Molybdenum in the structure of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides (pdb 1ogy)

The binding sites of Molybdenum atom in the structure of Crystal Structure of the Heterodimeric Nitrate Reductase From Rhodobacter Sphaeroides (pdb code 1ogy). This binding sites where shown with 5.0 Angstroms radius around Molybdenum atom. The 1ogy structure was solved by P.ARNOUX, M.SABATY, J.ALRIC, B.FRANGIONI, B.GUIGLIARELLI, J.-M.ADRIANO, D.PIGNOL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 30.0-3.2 Space group P1211 a (A) 123.000 b (A) 225.200 c (A) 154.600 alpha (°) 90.00 beta (°) 92.10 gamma (°) 90.00 Rfactor (%) 25.04 Rfree (%) 26.87 Molybdenum Binding Sites: Molybdenum binding site 1 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: A: Cys152, A: Met346, A: Gly383, A: Gln384, A: Arg694, A: His700, A: Mgd1803, A: Mgd1804, conact list: Atom Atom Distance (A) Mo CB A:Cys152 2.97 Mo SG A:Cys152 2.13 Mo CA A:Cys152 4.21 Mo CE A:Met346 4.87 Mo SD A:Met346 4.65 Mo N A:Gly383 4.53 Mo C A:Gly383 4.24 Mo CA A:Gly383 3.86 Mo NE2 A:Gln384 4.13 Mo N A:Gln384 3.97 Mo CD A:Gln384 4.75 Mo CG A:Gln384 4.31 Mo CA A:Gln384 4.97 Mo NH2 A:Arg694 4.72 Mo NH1 A:Arg694 4.76 Mo NE2 A:His700 4.88 Mo CE1 A:His700 4.80 Mo S13 A:Mgd1803 2.70 Mo C13 A:Mgd1803 3.60 Mo C12 A:Mgd1803 3.57 Mo S12 A:Mgd1803 2.50 Mo S13 A:Mgd1804 2.42 Mo C11 A:Mgd1804 4.89 Mo C13 A:Mgd1804 3.39 Mo C12 A:Mgd1804 3.38 Mo C14 A:Mgd1804 4.90 Mo S12 A:Mgd1804 2.38 interactive model: Molybdenum binding site 2 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: C: Cys152, C: Met346, C: Gly383, C: Gln384, C: Arg694, C: His700, C: Mgd1803, C: Mgd1804, conact list: Atom Atom Distance (A) Mo CB C:Cys152 2.95 Mo SG C:Cys152 2.26 Mo CA C:Cys152 4.21 Mo CE C:Met346 4.96 Mo SD C:Met346 4.61 Mo N C:Gly383 4.61 Mo C C:Gly383 4.28 Mo CA C:Gly383 3.93 Mo NE2 C:Gln384 3.93 Mo N C:Gln384 3.98 Mo CB C:Gln384 4.94 Mo CD C:Gln384 4.59 Mo CG C:Gln384 4.19 Mo CA C:Gln384 4.94 Mo NH2 C:Arg694 4.79 Mo NH1 C:Arg694 4.79 Mo NE2 C:His700 4.82 Mo CE1 C:His700 4.76 Mo S13 C:Mgd1803 2.72 Mo C11 C:Mgd1803 4.97 Mo C13 C:Mgd1803 3.54 Mo C12 C:Mgd1803 3.46 Mo S12 C:Mgd1803 2.40 Mo S13 C:Mgd1804 2.47 Mo C13 C:Mgd1804 3.48 Mo C12 C:Mgd1804 3.50 Mo C14 C:Mgd1804 4.97 Mo S12 C:Mgd1804 2.55 interactive model: Molybdenum binding site 3 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: E: Cys152, E: Met346, E: Gly383, E: Gln384, E: Arg694, E: His700, E: Mgd1803, E: Mgd1804, conact list: Atom Atom Distance (A) Mo N E:Cys152 4.97 Mo CB E:Cys152 2.88 Mo SG E:Cys152 2.13 Mo C E:Cys152 4.96 Mo CA E:Cys152 4.09 Mo CE E:Met346 4.84 Mo SD E:Met346 4.50 Mo N E:Gly383 4.65 Mo C E:Gly383 4.42 Mo CA E:Gly383 3.99 Mo NE2 E:Gln384 4.11 Mo N E:Gln384 4.13 Mo CD E:Gln384 4.79 Mo CG E:Gln384 4.42 Mo NH2 E:Arg694 4.67 Mo NH1 E:Arg694 4.74 Mo NE2 E:His700 4.87 Mo CE1 E:His700 4.81 Mo S13 E:Mgd1803 2.45 Mo C11 E:Mgd1803 4.96 Mo C13 E:Mgd1803 3.45 Mo C12 E:Mgd1803 3.46 Mo C14 E:Mgd1803 4.93 Mo S12 E:Mgd1803 2.41 Mo S13 E:Mgd1804 2.63 Mo C11 E:Mgd1804 4.94 Mo C13 E:Mgd1804 3.50 Mo C12 E:Mgd1804 3.44 Mo S12 E:Mgd1804 2.35 interactive model: Molybdenum binding site 4 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: G: Cys152, G: Met346, G: Gly383, G: Gln384, G: Arg694, G: His700, G: Mgd1803, G: Mgd1804, conact list: Atom Atom Distance (A) Mo N G:Cys152 4.96 Mo CB G:Cys152 2.83 Mo SG G:Cys152 2.17 Mo C G:Cys152 4.88 Mo CA G:Cys152 4.05 Mo CE G:Met346 4.73 Mo SD G:Met346 4.43 Mo N G:Gly383 4.56 Mo C G:Gly383 4.36 Mo CA G:Gly383 3.92 Mo NE2 G:Gln384 4.05 Mo N G:Gln384 4.09 Mo CD G:Gln384 4.76 Mo CG G:Gln384 4.39 Mo NH2 G:Arg694 4.70 Mo NH1 G:Arg694 4.77 Mo NE2 G:His700 4.97 Mo CE1 G:His700 4.90 Mo S13 G:Mgd1803 2.47 Mo C13 G:Mgd1803 3.50 Mo C12 G:Mgd1803 3.52 Mo S12 G:Mgd1803 2.51 Mo S13 G:Mgd1804 2.63 Mo C11 G:Mgd1804 4.90 Mo C13 G:Mgd1804 3.49 Mo C12 G:Mgd1804 3.40 Mo S12 G:Mgd1804 2.29 interactive model: Molybdenum binding site 5 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: I: Cys152, I: Met346, I: Gly383, I: Gln384, I: Arg694, I: His700, I: Mgd1803, I: Mgd1804, conact list: Atom Atom Distance (A) Mo N I:Cys152 4.99 Mo CB I:Cys152 2.80 Mo SG I:Cys152 2.28 Mo C I:Cys152 4.93 Mo CA I:Cys152 4.12 Mo SD I:Met346 4.58 Mo N I:Gly383 4.50 Mo C I:Gly383 4.21 Mo CA I:Gly383 3.82 Mo NE2 I:Gln384 3.76 Mo N I:Gln384 3.85 Mo CB I:Gln384 4.83 Mo CD I:Gln384 4.47 Mo CG I:Gln384 4.11 Mo CA I:Gln384 4.85 Mo NH2 I:Arg694 4.97 Mo NH1 I:Arg694 4.99 Mo NE2 I:His700 4.92 Mo CE1 I:His700 4.92 Mo S13 I:Mgd1803 2.76 Mo C11 I:Mgd1803 4.99 Mo C13 I:Mgd1803 3.63 Mo C12 I:Mgd1803 3.53 Mo S12 I:Mgd1803 2.41 Mo S13 I:Mgd1804 2.73 Mo C13 I:Mgd1804 3.65 Mo C12 I:Mgd1804 3.66 Mo S12 I:Mgd1804 2.63 interactive model: Molybdenum binding site 6 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: K: Cys152, K: Met346, K: Gly383, K: Gln384, K: Arg694, K: His700, K: Mgd1803, K: Mgd1804, conact list: Atom Atom Distance (A) Mo CB K:Cys152 2.84 Mo SG K:Cys152 2.28 Mo C K:Cys152 4.98 Mo CA K:Cys152 4.13 Mo CE K:Met346 4.87 Mo SD K:Met346 4.68 Mo N K:Gly383 4.61 Mo C K:Gly383 4.34 Mo CA K:Gly383 3.95 Mo NE2 K:Gln384 4.02 Mo N K:Gln384 4.04 Mo CD K:Gln384 4.72 Mo CG K:Gln384 4.33 Mo NH2 K:Arg694 4.67 Mo NH1 K:Arg694 4.79 Mo NE2 K:His700 4.89 Mo CE1 K:His700 4.82 Mo S13 K:Mgd1803 2.47 Mo C11 K:Mgd1803 5.00 Mo C13 K:Mgd1803 3.50 Mo C12 K:Mgd1803 3.50 Mo S12 K:Mgd1803 2.44 Mo S13 K:Mgd1804 2.53 Mo C11 K:Mgd1804 4.97 Mo C13 K:Mgd1804 3.48 Mo C12 K:Mgd1804 3.47 Mo C14 K:Mgd1804 4.99 Mo S12 K:Mgd1804 2.47 interactive model: Molybdenum binding site 7 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 7 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: M: Cys152, M: Met346, M: Gly383, M: Gln384, M: Arg694, M: His700, M: Mgd1803, M: Mgd1804, conact list: Atom Atom Distance (A) Mo CB M:Cys152 2.93 Mo SG M:Cys152 2.26 Mo CA M:Cys152 4.18 Mo CE M:Met346 4.94 Mo SD M:Met346 4.70 Mo N M:Gly383 4.59 Mo C M:Gly383 4.28 Mo CA M:Gly383 3.88 Mo NE2 M:Gln384 4.05 Mo N M:Gln384 4.01 Mo CD M:Gln384 4.71 Mo CG M:Gln384 4.29 Mo CA M:Gln384 5.00 Mo NH2 M:Arg694 4.72 Mo NH1 M:Arg694 4.72 Mo NE2 M:His700 4.84 Mo CE1 M:His700 4.75 Mo S13 M:Mgd1803 2.57 Mo C11 M:Mgd1803 4.99 Mo C13 M:Mgd1803 3.53 Mo C12 M:Mgd1803 3.52 Mo S12 M:Mgd1803 2.45 Mo S13 M:Mgd1804 2.47 Mo C11 M:Mgd1804 4.95 Mo C13 M:Mgd1804 3.43 Mo C12 M:Mgd1804 3.44 Mo C14 M:Mgd1804 4.94 Mo S12 M:Mgd1804 2.47 interactive model: Molybdenum binding site 8 out of 8 in 1ogy Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 8 of Molybdenum in the PDB 1ogy. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Molybdenum atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: O: Cys152, O: Met346, O: Gly383, O: Gln384, O: Arg694, O: His700, O: Mgd1803, O: Mgd1804, conact list: Atom Atom Distance (A) Mo CB O:Cys152 2.98 Mo SG O:Cys152 2.44 Mo CA O:Cys152 4.26 Mo CE O:Met346 4.93 Mo SD O:Met346 4.65 Mo N O:Gly383 4.48 Mo C O:Gly383 4.12 Mo CA O:Gly383 3.73 Mo NE2 O:Gln384 3.98 Mo N O:Gln384 3.86 Mo CB O:Gln384 4.95 Mo CD O:Gln384 4.65 Mo CG O:Gln384 4.23 Mo CA O:Gln384 4.88 Mo NH2 O:Arg694 4.74 Mo NH1 O:Arg694 4.80 Mo NE2 O:His700 4.81 Mo CE1 O:His700 4.75 Mo S13 O:Mgd1803 2.58 Mo C13 O:Mgd1803 3.60 Mo C12 O:Mgd1803 3.56 Mo S12 O:Mgd1803 2.51 Mo S13 O:Mgd1804 2.57 Mo C11 O:Mgd1804 4.91 Mo C13 O:Mgd1804 3.39 Mo C12 O:Mgd1804 3.38 Mo C14 O:Mgd1804 4.88 Mo S12 O:Mgd1804 2.44 interactive model: