Magnesium in the structure of Malk (pdb 1g29)

The binding sites of Magnesium atom in the structure of Malk (pdb code 1g29). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 1g29 structure was solved by K.DIEDERICHS, J.DIEZ, G.GRELLER, C.MUELLER, J.BREED, C.SCHNELL, C.VONRHEIN, W.BOOS, W.WELTE, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 34.3-1.9 Space group P21212 a (A) 190.718 b (A) 65.705 c (A) 77.912 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 21.1 Rfree (%) 24.7 Magnesium Binding Sites: Magnesium binding site 1 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 1g29. 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: 1: Tyr228, 1: Asp229, 1: Arg290, 1: Glu292, 1: Asp293, 1: Lys359, 1: Na376, 1: Na385, 1: Mg392, 1: Hoh835, 1: Hoh945, 1: Hoh975, conact list: Atom Atom Distance (A) Mg CE2 1:Tyr228 4.15 Mg CD2 1:Tyr228 4.82 Mg OD1 1:Asp229 4.33 Mg CB 1:Arg290 4.68 Mg CD 1:Arg290 3.88 Mg CG 1:Arg290 4.71 Mg NE 1:Arg290 4.59 Mg OE1 1:Glu292 4.01 Mg OE2 1:Glu292 2.85 Mg CD 1:Glu292 3.28 Mg CG 1:Glu292 3.66 Mg CB 1:Asp293 4.92 Mg OD2 1:Asp293 2.61 Mg OD1 1:Asp293 3.54 Mg CG 1:Asp293 3.45 Mg CB 1:Lys359 4.90 Mg CE 1:Lys359 3.11 Mg CD 1:Lys359 4.51 Mg CG 1:Lys359 4.84 Mg NZ 1:Lys359 2.54 Mg NA 1:Na376 4.24 Mg NA 1:Na385 2.63 Mg MG 1:Mg392 4.17 Mg O 1:Hoh835 4.29 Mg O 1:Hoh945 3.36 Mg O 1:Hoh975 3.91 interactive model: Magnesium binding site 2 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 1g29. 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: 1: Gln59, 1: Asp69, 1: Glu71, 1: Lys72, 1: Hoh845, conact list: Atom Atom Distance (A) Mg NE2 1:Gln59 3.57 Mg CD 1:Gln59 4.55 Mg CG 1:Gln59 4.98 Mg CB 1:Asp69 4.66 Mg OD2 1:Asp69 2.48 Mg OD1 1:Asp69 3.17 Mg CG 1:Asp69 3.17 Mg OE1 1:Glu71 3.56 Mg CB 1:Glu71 3.67 Mg CD 1:Glu71 4.21 Mg C 1:Glu71 4.77 Mg CG 1:Glu71 4.53 Mg CA 1:Glu71 4.69 Mg N 1:Lys72 4.72 Mg CB 1:Lys72 4.89 Mg CE 1:Lys72 4.22 Mg CD 1:Lys72 4.20 Mg CG 1:Lys72 3.80 Mg NZ 1:Lys72 3.17 Mg O 1:Hoh845 4.42 interactive model: Magnesium binding site 3 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Magnesium in the PDB 1g29. 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: 1: Tyr228, 1: Asp229, 1: Glu292, 1: Lys359, 1: Na376, 1: Mg378, 1: Na385, conact list: Atom Atom Distance (A) Mg CE2 1:Tyr228 3.94 Mg CD2 1:Tyr228 3.75 Mg CG 1:Tyr228 4.95 Mg CB 1:Asp229 4.87 Mg OD2 1:Asp229 3.36 Mg OD1 1:Asp229 2.66 Mg CG 1:Asp229 3.40 Mg OE2 1:Glu292 4.36 Mg NZ 1:Lys359 4.63 Mg NA 1:Na376 2.66 Mg MG 1:Mg378 4.17 Mg NA 1:Na385 4.05 interactive model: Magnesium binding site 4 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Magnesium in the PDB 1g29. 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: 1: Ser322, 1: Ser341, 1: Glu342, 1: Hoh847, 1: Hoh951, 1: Hoh997, conact list: Atom Atom Distance (A) Mg O 1:Ser322 4.63 Mg N 1:Ser341 4.16 Mg CB 1:Ser341 3.60 Mg OG 1:Ser341 3.97 Mg CA 1:Ser341 4.47 Mg N 1:Glu342 4.83 Mg OE1 1:Glu342 3.17 Mg OE2 1:Glu342 2.45 Mg CD 1:Glu342 3.19 Mg CG 1:Glu342 4.69 Mg O 1:Hoh847 2.87 Mg O 1:Hoh951 4.57 Mg O 1:Hoh997 4.99 interactive model: Magnesium binding site 5 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Magnesium in the PDB 1g29. 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: 2: Glu292, 2: Asp293, 2: Tyr295, 2: Asp356, 2: Lys359, 2: Na397, 2: Hoh628, 2: Hoh651, conact list: Atom Atom Distance (A) Mg O 2:Glu292 4.20 Mg C 2:Glu292 4.86 Mg O 2:Asp293 4.60 Mg N 2:Asp293 4.80 Mg CB 2:Asp293 3.96 Mg OD2 2:Asp293 4.86 Mg C 2:Asp293 4.62 Mg OD1 2:Asp293 2.80 Mg CG 2:Asp293 3.74 Mg CA 2:Asp293 3.86 Mg CE2 2:Tyr295 4.79 Mg CD1 2:Tyr295 4.80 Mg CZ 2:Tyr295 3.45 Mg CE1 2:Tyr295 3.44 Mg OH 2:Tyr295 2.61 Mg CB 2:Asp356 3.45 Mg OD2 2:Asp356 2.62 Mg OD1 2:Asp356 4.68 Mg CG 2:Asp356 3.45 Mg CA 2:Asp356 4.96 Mg CB 2:Lys359 4.97 Mg CE 2:Lys359 4.92 Mg CD 2:Lys359 4.56 Mg CG 2:Lys359 3.87 Mg NZ 2:Lys359 4.05 Mg NA 2:Na397 4.04 Mg O 2:Hoh628 3.80 Mg O 2:Hoh651 4.26 interactive model: Magnesium binding site 6 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Magnesium in the PDB 1g29. 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: 2: Tyr228, 2: Asp229, 2: Arg290, 2: Glu292, 2: Asp293, 2: Lys359, 2: Na388, 2: Na424, 2: Hoh505, 2: Hoh544, 2: Hoh633, 2: Hoh639, 2: Hoh651, conact list: Atom Atom Distance (A) Mg CE2 2:Tyr228 4.18 Mg CD2 2:Tyr228 4.89 Mg OD1 2:Asp229 4.44 Mg CB 2:Arg290 4.55 Mg CD 2:Arg290 3.82 Mg CG 2:Arg290 4.61 Mg NE 2:Arg290 4.52 Mg OE1 2:Glu292 3.96 Mg OE2 2:Glu292 2.57 Mg CD 2:Glu292 3.15 Mg CG 2:Glu292 3.59 Mg CB 2:Asp293 4.88 Mg OD2 2:Asp293 2.60 Mg OD1 2:Asp293 3.46 Mg CG 2:Asp293 3.42 Mg CB 2:Lys359 4.87 Mg CE 2:Lys359 3.37 Mg CD 2:Lys359 4.72 Mg CG 2:Lys359 4.94 Mg NZ 2:Lys359 2.91 Mg NA 2:Na388 2.57 Mg NA 2:Na424 3.70 Mg O 2:Hoh505 4.18 Mg O 2:Hoh544 4.20 Mg O 2:Hoh633 4.62 Mg O 2:Hoh639 4.16 Mg O 2:Hoh651 4.09 interactive model: Magnesium binding site 7 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Magnesium in the PDB 1g29. 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: 2: Glu347, 2: Nh4374, 2: Na377, 2: Hoh525, 2: Hoh561, conact list: Atom Atom Distance (A) Mg OE1 2:Glu347 2.72 Mg OE2 2:Glu347 3.29 Mg CD 2:Glu347 3.28 Mg CG 2:Glu347 4.63 Mg N 2:Nh4374 4.62 Mg NA 2:Na377 3.78 Mg O 2:Hoh525 2.93 Mg O 2:Hoh561 4.12 interactive model: Magnesium binding site 8 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Magnesium in the PDB 1g29. 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: 1: Lys79, 1: Asp80, 2: Lys11, 2: Phe13, 2: Glu53, 1: Hoh940, 2: Hoh506, 2: Hoh681, conact list: Atom Atom Distance (A) Mg O 1:Lys79 3.46 Mg CB 1:Lys79 4.06 Mg CE 1:Lys79 4.45 Mg CD 1:Lys79 4.44 Mg C 1:Lys79 3.78 Mg CG 1:Lys79 3.28 Mg CA 1:Lys79 4.57 Mg N 1:Asp80 4.13 Mg CB 1:Asp80 4.60 Mg OD2 1:Asp80 4.43 Mg OD1 1:Asp80 2.73 Mg CG 1:Asp80 3.74 Mg CA 1:Asp80 4.20 Mg CE 2:Lys11 3.61 Mg CD 2:Lys11 4.94 Mg NZ 2:Lys11 4.01 Mg CE2 2:Phe13 4.46 Mg CD1 2:Phe13 4.46 Mg CZ 2:Phe13 3.11 Mg CE1 2:Phe13 3.09 Mg OE1 2:Glu53 4.35 Mg CB 2:Glu53 4.84 Mg OE2 2:Glu53 2.68 Mg CD 2:Glu53 3.35 Mg CG 2:Glu53 3.56 Mg O 1:Hoh940 4.11 Mg O 2:Hoh506 4.22 Mg O 2:Hoh681 4.67 interactive model: Magnesium binding site 9 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 9 of Magnesium in the PDB 1g29. 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: 2: Asp225, 2: Na394, 2: Hoh517, conact list: Atom Atom Distance (A) Mg CB 2:Asp225 4.70 Mg OD2 2:Asp225 2.65 Mg OD1 2:Asp225 3.48 Mg CG 2:Asp225 3.36 Mg NA 2:Na394 3.68 Mg O 2:Hoh517 3.73 interactive model: Magnesium binding site 10 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 10 of Magnesium in the PDB 1g29. 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: 1: Ala91, 2: Thr43, 2: Asp164, 2: Glu165, 2: Val196, 2: Pop500, conact list: Atom Atom Distance (A) Mg CB 1:Ala91 4.43 Mg CB 2:Thr43 3.87 Mg CG2 2:Thr43 3.90 Mg OG1 2:Thr43 2.69 Mg CA 2:Thr43 4.83 Mg CB 2:Asp164 4.44 Mg OD2 2:Asp164 2.84 Mg OD1 2:Asp164 2.39 Mg CG 2:Asp164 2.96 Mg CB 2:Glu165 4.80 Mg CB 2:Val196 4.90 Mg CG1 2:Val196 3.98 Mg O4 2:Pop500 4.09 interactive model: Magnesium binding site 11 out of 11 in 1g29 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 11 of Magnesium in the PDB 1g29. 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: 2: Arg209, 2: Val221, 2: Gly222, 2: Ser223, 2: Glu226, conact list: Atom Atom Distance (A) Mg CD 2:Arg209 4.79 Mg CG 2:Arg209 4.33 Mg NE 2:Arg209 4.23 Mg NH2 2:Arg209 4.97 Mg O 2:Val221 4.82 Mg N 2:Gly222 4.92 Mg C 2:Gly222 4.13 Mg CA 2:Gly222 3.84 Mg N 2:Ser223 3.66 Mg CB 2:Ser223 4.58 Mg OG 2:Ser223 4.76 Mg CA 2:Ser223 4.63 Mg OE1 2:Glu226 2.38 Mg OE2 2:Glu226 3.39 Mg CD 2:Glu226 3.24 Mg CG 2:Glu226 4.65 interactive model: