Magnesium in the structure of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor (pdb 2nz4)

The binding sites of Magnesium atom in the structure of Structural Investigation of the Glms Ribozyme Bound to Its Catalytic Cofactor (pdb code 2nz4). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2nz4 structure was solved by J.C.COCHRANE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.9-2.5 Space group P1211 a (A) 48.127 b (A) 234.157 c (A) 105.003 alpha (°) 90.00 beta (°) 90.65 gamma (°) 90.00 Rfactor (%) 22.2 Rfree (%) 26.9 Magnesium Binding Sites: Magnesium binding site 1 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: A28, P: C52, P: G53, P: G54, P: Glp5001, P: Hoh9011, P: Hoh9012, P: Hoh9013, P: Hoh9014, P: Hoh9015, P: Hoh9016, conact list: Atom Atom Distance (A) Mg N6 P:A28 4.24 Mg N7 P:A28 4.63 Mg OP1 P:C52 4.80 Mg P P:C52 4.53 Mg OP2 P:C52 3.36 Mg C8 P:G53 4.94 Mg C6 P:G53 4.84 Mg C5 P:G53 4.74 Mg N7 P:G53 4.06 Mg OP2 P:G53 4.37 Mg O6 P:G53 4.34 Mg N7 P:G54 4.57 Mg O6 P:G54 4.45 Mg P P:Glp5001 4.77 Mg O3P P:Glp5001 4.15 Mg O2P P:Glp5001 4.25 Mg O P:Hoh9011 2.10 Mg O P:Hoh9012 2.28 Mg O P:Hoh9013 2.19 Mg O P:Hoh9014 1.94 Mg O P:Hoh9015 1.96 Mg O P:Hoh9016 2.02 interactive model: Magnesium binding site 2 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: C55, P: G56, P: Glp5001, P: Hoh9017, P: Hoh9018, P: Hoh9019, P: Hoh9020, P: Hoh9021, P: Hoh9022, conact list: Atom Atom Distance (A) Mg C5 P:C55 4.99 Mg N4 P:C55 4.72 Mg O6 P:G56 4.83 Mg C6 P:Glp5001 4.62 Mg P P:Glp5001 4.18 Mg O3P P:Glp5001 3.99 Mg O1P P:Glp5001 3.30 Mg O6 P:Glp5001 4.93 Mg O P:Hoh9017 2.03 Mg O P:Hoh9018 2.04 Mg O P:Hoh9019 3.27 Mg O P:Hoh9020 2.94 Mg O P:Hoh9021 1.95 Mg O P:Hoh9022 2.35 interactive model: Magnesium binding site 3 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: A2m0, E: C2, P: G30, P: A31, P: G32, E: Hoh131, P: Hoh9028, conact list: Atom Atom Distance (A) Mg OP1 E:A2m0 3.84 Mg C5' E:A2m0 4.92 Mg OP1 E:C2 3.71 Mg C3' P:G30 4.43 Mg O3' P:G30 4.45 Mg C5' P:G30 4.79 Mg OP1 P:A31 4.54 Mg C8 P:A31 4.74 Mg P P:A31 3.58 Mg N7 P:A31 4.65 Mg OP2 P:A31 2.13 Mg O5' P:A31 4.21 Mg N7 P:G32 4.54 Mg O6 P:G32 4.80 Mg O E:Hoh131 2.00 Mg O P:Hoh9028 2.38 interactive model: Magnesium binding site 4 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: G1, E: C2, P: A28, P: C29, P: G30, E: Hoh80, conact list: Atom Atom Distance (A) Mg C3' E:G1 4.51 Mg O3' E:G1 3.19 Mg C2' E:G1 4.89 Mg O2' E:G1 4.15 Mg OP1 E:C2 4.41 Mg P E:C2 3.20 Mg OP2 E:C2 2.15 Mg C5' E:C2 4.24 Mg O5' E:C2 4.12 Mg C3' P:A28 4.21 Mg O3' P:A28 3.14 Mg C2' P:A28 4.42 Mg O2' P:A28 3.50 Mg OP1 P:C29 4.41 Mg C3' P:C29 4.26 Mg P P:C29 3.20 Mg O3' P:C29 4.46 Mg OP2 P:C29 2.15 Mg C5' P:C29 4.75 Mg O5' P:C29 4.06 Mg OP1 P:G30 4.16 Mg C8 P:G30 4.82 Mg P P:G30 3.63 Mg N7 P:G30 5.00 Mg OP2 P:G30 2.32 Mg O5' P:G30 4.80 Mg O E:Hoh80 2.11 interactive model: Magnesium binding site 5 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: A-1, F: A2m0, F: G1, F: C2, Q: G30, Q: A31, Q: G32, conact list: Atom Atom Distance (A) Mg O3' F:A-1 4.78 Mg OP1 F:A2m0 4.68 Mg P F:A2m0 3.77 Mg OP2 F:A2m0 2.27 Mg C5' F:A2m0 4.64 Mg O5' F:A2m0 4.40 Mg C3' F:G1 4.93 Mg O3' F:G1 4.62 Mg OP1 F:C2 2.31 Mg P F:C2 3.51 Mg OP2 F:C2 3.85 Mg O5' F:C2 4.50 Mg C3' Q:G30 4.76 Mg OP2 Q:G30 4.65 Mg C5' Q:G30 3.96 Mg C4' Q:G30 4.95 Mg O5' Q:G30 4.93 Mg P Q:A31 4.84 Mg OP2 Q:A31 3.45 Mg O6 Q:G32 4.81 interactive model: Magnesium binding site 6 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: G1, Q: A28, Q: C52, Q: G53, Q: G54, F: Glp5002, F: Hoh33, F: Hoh35, Q: Hoh9013, Q: Hoh9014, Q: Hoh9015, Q: Hoh9016, conact list: Atom Atom Distance (A) Mg N2 F:G1 4.77 Mg N6 Q:A28 4.45 Mg N7 Q:A28 4.77 Mg OP1 Q:C52 4.90 Mg P Q:C52 4.78 Mg OP2 Q:C52 3.69 Mg N7 Q:G53 4.60 Mg OP2 Q:G53 4.42 Mg N7 Q:G54 4.74 Mg O6 Q:G54 4.92 Mg P F:Glp5002 4.10 Mg O3P F:Glp5002 4.89 Mg O1P F:Glp5002 3.37 Mg O2P F:Glp5002 3.80 Mg O F:Hoh33 2.52 Mg O F:Hoh35 2.13 Mg O Q:Hoh9013 2.15 Mg O Q:Hoh9014 2.17 Mg O Q:Hoh9015 2.08 Mg O Q:Hoh9016 2.28 interactive model: Magnesium binding site 7 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: Q: G56, Q: G57, F: Glp5002, F: Hoh37, F: Hoh40, F: Hoh42, F: Hoh82, Q: Hoh9017, Q: Hoh9018, Q: Hoh9019, conact list: Atom Atom Distance (A) Mg N7 Q:G56 4.25 Mg O6 Q:G56 4.51 Mg N7 Q:G57 4.66 Mg O6 Q:G57 4.58 Mg O3P F:Glp5002 4.68 Mg O2P F:Glp5002 4.87 Mg O F:Hoh37 1.84 Mg O F:Hoh40 2.12 Mg O F:Hoh42 2.50 Mg O F:Hoh82 3.76 Mg O Q:Hoh9017 2.14 Mg O Q:Hoh9018 2.00 Mg O Q:Hoh9019 1.83 interactive model: Magnesium binding site 8 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: F: G1, F: C2, Q: A28, Q: C29, Q: G30, Q: Hoh9027, conact list: Atom Atom Distance (A) Mg C3' F:G1 4.61 Mg O3' F:G1 3.37 Mg C2' F:G1 4.81 Mg O2' F:G1 3.96 Mg OP1 F:C2 4.55 Mg P F:C2 3.39 Mg OP2 F:C2 2.25 Mg C5' F:C2 4.32 Mg O5' F:C2 4.31 Mg C3' Q:A28 3.97 Mg C1' Q:A28 4.86 Mg O3' Q:A28 3.02 Mg C2' Q:A28 4.10 Mg O2' Q:A28 3.10 Mg OP1 Q:C29 4.43 Mg C3' Q:C29 4.19 Mg P Q:C29 3.20 Mg O3' Q:C29 4.37 Mg OP2 Q:C29 2.26 Mg C5' Q:C29 4.69 Mg O5' Q:C29 4.08 Mg OP1 Q:G30 4.17 Mg C8 Q:G30 4.99 Mg P Q:G30 3.71 Mg OP2 Q:G30 2.50 Mg O Q:Hoh9027 2.17 interactive model: Magnesium binding site 9 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: A-1, G: A2m0, G: G1, G: C2, R: G30, R: A31, R: G32, G: Hoh9020, conact list: Atom Atom Distance (A) Mg C5' G:A-1 4.65 Mg O5' G:A-1 3.29 Mg OP1 G:A2m0 4.04 Mg C5' G:A2m0 4.38 Mg O3' G:G1 4.93 Mg OP1 G:C2 2.45 Mg P G:C2 3.81 Mg OP2 G:C2 4.37 Mg O5' G:C2 4.66 Mg O5' R:G30 4.78 Mg P R:A31 4.81 Mg OP2 R:A31 3.39 Mg O6 R:G32 4.55 Mg O G:Hoh9020 2.30 interactive model: Magnesium binding site 10 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: R: C55, R: G56, R: G57, G: Glp5003, G: Hoh9014, G: Hoh9015, G: Hoh9018, R: Hoh9015, R: Hoh9016, R: Hoh9017, R: Hoh9018, conact list: Atom Atom Distance (A) Mg N4 R:C55 4.86 Mg C8 R:G56 4.94 Mg C6 R:G56 4.78 Mg C5 R:G56 4.70 Mg N7 R:G56 3.93 Mg O6 R:G56 4.16 Mg C6 R:G57 5.00 Mg N7 R:G57 4.34 Mg O6 R:G57 4.29 Mg C6 G:Glp5003 4.87 Mg O3P G:Glp5003 4.53 Mg O2P G:Glp5003 4.50 Mg O G:Hoh9014 2.00 Mg O G:Hoh9015 2.04 Mg O G:Hoh9018 4.13 Mg O R:Hoh9015 2.16 Mg O R:Hoh9016 2.27 Mg O R:Hoh9017 2.02 Mg O R:Hoh9018 1.86 interactive model: Magnesium binding site 11 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: R: A28, R: C52, R: G53, R: G54, G: Glp5003, G: Hoh9016, G: Hoh9017, R: Hoh9019, R: Hoh9020, R: Hoh9021, R: Hoh9022, conact list: Atom Atom Distance (A) Mg N6 R:A28 4.69 Mg N7 R:A28 4.69 Mg P R:C52 4.67 Mg OP2 R:C52 3.51 Mg C8 R:G53 4.98 Mg C6 R:G53 4.83 Mg C5 R:G53 4.74 Mg N7 R:G53 4.12 Mg OP2 R:G53 4.54 Mg O6 R:G53 4.36 Mg C6 R:G54 4.96 Mg N7 R:G54 4.36 Mg O6 R:G54 4.11 Mg P G:Glp5003 4.97 Mg O1P G:Glp5003 4.29 Mg O2P G:Glp5003 4.52 Mg O G:Hoh9016 2.05 Mg O G:Hoh9017 1.92 Mg O R:Hoh9019 1.86 Mg O R:Hoh9020 2.23 Mg O R:Hoh9021 1.92 Mg O R:Hoh9022 2.10 interactive model: Magnesium binding site 12 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 12 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: G1, G: C2, R: A28, R: C29, R: G30, G: Hoh9020, R: Hoh9038, conact list: Atom Atom Distance (A) Mg O3' G:G1 3.96 Mg O2' G:G1 4.90 Mg OP1 G:C2 4.53 Mg P G:C2 3.46 Mg OP2 G:C2 2.01 Mg C5' G:C2 4.30 Mg O5' G:C2 4.18 Mg C3' R:A28 4.77 Mg O3' R:A28 3.74 Mg O2' R:A28 4.56 Mg OP1 R:C29 4.63 Mg C3' R:C29 4.64 Mg P R:C29 3.53 Mg O3' R:C29 4.54 Mg OP2 R:C29 2.29 Mg C5' R:C29 4.74 Mg O5' R:C29 4.45 Mg OP1 R:G30 3.78 Mg P R:G30 3.42 Mg OP2 R:G30 2.24 Mg O5' R:G30 4.25 Mg O G:Hoh9020 4.07 Mg O R:Hoh9038 1.97 interactive model: Magnesium binding site 13 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 13 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: H: A-1, H: A2m0, H: C2, S: G30, S: A31, S: G32, H: Hoh132, H: Hoh185, conact list: Atom Atom Distance (A) Mg O5' H:A-1 4.23 Mg OP1 H:A2m0 4.10 Mg C5' H:A2m0 4.60 Mg O5' H:A2m0 4.79 Mg OP1 H:C2 3.11 Mg P H:C2 4.48 Mg C3' S:G30 4.65 Mg O3' S:G30 4.87 Mg C8 S:A31 4.99 Mg P S:A31 4.20 Mg N7 S:A31 4.74 Mg OP2 S:A31 2.73 Mg N7 S:G32 4.65 Mg O6 S:G32 4.26 Mg O H:Hoh132 1.83 Mg O H:Hoh185 2.77 interactive model: Magnesium binding site 14 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 14 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: H: G1, H: C2, S: A28, S: C29, S: G30, S: Hoh9010, S: Hoh9013, S: Hoh9014, conact list: Atom Atom Distance (A) Mg C3' H:G1 4.82 Mg O3' H:G1 3.49 Mg O2' H:G1 4.58 Mg OP1 H:C2 4.28 Mg P H:C2 3.16 Mg OP2 H:C2 1.80 Mg C5' H:C2 4.17 Mg O5' H:C2 4.02 Mg C3' S:A28 4.68 Mg O3' S:A28 3.67 Mg C2' S:A28 4.98 Mg O2' S:A28 4.12 Mg OP1 S:C29 4.76 Mg C3' S:C29 4.54 Mg P S:C29 3.58 Mg O3' S:C29 4.53 Mg OP2 S:C29 2.31 Mg C5' S:C29 4.80 Mg O5' S:C29 4.40 Mg OP1 S:G30 4.17 Mg P S:G30 3.43 Mg OP2 S:G30 2.09 Mg O5' S:G30 3.92 Mg O S:Hoh9010 1.86 Mg O S:Hoh9013 1.89 Mg O S:Hoh9014 2.00 interactive model: Magnesium binding site 15 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 15 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: S: G56, S: G57, H: Glp5004, conact list: Atom Atom Distance (A) Mg C6 S:G56 4.91 Mg C5 S:G56 4.96 Mg N7 S:G56 4.27 Mg O6 S:G56 4.19 Mg N7 S:G57 4.80 Mg O6 S:G57 4.34 Mg C6 H:Glp5004 4.55 Mg P H:Glp5004 4.96 Mg O3P H:Glp5004 4.41 Mg O1P H:Glp5004 4.47 interactive model: Magnesium binding site 16 out of 16 in 2nz4 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 16 of Magnesium in the PDB 2nz4. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Magnesium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: S: A28, S: C52, S: G53, S: G54, H: Glp5004, H: Hoh14, H: Hoh17, S: Hoh9005, S: Hoh9006, S: Hoh9007, S: Hoh9008, conact list: Atom Atom Distance (A) Mg N6 S:A28 4.59 Mg N7 S:A28 4.56 Mg OP2 S:C52 3.67 Mg C8 S:G53 4.96 Mg C6 S:G53 4.80 Mg C5 S:G53 4.72 Mg N7 S:G53 4.07 Mg OP2 S:G53 4.73 Mg O6 S:G53 4.29 Mg C6 S:G54 4.97 Mg C5 S:G54 4.99 Mg N7 S:G54 4.25 Mg O6 S:G54 4.24 Mg P H:Glp5004 4.79 Mg O3P H:Glp5004 4.26 Mg O2P H:Glp5004 4.08 Mg O H:Hoh14 1.83 Mg O H:Hoh17 2.07 Mg O S:Hoh9005 1.86 Mg O S:Hoh9006 2.09 Mg O S:Hoh9007 2.02 Mg O S:Hoh9008 2.18 interactive model: