Manganese in the structure of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum (pdb 2woc)

The binding sites of Manganese atom in the structure of Crystal Structure of the Dinitrogenase Reductase-Activating Glycohydrolase (Drag) From Rhodospirillum Rubrum (pdb code 2woc). This binding sites where shown with 5.0 Angstroms radius around Manganese atom. The 2woc structure was solved by C.L.BERTHOLD, H.WANG, S.NORDLUND, M.HOGBOM, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 40.0-2.2 Space group P1 a (A) 44.771 b (A) 47.537 c (A) 95.212 alpha (°) 80.84 beta (°) 86.56 gamma (°) 85.83 Rfactor (%) 17.425 Rfree (%) 24.016 Manganese Binding Sites: Manganese binding site 1 out of 6 in 2woc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Manganese in the PDB 2woc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu28, A: Asp60, A: Asp61, A: Asn126, A: Asp243, A: Asp245, A: Thr246, A: Mn401, A: Fmt402, A: Hoh2012, conact list: Atom Atom Distance (A) Mn OE2 A:Glu28 4.47 Mn CD A:Glu28 4.68 Mn OD1 A:Asp60 4.86 Mn OD2 A:Asp61 4.43 Mn OD1 A:Asp61 4.53 Mn CG A:Asp61 4.93 Mn ND2 A:Asn126 4.64 Mn OD1 A:Asn126 4.18 Mn CG A:Asn126 4.84 Mn O A:Asp243 4.58 Mn CB A:Asp243 4.38 Mn OD2 A:Asp243 2.64 Mn C A:Asp243 4.93 Mn OD1 A:Asp243 2.54 Mn CG A:Asp243 2.91 Mn CA A:Asp243 4.95 Mn CB A:Asp245 4.42 Mn OD2 A:Asp245 2.63 Mn C A:Asp245 4.89 Mn OD1 A:Asp245 2.52 Mn CG A:Asp245 2.92 Mn N A:Thr246 4.12 Mn CB A:Thr246 3.58 Mn CG2 A:Thr246 4.65 Mn OG1 A:Thr246 2.38 Mn CA A:Thr246 4.42 Mn MN A:Mn401 4.44 Mn O1 A:Fmt402 2.72 Mn O2 A:Fmt402 2.77 Mn C A:Fmt402 3.07 Mn O A:Hoh2012 2.61 interactive model: Manganese binding site 2 out of 6 in 2woc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Manganese in the PDB 2woc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Glu28, A: Leu51, A: Thr59, A: Asp60, A: Asp61, A: Asp97, A: Asp245, A: Mn400, A: Fmt402, A: Hoh2012, conact list: Atom Atom Distance (A) Mn OE1 A:Glu28 3.01 Mn OE2 A:Glu28 3.63 Mn CD A:Glu28 3.66 Mn CD1 A:Leu51 4.23 Mn CB A:Thr59 3.38 Mn CG2 A:Thr59 3.90 Mn OG1 A:Thr59 2.97 Mn CA A:Thr59 4.80 Mn N A:Asp60 4.32 Mn OD2 A:Asp60 4.71 Mn OD1 A:Asp60 3.00 Mn CG A:Asp60 4.09 Mn OD2 A:Asp61 4.13 Mn CB A:Asp97 4.03 Mn OD2 A:Asp97 2.59 Mn OD1 A:Asp97 4.76 Mn CG A:Asp97 3.66 Mn CB A:Asp245 4.08 Mn OD2 A:Asp245 2.93 Mn OD1 A:Asp245 4.16 Mn CG A:Asp245 3.49 Mn MN A:Mn400 4.44 Mn O1 A:Fmt402 4.29 Mn O A:Hoh2012 3.17 interactive model: Manganese binding site 3 out of 6 in 2woc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Manganese in the PDB 2woc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Glu28, B: Asp60, B: Asp61, B: Asn126, B: Asp243, B: Asp245, B: Thr246, B: Mn401, B: Fmt402, B: Hoh2013, B: Hoh2014, B: Hoh2052, B: Hoh2125, conact list: Atom Atom Distance (A) Mn OE1 B:Glu28 4.80 Mn OE2 B:Glu28 4.70 Mn CD B:Glu28 4.72 Mn OD1 B:Asp60 4.81 Mn OD2 B:Asp61 4.49 Mn OD1 B:Asp61 4.61 Mn CG B:Asp61 4.99 Mn ND2 B:Asn126 4.78 Mn OD1 B:Asn126 4.36 Mn CG B:Asn126 4.98 Mn O B:Asp243 4.73 Mn CB B:Asp243 4.37 Mn OD2 B:Asp243 2.60 Mn OD1 B:Asp243 2.52 Mn CG B:Asp243 2.88 Mn CA B:Asp243 4.98 Mn CB B:Asp245 4.45 Mn OD2 B:Asp245 2.67 Mn C B:Asp245 4.95 Mn OD1 B:Asp245 2.54 Mn CG B:Asp245 2.95 Mn N B:Thr246 4.18 Mn CB B:Thr246 3.69 Mn CG2 B:Thr246 4.77 Mn OG1 B:Thr246 2.53 Mn CA B:Thr246 4.52 Mn MN B:Mn401 4.41 Mn O1 B:Fmt402 2.66 Mn O2 B:Fmt402 2.69 Mn C B:Fmt402 2.97 Mn O B:Hoh2013 2.72 Mn O B:Hoh2014 4.47 Mn O B:Hoh2052 4.64 Mn O B:Hoh2125 4.63 interactive model: Manganese binding site 4 out of 6 in 2woc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Manganese in the PDB 2woc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: B: Asp21, B: Ala25, B: Glu28, B: Leu51, B: Thr59, B: Asp60, B: Asp61, B: Asp97, B: Asp245, B: Mn400, B: Fmt402, B: Hoh2013, B: Hoh2052, conact list: Atom Atom Distance (A) Mn OD1 B:Asp21 4.82 Mn CB B:Ala25 4.99 Mn OE1 B:Glu28 3.04 Mn OE2 B:Glu28 3.82 Mn CD B:Glu28 3.80 Mn CD1 B:Leu51 4.35 Mn CB B:Thr59 3.42 Mn CG2 B:Thr59 4.04 Mn OG1 B:Thr59 2.77 Mn CA B:Thr59 4.79 Mn N B:Asp60 4.32 Mn CB B:Asp60 4.97 Mn OD2 B:Asp60 4.52 Mn OD1 B:Asp60 2.80 Mn CG B:Asp60 3.92 Mn OD2 B:Asp61 3.95 Mn CB B:Asp97 4.16 Mn OD2 B:Asp97 2.71 Mn OD1 B:Asp97 4.89 Mn CG B:Asp97 3.79 Mn CB B:Asp245 3.95 Mn OD2 B:Asp245 2.84 Mn OD1 B:Asp245 4.04 Mn CG B:Asp245 3.38 Mn MN B:Mn400 4.41 Mn O1 B:Fmt402 4.68 Mn O B:Hoh2013 3.39 Mn O B:Hoh2052 3.78 interactive model: Manganese binding site 5 out of 6 in 2woc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Manganese in the PDB 2woc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Glu28, C: Asp60, C: Asp61, C: Asn126, C: Asp243, C: Asp245, C: Thr246, C: Mn401, C: Fmt402, C: Hoh2101, conact list: Atom Atom Distance (A) Mn OE1 C:Glu28 4.62 Mn OE2 C:Glu28 4.43 Mn CD C:Glu28 4.50 Mn OD1 C:Asp60 4.92 Mn OD2 C:Asp61 4.47 Mn OD1 C:Asp61 4.58 Mn CG C:Asp61 4.97 Mn ND2 C:Asn126 4.74 Mn OD1 C:Asn126 4.30 Mn CG C:Asn126 4.94 Mn O C:Asp243 4.56 Mn CB C:Asp243 4.29 Mn OD2 C:Asp243 2.52 Mn C C:Asp243 4.89 Mn OD1 C:Asp243 2.54 Mn CG C:Asp243 2.84 Mn CA C:Asp243 4.85 Mn CB C:Asp245 4.34 Mn OD2 C:Asp245 2.48 Mn C C:Asp245 4.87 Mn OD1 C:Asp245 2.51 Mn CG C:Asp245 2.83 Mn N C:Thr246 4.07 Mn CB C:Thr246 3.65 Mn CG2 C:Thr246 4.75 Mn OG1 C:Thr246 2.47 Mn CA C:Thr246 4.45 Mn MN C:Mn401 4.45 Mn O1 C:Fmt402 2.74 Mn O2 C:Fmt402 2.89 Mn C C:Fmt402 3.15 Mn O C:Hoh2101 2.55 interactive model: Manganese binding site 6 out of 6 in 2woc Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Manganese in the PDB 2woc. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Manganese atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Asp21, C: Glu28, C: Leu51, C: Thr59, C: Asp60, C: Asp61, C: Asp97, C: Asp245, C: Mn400, C: Fmt402, C: Hoh2101, conact list: Atom Atom Distance (A) Mn OD1 C:Asp21 4.75 Mn OE1 C:Glu28 2.99 Mn OE2 C:Glu28 3.90 Mn CD C:Glu28 3.82 Mn CD1 C:Leu51 4.31 Mn CB C:Thr59 3.36 Mn CG2 C:Thr59 3.88 Mn OG1 C:Thr59 2.73 Mn CA C:Thr59 4.77 Mn N C:Asp60 4.34 Mn CB C:Asp60 4.98 Mn OD2 C:Asp60 4.29 Mn OD1 C:Asp60 2.85 Mn CG C:Asp60 3.84 Mn OD2 C:Asp61 3.89 Mn CB C:Asp97 4.12 Mn OD2 C:Asp97 2.78 Mn OD1 C:Asp97 4.95 Mn CG C:Asp97 3.82 Mn CB C:Asp245 3.93 Mn OD2 C:Asp245 2.95 Mn OD1 C:Asp245 4.15 Mn CG C:Asp245 3.44 Mn MN C:Mn400 4.45 Mn O2 C:Fmt402 4.65 Mn O C:Hoh2101 3.25 interactive model: