Magnesium in the structure of The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis (pdb 2vbf)

The binding sites of Magnesium atom in the structure of The Holostructure of the Branched-Chain Keto Acid Decarboxylase (Kdca) From Lactococcus Lactis (pdb code 2vbf). This binding sites where shown with 5.0 Angstroms radius around Magnesium atom. The 2vbf structure was solved by C.L.BERTHOLD, D.GOCKE, M.D.WOOD, F.LEEPER, M.POHL, G.SCHNEIDER, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-1.6 Space group P212121 a (A) 65.603 b (A) 108.421 c (A) 146.593 alpha (°) 90.00 beta (°) 90.00 gamma (°) 90.00 Rfactor (%) 16.3 Rfree (%) 20 Magnesium Binding Sites: Magnesium binding site 1 out of 2 in 2vbf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Magnesium in the PDB 2vbf. 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: Gly428, B: Asp429, B: Gly430, B: Ile454, B: Asn456, B: Asp457, B: Gly458, B: Tyr459, B: Thr460, B: Tpp1549, B: Hoh2447, B: Hoh2450, conact list: Atom Atom Distance (A) Mg C B:Gly428 4.69 Mg CA B:Gly428 4.64 Mg N B:Asp429 3.99 Mg CB B:Asp429 4.46 Mg OD2 B:Asp429 3.73 Mg C B:Asp429 4.90 Mg OD1 B:Asp429 2.06 Mg CG B:Asp429 3.22 Mg CA B:Asp429 4.62 Mg N B:Gly430 4.09 Mg CA B:Gly430 4.92 Mg O B:Ile454 4.02 Mg O B:Asn456 4.99 Mg N B:Asn456 4.44 Mg CB B:Asn456 4.50 Mg ND2 B:Asn456 3.48 Mg C B:Asn456 4.73 Mg OD1 B:Asn456 2.16 Mg CG B:Asn456 3.14 Mg CA B:Asn456 4.78 Mg N B:Asp457 4.98 Mg O B:Gly458 2.03 Mg N B:Gly458 4.13 Mg C B:Gly458 3.25 Mg CA B:Gly458 4.19 Mg N B:Tyr459 4.17 Mg C B:Tyr459 4.74 Mg CA B:Tyr459 4.27 Mg N B:Thr460 4.11 Mg CB B:Thr460 4.94 Mg OG1 B:Thr460 4.76 Mg O3B B:Tpp1549 2.11 Mg PA B:Tpp1549 3.21 Mg O2A B:Tpp1549 2.01 Mg O1B B:Tpp1549 4.54 Mg PB B:Tpp1549 3.24 Mg O2B B:Tpp1549 3.73 Mg O7 B:Tpp1549 4.18 Mg O3A B:Tpp1549 3.52 Mg O1A B:Tpp1549 4.32 Mg O B:Hoh2447 2.20 Mg O B:Hoh2450 4.51 interactive model: Magnesium binding site 2 out of 2 in 2vbf Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Magnesium in the PDB 2vbf. 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: Gly428, A: Asp429, A: Gly430, A: Ile454, A: Asn456, A: Gly458, A: Tyr459, A: Thr460, B: Tpp1551, A: Hoh2431, A: Hoh2437, conact list: Atom Atom Distance (A) Mg C A:Gly428 4.68 Mg CA A:Gly428 4.57 Mg N A:Asp429 4.03 Mg CB A:Asp429 4.43 Mg OD2 A:Asp429 3.67 Mg C A:Asp429 4.93 Mg OD1 A:Asp429 1.97 Mg CG A:Asp429 3.15 Mg CA A:Asp429 4.64 Mg N A:Gly430 4.15 Mg CA A:Gly430 5.00 Mg O A:Ile454 3.99 Mg N A:Asn456 4.38 Mg CB A:Asn456 4.46 Mg ND2 A:Asn456 3.47 Mg C A:Asn456 4.75 Mg OD1 A:Asn456 2.14 Mg CG A:Asn456 3.12 Mg CA A:Asn456 4.72 Mg O A:Gly458 2.05 Mg N A:Gly458 4.18 Mg C A:Gly458 3.28 Mg CA A:Gly458 4.21 Mg N A:Tyr459 4.21 Mg C A:Tyr459 4.81 Mg CA A:Tyr459 4.32 Mg N A:Thr460 4.17 Mg CB A:Thr460 4.91 Mg OG1 A:Thr460 4.74 Mg O3B B:Tpp1551 2.14 Mg PA B:Tpp1551 3.27 Mg O2A B:Tpp1551 2.09 Mg O1B B:Tpp1551 4.54 Mg PB B:Tpp1551 3.23 Mg O2B B:Tpp1551 3.74 Mg O7 B:Tpp1551 4.20 Mg O3A B:Tpp1551 3.54 Mg O1A B:Tpp1551 4.36 Mg O A:Hoh2431 2.12 Mg O A:Hoh2437 4.59 interactive model: