Magnesium in the structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb 3m32)

The binding sites of Magnesium atom in the structure of Structural Insight Into Methyl-Coenzyme M Reductase Chemistry Using Coenzyme B Analogues (pdb code 3m32). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 3m32 structure was solved by P.E.CEDERVALL, M.DEY, S.W.RAGSDALE, C.M.WILMOT, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 20.3-1.4 Space group P1211 a (A) 82.016 b (A) 118.260 c (A) 122.387 alpha (°) 90.00 beta (°) 91.84 gamma (°) 90.00 Rfactor (%) 14 Rfree (%) 15.7 Magnesium Binding Sites: Magnesium binding site 1 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 3m32. 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: A: Asp516, A: Asp521, A: Mg552, A: Hoh716, A: Hoh739, A: Hoh996, A: Hoh1286, A: Hoh1356, A: Hoh1590, A: Hoh1599, A: Hoh2583, A: Hoh2603, A: Hoh3581, A: Hoh3828, A: Hoh3907, A: Hoh3971, conact list: Atom Atom Distance (A) Mg O A:Asp516 4.50 Mg CB A:Asp516 4.49 Mg OD1 A:Asp516 4.82 Mg CB A:Asp521 4.66 Mg OD2 A:Asp521 4.51 Mg CG A:Asp521 4.68 Mg MG A:Mg552 4.08 Mg O A:Hoh716 4.46 Mg O A:Hoh739 4.10 Mg O A:Hoh996 4.56 Mg O A:Hoh1286 4.92 Mg O A:Hoh1356 2.05 Mg O A:Hoh1590 2.08 Mg O A:Hoh1599 2.19 Mg O A:Hoh1599 2.37 Mg O A:Hoh2583 2.11 Mg O A:Hoh2603 2.29 Mg O A:Hoh3581 1.94 Mg O A:Hoh3828 4.54 Mg O A:Hoh3907 4.37 Mg O A:Hoh3971 3.70 interactive model: Magnesium binding site 2 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 3m32. 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: A: Val519, A: Glu528, A: Lys531, A: Mg551, A: Act556, A: Hoh641, A: Hoh716, A: Hoh1396, A: Hoh1599, A: Hoh2285, A: Hoh2583, A: Hoh3581, A: Hoh3828, A: Hoh3971, conact list: Atom Atom Distance (A) Mg O A:Val519 4.52 Mg OE1 A:Glu528 4.34 Mg OE2 A:Glu528 4.14 Mg CD A:Glu528 4.69 Mg CE A:Lys531 4.95 Mg CD A:Lys531 4.92 Mg NZ A:Lys531 3.82 Mg MG A:Mg551 4.08 Mg O A:Act556 4.18 Mg CH3 A:Act556 3.40 Mg C A:Act556 3.04 Mg OXT A:Act556 1.99 Mg O A:Hoh641 3.79 Mg O A:Hoh716 2.11 Mg O A:Hoh1396 4.11 Mg O A:Hoh1599 3.68 Mg O A:Hoh1599 2.07 Mg O A:Hoh2285 2.33 Mg O A:Hoh2583 3.89 Mg O A:Hoh3581 2.72 Mg O A:Hoh3828 2.16 Mg O A:Hoh3971 2.15 interactive model: Magnesium binding site 3 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 3m32. 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: B: Asn250, B: Asp254, B: Hoh1305, B: Hoh3031, B: Hoh3225, B: Hoh3325, B: Hoh3430, B: Hoh3547, B: Hoh3548, B: Hoh3549, B: Hoh3550, B: Hoh3714, conact list: Atom Atom Distance (A) Mg ND2 B:Asn250 4.11 Mg OD2 B:Asp254 4.10 Mg OD1 B:Asp254 4.12 Mg CG B:Asp254 4.51 Mg O B:Hoh1305 2.07 Mg O B:Hoh3031 4.37 Mg O B:Hoh3225 4.06 Mg O B:Hoh3325 4.58 Mg O B:Hoh3430 4.96 Mg O B:Hoh3547 2.02 Mg O B:Hoh3548 2.07 Mg O B:Hoh3549 2.00 Mg O B:Hoh3550 2.02 Mg O B:Hoh3714 2.23 interactive model: Magnesium binding site 4 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 3m32. 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: C: Lys27, C: Glu30, C: Ile31, C: Lys135, C: Glu139, C: Hoh722, C: Hoh1095, C: Hoh1319, C: Hoh1542, C: Hoh2304, C: Hoh3555, C: Hoh3556, C: Hoh3557, C: Hoh3558, C: Hoh3795, conact list: Atom Atom Distance (A) Mg NZ C:Lys27 4.47 Mg OE1 C:Glu30 3.40 Mg OE2 C:Glu30 2.03 Mg CD C:Glu30 3.07 Mg CG C:Glu30 4.45 Mg O C:Ile31 4.11 Mg CE C:Lys135 4.89 Mg NZ C:Lys135 3.90 Mg OE2 C:Glu139 4.26 Mg O C:Hoh722 3.90 Mg O C:Hoh1095 2.11 Mg O C:Hoh1319 4.40 Mg O C:Hoh1542 4.20 Mg O C:Hoh2304 4.12 Mg O C:Hoh3555 2.08 Mg O C:Hoh3556 2.16 Mg O C:Hoh3557 2.11 Mg O C:Hoh3558 2.03 Mg O C:Hoh3795 4.36 interactive model: Magnesium binding site 5 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 3m32. 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: B: Ser267, B: Asp271, B: Glu274, B: Hoh564, B: Hoh811, B: Hoh973, B: Hoh1206, B: Hoh3076, B: Hoh4161, conact list: Atom Atom Distance (A) Mg O B:Ser267 4.54 Mg N B:Asp271 4.65 Mg CB B:Asp271 4.35 Mg OD2 B:Asp271 3.38 Mg OD1 B:Asp271 1.98 Mg CG B:Asp271 3.01 Mg CA B:Asp271 4.61 Mg OE1 B:Glu274 4.73 Mg OE1 B:Glu274 4.68 Mg OE2 B:Glu274 4.29 Mg CD B:Glu274 4.87 Mg O B:Hoh564 2.23 Mg O B:Hoh811 2.31 Mg O B:Hoh811 1.97 Mg O B:Hoh973 4.26 Mg O B:Hoh1206 2.74 Mg O B:Hoh1206 2.02 Mg O B:Hoh3076 2.27 Mg O B:Hoh4161 1.97 interactive model: Magnesium binding site 6 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 3m32. 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: D: Asp516, D: Asp521, D: Hoh674, D: Hoh992, D: Hoh1116, D: Hoh3559, D: Hoh3560, D: Hoh3561, D: Hoh3562, D: Hoh3563, conact list: Atom Atom Distance (A) Mg O D:Asp516 4.47 Mg CB D:Asp516 4.76 Mg OD1 D:Asp516 4.29 Mg CG D:Asp516 4.88 Mg CB D:Asp521 4.64 Mg OD2 D:Asp521 4.42 Mg CG D:Asp521 4.68 Mg O D:Hoh674 4.03 Mg O D:Hoh992 4.63 Mg O D:Hoh1116 2.11 Mg O D:Hoh3559 2.00 Mg O D:Hoh3560 2.08 Mg O D:Hoh3561 2.05 Mg O D:Hoh3562 2.05 Mg O D:Hoh3563 2.06 interactive model: Magnesium binding site 7 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 3m32. 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: D: Glu376, F: Arg225, D: Hoh1011, D: Hoh3543, D: Hoh3544, D: Hoh3546, D: Hoh4148, F: Hoh807, F: Hoh3542, F: Hoh3545, conact list: Atom Atom Distance (A) Mg OE1 D:Glu376 4.52 Mg OE2 D:Glu376 4.40 Mg CD D:Glu376 4.91 Mg CZ F:Arg225 4.98 Mg NH2 F:Arg225 4.14 Mg O D:Hoh1011 4.39 Mg O D:Hoh3543 2.14 Mg O D:Hoh3544 2.11 Mg O D:Hoh3546 2.05 Mg O D:Hoh4148 4.37 Mg O F:Hoh807 4.59 Mg O F:Hoh3542 2.06 Mg O F:Hoh3545 2.02 interactive model: Magnesium binding site 8 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 3m32. 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: Glu287, E: Lys292, E: Hoh2118, E: Hoh2200, E: Hoh2328, E: Hoh3583, E: Hoh3584, E: Hoh3585, E: Hoh3601, E: Hoh3758, F: Hoh3202, conact list: Atom Atom Distance (A) Mg OE1 E:Glu287 3.99 Mg OE2 E:Glu287 4.65 Mg CD E:Glu287 4.53 Mg CE E:Lys292 5.00 Mg NZ E:Lys292 4.53 Mg O E:Hoh2118 4.47 Mg O E:Hoh2200 2.11 Mg O E:Hoh2328 2.02 Mg O E:Hoh3583 1.94 Mg O E:Hoh3584 2.24 Mg O E:Hoh3585 2.09 Mg O E:Hoh3601 4.05 Mg O E:Hoh3758 4.37 Mg O F:Hoh3202 3.95 interactive model: Magnesium binding site 9 out of 9 in 3m32 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 3m32. 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: Lys27, F: Glu30, F: Ile31, F: Lys135, F: Glu139, F: Hoh715, F: Hoh752, F: Hoh1096, F: Hoh1294, F: Hoh3551, F: Hoh3552, F: Hoh3553, F: Hoh3554, F: Hoh3665, conact list: Atom Atom Distance (A) Mg NZ F:Lys27 4.37 Mg OE1 F:Glu30 3.38 Mg OE2 F:Glu30 2.07 Mg CD F:Glu30 3.11 Mg CG F:Glu30 4.34 Mg O F:Ile31 4.07 Mg C F:Ile31 4.99 Mg CE F:Lys135 4.94 Mg NZ F:Lys135 3.95 Mg OE2 F:Glu139 4.19 Mg O F:Hoh715 4.37 Mg O F:Hoh752 3.94 Mg O F:Hoh1096 4.30 Mg O F:Hoh1294 2.08 Mg O F:Hoh3551 2.09 Mg O F:Hoh3552 2.06 Mg O F:Hoh3553 2.12 Mg O F:Hoh3554 2.05 Mg O F:Hoh3665 4.23 interactive model: