Sodium in the structure of Mature Metal Chelatase Catalytic Antibody With Hapten (pdb 3fct)

The binding sites of Sodium atom in the structure of Mature Metal Chelatase Catalytic Antibody With Hapten (pdb code 3fct). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3fct structure was solved by F.E.ROMESBERG, B.D.SANTARSIERO, D.BARNES, J.YIN, B.SPILLER, P.G.SCHULTZ, R.C.STEVENS, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 50.0-2.4 Space group P21212 a (A) 134.290 b (A) 100.689 c (A) 73.537 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 20.6 Rfree (%) 29.3 Sodium Binding Sites: Sodium binding site 1 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys39, A: Gln42, A: Lys45, A: Hoh973, A: Hoh1030, conact list: Atom Atom Distance (A) Na CE A:Lys39 3.21 Na CD A:Lys39 3.75 Na NZ A:Lys39 4.41 Na NE2 A:Gln42 4.19 Na OE1 A:Gln42 3.68 Na CD A:Gln42 4.37 Na CE A:Lys45 4.09 Na CD A:Lys45 4.95 Na NZ A:Lys45 2.89 Na O A:Hoh973 4.72 Na O A:Hoh1030 2.90 interactive model: Sodium binding site 2 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asn198, B: Asn200, B: Lys207, B: Val208, B: Asp209, B: Hoh948, B: Hoh1055, conact list: Atom Atom Distance (A) Na CB B:Asn198 4.25 Na ND2 B:Asn198 4.04 Na CG B:Asn198 4.64 Na OD1 B:Asn200 4.77 Na CD B:Lys207 3.96 Na CG B:Lys207 3.82 Na O B:Val208 4.64 Na CB B:Asp209 4.77 Na OD2 B:Asp209 2.87 Na OD1 B:Asp209 2.94 Na CG B:Asp209 3.28 Na O B:Hoh948 3.76 Na O B:Hoh1055 2.87 interactive model: Sodium binding site 3 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Tyr27, B: Thr28, B: Phe29, B: Tyr32, B: Trp33, B: Met34, B: Pro53, B: Arg98, conact list: Atom Atom Distance (A) Na CE2 B:Tyr27 3.61 Na CD2 B:Tyr27 4.89 Na CZ B:Tyr27 3.70 Na OH B:Tyr27 2.97 Na O B:Thr28 4.96 Na O B:Phe29 3.11 Na CD1 B:Phe29 3.54 Na CZ B:Phe29 4.84 Na C B:Phe29 4.08 Na CE1 B:Phe29 3.74 Na CG B:Phe29 4.52 Na CA B:Phe29 4.35 Na O B:Tyr32 2.80 Na N B:Tyr32 4.03 Na CB B:Tyr32 3.72 Na C B:Tyr32 3.59 Na CG B:Tyr32 4.92 Na CA B:Tyr32 3.97 Na N B:Trp33 4.64 Na C B:Trp33 4.51 Na O B:Trp33 4.32 Na N B:Met34 4.81 Na CB B:Met34 4.60 Na CE B:Met34 3.53 Na SD B:Met34 4.67 Na CA B:Met34 4.99 Na CB B:Pro53 4.53 Na CD B:Pro53 4.67 Na CG B:Pro53 3.87 Na CD B:Arg98 4.46 Na CG B:Arg98 4.91 interactive model: Sodium binding site 4 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asn138, C: Asp167, C: Asp170, C: Thr172, D: His165, C: Hoh969, C: Hoh972, C: Hoh997, D: Hoh283, conact list: Atom Atom Distance (A) Na CB C:Asn138 4.35 Na ND2 C:Asn138 3.73 Na OD1 C:Asn138 2.71 Na CG C:Asn138 3.33 Na OD2 C:Asp167 3.27 Na OD1 C:Asp167 4.78 Na CG C:Asp167 4.22 Na CB C:Asp170 4.70 Na OD2 C:Asp170 2.64 Na OD1 C:Asp170 4.71 Na CG C:Asp170 3.87 Na OG1 C:Thr172 4.61 Na NE2 D:His165 3.82 Na CE1 D:His165 3.83 Na O C:Hoh969 4.21 Na O C:Hoh972 3.36 Na O C:Hoh997 2.81 Na O D:Hoh283 4.20 interactive model: Sodium binding site 5 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Pro59, C: Asp60, C: Arg61, C: Hoh940, C: Hoh950, C: Hoh987, C: Hoh992, conact list: Atom Atom Distance (A) Na O C:Pro59 4.73 Na CB C:Pro59 3.37 Na C C:Pro59 3.86 Na CG C:Pro59 4.72 Na CA C:Pro59 3.97 Na O C:Asp60 4.90 Na N C:Asp60 3.37 Na CB C:Asp60 4.58 Na OD2 C:Asp60 4.81 Na C C:Asp60 3.86 Na OD1 C:Asp60 2.66 Na CG C:Asp60 3.86 Na CA C:Asp60 4.07 Na N C:Arg61 2.99 Na CB C:Arg61 3.23 Na CD C:Arg61 3.86 Na CZ C:Arg61 4.51 Na C C:Arg61 4.99 Na CG C:Arg61 3.26 Na NE C:Arg61 4.64 Na NH1 C:Arg61 3.49 Na CA C:Arg61 3.66 Na O C:Hoh940 3.72 Na O C:Hoh950 4.13 Na O C:Hoh987 2.76 Na O C:Hoh992 4.56 interactive model: Sodium binding site 6 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Gln37, C: Lys39, C: Gln42, C: Lys45, C: Hoh933, C: Hoh937, C: Hoh962, C: Hoh1014, C: Hoh1036, conact list: Atom Atom Distance (A) Na NE2 C:Gln37 4.79 Na CE C:Lys39 3.74 Na CD C:Lys39 4.43 Na NZ C:Lys39 4.95 Na NE2 C:Gln42 4.58 Na OE1 C:Gln42 3.87 Na CD C:Gln42 4.66 Na CE C:Lys45 3.20 Na CD C:Lys45 4.07 Na NZ C:Lys45 4.09 Na O C:Hoh933 2.65 Na O C:Hoh937 4.62 Na O C:Hoh962 2.79 Na O C:Hoh1014 3.71 Na O C:Hoh1036 2.84 interactive model: Sodium binding site 7 out of 7 in 3fct Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Sodium in the PDB 3fct. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Met4, C: Thr5, C: Gln6, C: Lys9, C: Gly99, C: Gly100, C: Hoh983, conact list: Atom Atom Distance (A) Na O C:Met4 2.89 Na C C:Met4 3.85 Na O C:Thr5 4.94 Na N C:Thr5 4.09 Na CB C:Thr5 4.40 Na CG2 C:Thr5 4.60 Na OG1 C:Thr5 4.59 Na C C:Thr5 3.75 Na CA C:Thr5 3.36 Na O C:Gln6 4.63 Na N C:Gln6 3.20 Na CB C:Gln6 4.29 Na C C:Gln6 4.97 Na CA C:Gln6 4.29 Na NZ C:Lys9 4.94 Na O C:Gly99 4.92 Na C C:Gly99 3.86 Na CA C:Gly99 4.12 Na N C:Gly100 2.87 Na C C:Gly100 4.76 Na CA C:Gly100 3.45 Na O C:Hoh983 3.50 interactive model: