Sodium in the structure of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. (pdb 3i01)

The binding sites of Sodium atom in the structure of Native Structure of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl- Coa Synthase From Moorella Thermoacetica, Water-Bound C-Cluster. (pdb code 3i01). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 3i01 structure was solved by Y.KUNG, T.I.DOUKOV, C.L.DRENNAN, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 37.0-2.1 Space group P1 a (A) 99.651 b (A) 136.870 c (A) 140.864 alpha (°) 101.26 beta (°) 109.11 gamma (°) 104.08 Rfactor (%) 18.6 Rfree (%) 24.2 Sodium Binding Sites: Sodium binding site 1 out of 4 in 3i01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3i01. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: M: Phe328, M: Glu329, M: Glu331, M: Ile411, M: Asn412, M: Tyr413, M: Gly414, M: Glu415, M: Gly416, M: Leu417, M: Trp418, M: Hoh1431, conact list: Atom Atom Distance (A) Na O M:Phe328 2.75 Na CB M:Phe328 4.02 Na C M:Phe328 3.62 Na CA M:Phe328 4.36 Na O M:Glu329 4.54 Na N M:Glu329 4.45 Na C M:Glu329 4.81 Na CA M:Glu329 4.53 Na OE1 M:Glu331 2.52 Na CB M:Glu331 4.80 Na OE2 M:Glu331 4.63 Na CD M:Glu331 3.44 Na CG M:Glu331 3.58 Na O M:Ile411 4.49 Na O M:Asn412 2.12 Na N M:Asn412 4.82 Na CB M:Asn412 4.36 Na C M:Asn412 3.12 Na OD1 M:Asn412 4.52 Na CG M:Asn412 4.93 Na CA M:Asn412 3.62 Na N M:Tyr413 4.26 Na C M:Tyr413 4.32 Na CA M:Tyr413 4.65 Na O M:Gly414 2.27 Na N M:Gly414 3.91 Na C M:Gly414 3.45 Na CA M:Gly414 4.31 Na N M:Glu415 4.37 Na C M:Glu415 4.84 Na CA M:Glu415 4.52 Na N M:Gly416 4.30 Na C M:Gly416 4.88 Na O M:Leu417 2.45 Na N M:Leu417 3.93 Na CB M:Leu417 4.63 Na C M:Leu417 3.56 Na CA M:Leu417 4.23 Na N M:Trp418 4.60 Na CA M:Trp418 4.81 Na O M:Hoh1431 2.50 interactive model: Sodium binding site 2 out of 4 in 3i01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3i01. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: N: Phe328, N: Glu329, N: Glu331, N: Ile411, N: Asn412, N: Tyr413, N: Gly414, N: Glu415, N: Gly416, N: Leu417, N: Trp418, N: Hoh1432, conact list: Atom Atom Distance (A) Na O N:Phe328 2.64 Na CB N:Phe328 3.87 Na C N:Phe328 3.55 Na CA N:Phe328 4.22 Na O N:Glu329 4.88 Na N N:Glu329 4.51 Na C N:Glu329 4.96 Na CA N:Glu329 4.67 Na OE1 N:Glu331 4.58 Na CB N:Glu331 4.51 Na OE2 N:Glu331 2.46 Na CD N:Glu331 3.45 Na CG N:Glu331 3.75 Na O N:Ile411 4.49 Na O N:Asn412 2.29 Na N N:Asn412 4.99 Na CB N:Asn412 4.68 Na C N:Asn412 3.36 Na OD1 N:Asn412 4.49 Na CA N:Asn412 3.88 Na N N:Tyr413 4.45 Na C N:Tyr413 4.48 Na CA N:Tyr413 4.79 Na O N:Gly414 2.53 Na N N:Gly414 4.16 Na C N:Gly414 3.72 Na CA N:Gly414 4.55 Na N N:Glu415 4.63 Na C N:Glu415 4.92 Na CA N:Glu415 4.66 Na N N:Gly416 4.25 Na C N:Gly416 4.83 Na O N:Leu417 2.29 Na N N:Leu417 4.00 Na CB N:Leu417 4.71 Na C N:Leu417 3.50 Na CA N:Leu417 4.24 Na N N:Trp418 4.52 Na CA N:Trp418 4.68 Na O N:Hoh1432 2.14 interactive model: Sodium binding site 3 out of 4 in 3i01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3i01. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: O: Phe328, O: Glu329, O: Glu331, O: Asn412, O: Tyr413, O: Gly414, O: Glu415, O: Gly416, O: Leu417, O: Trp418, O: Hoh1433, conact list: Atom Atom Distance (A) Na O O:Phe328 2.40 Na CB O:Phe328 4.26 Na C O:Phe328 3.56 Na CA O:Phe328 4.48 Na O O:Glu329 4.62 Na N O:Glu329 4.45 Na C O:Glu329 4.70 Na CA O:Glu329 4.50 Na OE2 O:Glu331 3.16 Na CD O:Glu331 3.90 Na CG O:Glu331 3.92 Na O O:Asn412 2.74 Na CB O:Asn412 4.92 Na C O:Asn412 3.74 Na OD1 O:Asn412 4.48 Na CA O:Asn412 4.26 Na N O:Tyr413 4.79 Na C O:Tyr413 4.81 Na O O:Gly414 2.56 Na N O:Gly414 4.50 Na C O:Gly414 3.66 Na CA O:Gly414 4.70 Na N O:Glu415 4.38 Na C O:Glu415 4.34 Na CA O:Glu415 4.29 Na N O:Gly416 3.56 Na C O:Gly416 4.42 Na CA O:Gly416 4.34 Na O O:Leu417 2.54 Na N O:Leu417 3.65 Na CB O:Leu417 4.66 Na C O:Leu417 3.66 Na CA O:Leu417 4.19 Na N O:Trp418 4.80 Na O O:Hoh1433 2.71 interactive model: Sodium binding site 4 out of 4 in 3i01 Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3i01. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere Residues shown as a stick model or VDW spheres: P: Phe328, P: Glu329, P: Glu331, P: Ile411, P: Asn412, P: Tyr413, P: Gly414, P: Glu415, P: Gly416, P: Leu417, P: Trp418, P: Hoh1434, conact list: Atom Atom Distance (A) Na O P:Phe328 2.58 Na CB P:Phe328 4.45 Na C P:Phe328 3.72 Na CA P:Phe328 4.70 Na O P:Glu329 4.77 Na N P:Glu329 4.51 Na C P:Glu329 4.90 Na CA P:Glu329 4.54 Na OE1 P:Glu331 4.72 Na OE2 P:Glu331 2.80 Na CD P:Glu331 3.73 Na CG P:Glu331 4.16 Na O P:Ile411 4.50 Na O P:Asn412 2.30 Na N P:Asn412 4.94 Na CB P:Asn412 4.51 Na C P:Asn412 3.28 Na OD1 P:Asn412 4.47 Na CG P:Asn412 5.00 Na CA P:Asn412 3.75 Na O P:Tyr413 4.92 Na N P:Tyr413 4.41 Na C P:Tyr413 4.43 Na CA P:Tyr413 4.83 Na O P:Gly414 2.47 Na N P:Gly414 4.07 Na C P:Gly414 3.52 Na CA P:Gly414 4.40 Na N P:Glu415 4.34 Na C P:Glu415 4.77 Na CA P:Glu415 4.45 Na N P:Gly416 4.34 Na C P:Gly416 4.86 Na O P:Leu417 2.28 Na N P:Leu417 3.77 Na CB P:Leu417 4.53 Na C P:Leu417 3.44 Na CA P:Leu417 4.08 Na N P:Trp418 4.54 Na CA P:Trp418 4.79 Na O P:Hoh1434 2.64 interactive model: