3.26 interactive model: Cobalt binding site 2 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Cobalt in the PDB 1gql. 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: Asp6, A: Gly7, A: Asn452, A: Pro457, A: Gln460, A: Arg641, A: Gln644, A: Hoh2007, A: Hoh2489, A: Hoh2652, conact list: Atom Atom Distance (A) Co O A:Asp6 4.36 Co C A:Asp6 4.42 Co O A:Gly7 4.97 Co N A:Gly7 4.12 Co C A:Gly7 4.74 Co CA A:Gly7 3.60 Co CB A:Asn452 3.56 Co ND2 A:Asn452 3.30 Co CG A:Asn452 3.96 Co CA A:Asn452 4.94 Co N A:Pro457 4.76 Co CB A:Pro457 3.58 Co CD A:Pro457 4.70 Co CG A:Pro457 3.61 Co CA A:Pro457 4.02 Co NE2 A:Gln460 3.72 Co OE1 A:Gln460 4.43 Co CD A:Gln460 4.40 Co CD A:Arg641 3.70 Co CG A:Arg641 4.08 Co OE1 A:Gln644 4.42 Co O A:Hoh2007 4.86 Co O A:Hoh2489 3.03 Co O A:Hoh2652 2.99 interactive model: Cobalt binding site 3 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Cobalt in the PDB 1gql. 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: Asn607, A: Trp609, A: Gln610, A: Arg673, A: Pro674, conact list: Atom Atom Distance (A) Co ND2 A:Asn607 3.36 Co OD1 A:Asn607 4.15 Co CG A:Asn607 4.20 Co CB A:Trp609 4.56 Co CD1 A:Trp609 3.67 Co CG A:Trp609 4.45 Co NE1 A:Trp609 4.59 Co NE2 A:Gln610 4.26 Co CD A:Gln610 4.62 Co CG A:Gln610 4.58 Co CB A:Arg673 4.33 Co CD A:Arg673 3.83 Co CZ A:Arg673 4.25 Co CG A:Arg673 4.29 Co NE A:Arg673 4.45 Co NH1 A:Arg673 3.27 Co CD A:Pro674 4.77 interactive model: Cobalt binding site 4 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Cobalt in the PDB 1gql. 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: Asn162, A: Asn164, A: Val166, A: Trp702, A: Hoh2213, A: Hoh2695, A: Hoh2696, A: Hoh2705, B: Hoh2703, conact list: Atom Atom Distance (A) Co CB A:Asn162 4.55 Co ND2 A:Asn162 3.29 Co CG A:Asn162 4.34 Co ND2 A:Asn164 3.35 Co OD1 A:Asn164 3.99 Co CG A:Asn164 4.11 Co CB A:Val166 3.82 Co CG2 A:Val166 4.37 Co CG1 A:Val166 3.98 Co CD1 A:Trp702 3.73 Co CG A:Trp702 4.89 Co NE1 A:Trp702 4.19 Co O A:Hoh2213 4.73 Co O A:Hoh2695 4.95 Co O A:Hoh2696 3.22 Co O A:Hoh2705 3.12 Co O B:Hoh2703 4.88 interactive model: Cobalt binding site 5 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Cobalt in the PDB 1gql. 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: Met502, B: Val505, B: Ala625, B: Met626, B: Thr629, B: Hoh2229, B: Hoh2261, B: Hoh2509, B: Hoh2621, B: Hoh2625, B: Hoh2631, B: Hoh2714, conact list: Atom Atom Distance (A) Co N B:Met502 4.39 Co CB B:Met502 3.77 Co CG B:Met502 3.89 Co CA B:Met502 3.78 Co CG1 B:Val505 4.62 Co O B:Ala625 3.73 Co C B:Ala625 3.86 Co CB B:Ala625 4.48 Co CA B:Ala625 4.82 Co N B:Met626 3.85 Co CB B:Met626 4.45 Co C B:Met626 4.90 Co CG B:Met626 4.01 Co CA B:Met626 3.75 Co CB B:Thr629 3.74 Co CG2 B:Thr629 4.21 Co OG1 B:Thr629 3.03 Co O B:Hoh2229 4.92 Co O B:Hoh2261 4.99 Co O B:Hoh2509 3.52 Co O B:Hoh2621 3.07 Co O B:Hoh2625 4.25 Co O B:Hoh2631 4.78 Co O B:Hoh2714 3.32 interactive model: Cobalt binding site 6 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Cobalt in the PDB 1gql. 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: Asp6, B: Gly7, B: Asn452, B: Pro457, B: Gln460, B: Arg641, B: Gln644, B: Hoh2006, B: Hoh2481, B: Hoh2654, conact list: Atom Atom Distance (A) Co O B:Asp6 4.34 Co C B:Asp6 4.36 Co O B:Gly7 4.93 Co N B:Gly7 4.06 Co C B:Gly7 4.72 Co CA B:Gly7 3.55 Co CB B:Asn452 3.52 Co ND2 B:Asn452 3.31 Co CG B:Asn452 3.95 Co CA B:Asn452 4.89 Co N B:Pro457 4.77 Co CB B:Pro457 3.60 Co CD B:Pro457 4.71 Co CG B:Pro457 3.63 Co CA B:Pro457 4.02 Co NE2 B:Gln460 3.66 Co OE1 B:Gln460 4.47 Co CD B:Gln460 4.41 Co CD B:Arg641 3.68 Co CG B:Arg641 4.10 Co OE1 B:Gln644 4.42 Co O B:Hoh2006 4.82 Co O B:Hoh2481 3.07 Co O B:Hoh2654 2.99 interactive model: Cobalt binding site 7 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Cobalt in the PDB 1gql. 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: Asn162, B: Asn164, B: Val166, B: Trp702, A: Hoh2695, B: Hoh2220, B: Hoh2703, B: Hoh2706, B: Hoh2715, B: Hoh2716, B: Hoh2717, conact list: Atom Atom Distance (A) Co CB B:Asn162 4.55 Co ND2 B:Asn162 3.26 Co CG B:Asn162 4.32 Co ND2 B:Asn164 3.30 Co OD1 B:Asn164 3.96 Co CG B:Asn164 4.07 Co O B:Val166 5.00 Co CB B:Val166 3.80 Co CG2 B:Val166 4.33 Co CG1 B:Val166 3.91 Co CD1 B:Trp702 3.77 Co CG B:Trp702 4.94 Co NE1 B:Trp702 4.23 Co O A:Hoh2695 4.91 Co O B:Hoh2220 4.74 Co O B:Hoh2703 5.00 Co O B:Hoh2706 3.23 Co O B:Hoh2715 3.03 Co O B:Hoh2716 3.40 Co O B:Hoh2717 3.21 interactive model: Cobalt binding site 8 out of 8 in 1gql Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Cobalt in the PDB 1gql. 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: Asn607, B: Trp609, B: Gln610, B: Arg673, B: Pro674, B: Hoh2675, conact list: Atom Atom Distance (A) Co ND2 B:Asn607 3.40 Co OD1 B:Asn607 4.21 Co CG B:Asn607 4.25 Co CB B:Trp609 4.58 Co CD1 B:Trp609 3.68 Co CG B:Trp609 4.48 Co NE1 B:Trp609 4.60 Co NE2 B:Gln610 4.33 Co CD B:Gln610 4.68 Co CG B:Gln610 4.55 Co CB B:Arg673 4.25 Co CD B:Arg673 3.71 Co CZ B:Arg673 4.29 Co CG B:Arg673 4.16 Co NE B:Arg673 4.44 Co NH1 B:Arg673 3.31 Co CD B:Pro674 4.75 Co O B:Hoh2675 3.35 interactive model: