Platinum in the structure of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis (pdb 1rli)

The binding sites of Platinum atom in the structure of The Structure of Trp Repressor Binding Protein From Bacillus Subtilis (pdb code 1rli). This binding sites where shown with 5.0 Angstroms radius around Platinum atom. The 1rli structure was solved by Y.KIM, P.QUARTEY, A.JOACHIMIAK, MIDWEST CENTER FOR STRUCTURALGENOMICS (MCSG), with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 36.8-1.8 Space group P1211 a (A) 60.993 b (A) 90.666 c (A) 63.446 alpha (°) 90.00 beta (°) 97.02 gamma (°) 90.00 Rfactor (%) 19.6 Rfree (%) 23 Platinum Binding Sites: Platinum binding site 1 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly82, A: Met83, A: Lys88, A: Leu132, A: Gln135, D: Lys88, D: Gln135, A: Hoh607, A: Hoh613, A: Hoh646, A: Hoh689, A: Hoh690, D: Hoh624, conact list: Atom Atom Distance (A) Pt C A:Gly82 4.72 Pt CA A:Gly82 4.71 Pt N A:Met83 3.74 Pt CB A:Met83 4.00 Pt CE A:Met83 3.19 Pt CG A:Met83 2.83 Pt SD A:Met83 3.46 Pt CA A:Met83 4.46 Pt CB A:Lys88 4.62 Pt CE A:Lys88 4.72 Pt CD A:Lys88 4.14 Pt CG A:Lys88 4.76 Pt NZ A:Lys88 4.95 Pt CD1 A:Leu132 4.61 Pt OE1 A:Gln135 4.04 Pt CD A:Gln135 4.80 Pt CE D:Lys88 4.86 Pt NE2 D:Gln135 4.76 Pt O A:Hoh607 2.12 Pt O A:Hoh613 3.51 Pt O A:Hoh646 2.50 Pt O A:Hoh689 2.47 Pt O A:Hoh690 2.30 Pt O D:Hoh624 3.82 interactive model: Platinum binding site 2 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Lys2, A: Ile3, A: His70, A: Hoh705, A: Hoh706, A: Hoh707, conact list: Atom Atom Distance (A) Pt CB A:Lys2 3.82 Pt CE A:Lys2 3.40 Pt CD A:Lys2 3.49 Pt CG A:Lys2 4.26 Pt NZ A:Lys2 3.22 Pt CG2 A:Ile3 4.72 Pt NE2 A:His70 2.45 Pt ND1 A:His70 4.56 Pt CD2 A:His70 3.32 Pt CE1 A:His70 3.48 Pt CG A:His70 4.52 Pt O A:Hoh705 2.43 Pt O A:Hoh706 4.11 Pt O A:Hoh707 2.94 interactive model: Platinum binding site 3 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Gly14, A: Asn15, A: Thr16, A: Pro77, A: Val120, A: Hoh628, A: Hoh649, A: Hoh672, A: Hoh674, A: Hoh709, A: Hoh710, A: Hoh713, conact list: Atom Atom Distance (A) Pt C A:Gly14 4.51 Pt CA A:Gly14 4.90 Pt N A:Asn15 3.75 Pt CB A:Asn15 3.76 Pt ND2 A:Asn15 4.67 Pt C A:Asn15 4.14 Pt CG A:Asn15 4.69 Pt CA A:Asn15 4.05 Pt N A:Thr16 3.33 Pt CB A:Thr16 3.91 Pt OG1 A:Thr16 3.27 Pt CA A:Thr16 4.20 Pt CB A:Pro77 4.16 Pt CA A:Pro77 4.82 Pt O A:Val120 4.99 Pt CB A:Val120 4.91 Pt CG1 A:Val120 4.87 Pt O A:Hoh628 4.65 Pt O A:Hoh649 3.60 Pt O A:Hoh672 2.88 Pt O A:Hoh674 3.86 Pt O A:Hoh709 2.68 Pt O A:Hoh710 2.16 Pt O A:Hoh713 3.79 interactive model: Platinum binding site 4 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Gly82, B: Met83, B: Lys88, B: Leu132, B: Gln135, C: Lys88, C: Gln135, B: Hoh642, B: Hoh701, B: Hoh702, C: Hoh613, C: Hoh621, C: Hoh653, conact list: Atom Atom Distance (A) Pt C B:Gly82 4.88 Pt CA B:Gly82 4.88 Pt N B:Met83 3.86 Pt N B:Met83 3.87 Pt CB B:Met83 3.83 Pt CB B:Met83 4.03 Pt CE B:Met83 3.87 Pt CE B:Met83 3.59 Pt CG B:Met83 4.15 Pt CG B:Met83 2.76 Pt SD B:Met83 3.76 Pt SD B:Met83 3.39 Pt CA B:Met83 4.44 Pt CA B:Met83 4.52 Pt CB B:Lys88 4.51 Pt CE B:Lys88 4.75 Pt CD B:Lys88 4.23 Pt CG B:Lys88 4.74 Pt CD1 B:Leu132 4.72 Pt NE2 B:Gln135 2.67 Pt OE1 B:Gln135 4.25 Pt OE1 B:Gln135 4.14 Pt CD B:Gln135 3.84 Pt CD B:Gln135 4.89 Pt CE C:Lys88 4.70 Pt NE2 C:Gln135 4.87 Pt O B:Hoh642 3.71 Pt O B:Hoh701 2.32 Pt O B:Hoh702 2.36 Pt O C:Hoh613 2.29 Pt O C:Hoh621 4.06 Pt O C:Hoh653 2.42 interactive model: Platinum binding site 5 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: His70, B: Ile71, B: Po4614, B: Hoh726, B: Hoh745, conact list: Atom Atom Distance (A) Pt NE2 B:His70 4.37 Pt CB B:His70 3.63 Pt ND1 B:His70 2.38 Pt CD2 B:His70 4.43 Pt CE1 B:His70 3.27 Pt CG B:His70 3.34 Pt CD1 B:Ile71 4.77 Pt CG1 B:Ile71 4.81 Pt O1 B:Po4614 4.37 Pt O2 B:Po4614 3.66 Pt P B:Po4614 3.40 Pt O4 B:Po4614 2.11 Pt O3 B:Po4614 4.27 Pt O B:Hoh726 2.58 Pt O B:Hoh745 3.40 interactive model: Platinum binding site 6 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Lys36, C: Gly50, C: Phe52, C: Tyr79, C: Gly85, C: Thr86, B: Hoh643, B: Hoh703, C: Hoh614, C: Hoh623, C: Hoh636, C: Hoh658, C: Hoh703, conact list: Atom Atom Distance (A) Pt CE C:Lys36 4.64 Pt CD C:Lys36 4.00 Pt NZ C:Lys36 4.00 Pt N C:Gly50 4.59 Pt CA C:Gly50 4.91 Pt O C:Phe52 4.55 Pt N C:Phe52 4.83 Pt CB C:Phe52 4.30 Pt CD1 C:Phe52 4.68 Pt C C:Phe52 4.77 Pt CG C:Phe52 4.96 Pt CA C:Phe52 4.90 Pt CE2 C:Tyr79 4.56 Pt N C:Gly85 4.51 Pt CA C:Gly85 4.65 Pt N C:Thr86 4.82 Pt CG2 C:Thr86 4.90 Pt O B:Hoh643 3.27 Pt O B:Hoh703 2.22 Pt O C:Hoh614 2.25 Pt O C:Hoh623 2.51 Pt O C:Hoh636 2.49 Pt O C:Hoh658 4.74 Pt O C:Hoh703 3.27 interactive model: Platinum binding site 7 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Thr10, C: Gly14, C: Asn15, C: Thr16, C: Pro77, C: Hoh693, C: Hoh697, C: Hoh699, C: Hoh700, C: Hoh711, C: Hoh715, conact list: Atom Atom Distance (A) Pt O C:Thr10 4.90 Pt C C:Gly14 4.27 Pt CA C:Gly14 4.10 Pt N C:Asn15 3.66 Pt CB C:Asn15 4.37 Pt ND2 C:Asn15 4.52 Pt C C:Asn15 4.90 Pt CG C:Asn15 4.82 Pt CA C:Asn15 4.50 Pt N C:Thr16 4.20 Pt CB C:Thr16 4.80 Pt OG1 C:Thr16 4.25 Pt CB C:Pro77 4.72 Pt O C:Hoh693 4.48 Pt O C:Hoh697 2.55 Pt O C:Hoh699 1.97 Pt O C:Hoh700 2.56 Pt O C:Hoh711 3.59 Pt O C:Hoh715 3.07 interactive model: Platinum binding site 8 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Lys2, C: His70, C: Hoh694, C: Hoh695, C: Hoh696, conact list: Atom Atom Distance (A) Pt CE C:Lys2 3.76 Pt CD C:Lys2 4.82 Pt CG C:Lys2 4.64 Pt NZ C:Lys2 2.87 Pt NE2 C:His70 4.45 Pt CB C:His70 3.39 Pt ND1 C:His70 2.42 Pt CD2 C:His70 4.39 Pt CE1 C:His70 3.42 Pt CG C:His70 3.24 Pt CA C:His70 4.91 Pt O C:Hoh694 2.36 Pt O C:Hoh695 2.29 Pt O C:Hoh696 4.69 interactive model: Platinum binding site 9 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Lys36, D: Gly50, D: Phe52, D: Tyr79, D: Gly85, D: Thr86, A: Hoh636, A: Hoh691, D: Hoh615, D: Hoh626, D: Hoh636, D: Hoh692, D: Hoh711, conact list: Atom Atom Distance (A) Pt CE D:Lys36 4.84 Pt CD D:Lys36 4.19 Pt NZ D:Lys36 4.39 Pt N D:Gly50 4.38 Pt CA D:Gly50 4.73 Pt O D:Phe52 4.52 Pt N D:Phe52 4.79 Pt CB D:Phe52 4.24 Pt CD1 D:Phe52 4.82 Pt C D:Phe52 4.73 Pt CG D:Phe52 4.96 Pt CA D:Phe52 4.84 Pt CE2 D:Tyr79 4.30 Pt CD2 D:Tyr79 4.90 Pt N D:Gly85 4.52 Pt CA D:Gly85 4.66 Pt N D:Thr86 4.83 Pt CG2 D:Thr86 4.91 Pt O A:Hoh636 3.36 Pt O A:Hoh691 2.22 Pt O D:Hoh615 2.35 Pt O D:Hoh626 4.42 Pt O D:Hoh636 2.43 Pt O D:Hoh692 3.03 Pt O D:Hoh711 2.34 interactive model: Platinum binding site 10 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Lys2, D: His70, D: Hoh736, D: Hoh764, conact list: Atom Atom Distance (A) Pt CE D:Lys2 3.13 Pt CD D:Lys2 4.28 Pt NZ D:Lys2 2.67 Pt NE2 D:His70 4.33 Pt CB D:His70 3.65 Pt ND1 D:His70 2.85 Pt CD2 D:His70 4.25 Pt CE1 D:His70 3.57 Pt CG D:His70 3.37 Pt O D:Hoh736 2.62 Pt O D:Hoh764 4.27 interactive model: Platinum binding site 11 out of 11 in 1rli Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Platinum in the PDB 1rli. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Platinum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: D: Thr10, D: Gly14, D: Asn15, D: Thr16, D: Pro77, D: Hoh698, D: Hoh737, D: Hoh738, D: Hoh739, D: Hoh740, D: Hoh756, conact list: Atom Atom Distance (A) Pt OG1 D:Thr10 4.16 Pt C D:Gly14 4.48 Pt CA D:Gly14 4.39 Pt N D:Asn15 3.72 Pt CB D:Asn15 4.17 Pt ND2 D:Asn15 3.89 Pt C D:Asn15 4.99 Pt CG D:Asn15 4.40 Pt CA D:Asn15 4.47 Pt N D:Thr16 4.41 Pt OG1 D:Thr16 4.57 Pt CB D:Pro77 4.63 Pt O D:Hoh698 3.24 Pt O D:Hoh737 2.42 Pt O D:Hoh738 2.42 Pt O D:Hoh739 2.41 Pt O D:Hoh740 2.49 Pt O D:Hoh756 4.25 interactive model: