Sodium in the structure of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network At the Active Site (pdb 1ghv)

The binding sites of Sodium atom in the structure of A Novel Serine Protease Inhibition Motif Involving A Multi-Centered Short Hydrogen Bonding Network At the Active Site (pdb code 1ghv). This binding sites where shown with 5.0 Angstroms radius around Sodium atom. The 1ghv structure was solved by B.A.KATZ, K.ELROD, C.LUONG, M.RICE, R.L.MACKMAN, P.A.SPRENGELER, J.SPENCER, J.HATAYTE, J.JANC, J.LINK, J.LITVAK, R.RAI, K.RICE, S.SIDERIS, E.VERNER, W.YOUNG, with X-Ray Crystallography technique, brief refinement statistics is given in the table below: Resolution (A) 7.0-1.9 Space group C121 a (A) 71.620 b (A) 72.070 c (A) 73.200 alpha (°) 90.00 beta (°) 101.14 gamma (°) 90.00 Rfactor (%) 18.8 Rfree (%) 23.5 Sodium Binding Sites: Sodium binding site 1 out of 1 in 1ghv Click to enlarge Click to enlarge Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 1ghv. 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: H: Tyr184A, H: Arg187, H: Asp221, H: Arg221A, H: Asp222, H: Gly223, H: Lys224, H: Tyr225, H: Hoh410, H: Hoh416, H: Hoh419, H: Hoh423, H: Hoh427, H: Hoh430, H: Hoh445, H: Hoh447, conact list: Atom Atom Distance (A) Na O H:Tyr184A 4.26 Na HH21 H:Arg187 4.71 Na O H:Asp221 4.69 Na HA H:Asp221 3.81 Na OD1 H:Asp221 4.87 Na C H:Asp221 4.24 Na CA H:Asp221 4.57 Na HB2 H:Arg221A 4.92 Na N H:Arg221A 4.04 Na C H:Arg221A 3.47 Na CA H:Arg221A 4.46 Na O H:Arg221A 2.41 Na H H:Arg221A 4.06 Na N H:Asp222 4.19 Na HA H:Asp222 3.25 Na C H:Asp222 4.30 Na CA H:Asp222 4.03 Na N H:Gly223 4.09 Na H H:Gly223 3.69 Na C H:Gly223 4.67 Na HB2 H:Lys224 3.82 Na N H:Lys224 3.72 Na CB H:Lys224 4.50 Na C H:Lys224 3.47 Na CA H:Lys224 4.09 Na O H:Lys224 2.44 Na H H:Lys224 3.12 Na N H:Tyr225 4.51 Na CA H:Tyr225 4.81 Na HA H:Tyr225 4.04 Na O H:Hoh410 4.43 Na H1 H:Hoh410 3.64 Na H2 H:Hoh410 4.71 Na O H:Hoh416 2.69 Na H1 H:Hoh416 2.91 Na H2 H:Hoh416 3.22 Na O H:Hoh419 2.74 Na H1 H:Hoh419 3.10 Na H2 H:Hoh419 3.08 Na O H:Hoh423 4.80 Na H1 H:Hoh423 4.76 Na O H:Hoh427 3.97 Na H1 H:Hoh427 4.46 Na H2 H:Hoh427 3.40 Na O H:Hoh430 4.00 Na H1 H:Hoh430 4.67 Na H2 H:Hoh430 4.73 Na O H:Hoh445 2.59 Na H1 H:Hoh445 3.24 Na H2 H:Hoh445 2.95 Na O H:Hoh447 2.63 Na H1 H:Hoh447 3.14 Na H2 H:Hoh447 3.38 interactive model: