The binding sites of Sodium atom in the structure of Oxidized (CU2+) Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) With Bound Azide, Obtained in the Presence of Substrate (pdb code 3mih). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3mih structure was solved by E.E.CHUFAN, B.A.EIPPER, R.E.MAINS, L.M.AMZEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 52.0-2.7 | | Space group | P212121 | | a (A) | 68.110 | | b (A) | 68.800 | | c (A) | 79.791 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 23.7 | | Rfree (%) | 29.6 |
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Sodium binding site 1 out of 4 in 3mih
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3mih. 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: A: Asp96, A: His192, A: Iod360, A: Azi1, | conact list:
| Atom | Atom | Distance (A) | | Na | CB A:Asp96 | 3.81 | | Na | OD2 A:Asp96 | 2.68 | | Na | OD1 A:Asp96 | 4.80 | | Na | CG A:Asp96 | 3.64 | | Na | NE2 A:His192 | 4.86 | | Na | CB A:His192 | 4.15 | | Na | ND1 A:His192 | 2.86 | | Na | CD2 A:His192 | 4.98 | | Na | CE1 A:His192 | 3.68 | | Na | CG A:His192 | 3.88 | | Na | I A:Iod360 | 4.59 | | Na | N1 A:Azi1 | 2.66 | | Na | N3 A:Azi1 | 3.32 | | Na | N2 A:Azi1 | 2.76 |
| interactive model:
| Sodium binding site 2 out of 4 in 3mih
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Sodium in the PDB 3mih. 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: A: Azi5, A: Hoh377, | conact list:
| Atom | Atom | Distance (A) | | Na | N1 A:Azi5 | 4.81 | | Na | N3 A:Azi5 | 3.18 | | Na | N2 A:Azi5 | 3.92 | | Na | O A:Hoh377 | 4.72 |
| interactive model:
| Sodium binding site 3 out of 4 in 3mih
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Sodium in the PDB 3mih. 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: A: Leu246, A: Glu298, A: Gly299, A: Arg300, A: Azi7, | conact list:
| Atom | Atom | Distance (A) | | Na | CD2 A:Leu246 | 4.05 | | Na | O A:Glu298 | 3.98 | | Na | C A:Glu298 | 4.87 | | Na | O A:Gly299 | 3.09 | | Na | N A:Gly299 | 4.98 | | Na | C A:Gly299 | 3.78 | | Na | CA A:Gly299 | 4.11 | | Na | N A:Arg300 | 4.78 | | Na | CD A:Arg300 | 4.08 | | Na | CZ A:Arg300 | 4.54 | | Na | CG A:Arg300 | 4.24 | | Na | NE A:Arg300 | 3.53 | | Na | NH2 A:Arg300 | 4.64 | | Na | N1 A:Azi7 | 4.88 | | Na | N3 A:Azi7 | 2.58 | | Na | N2 A:Azi7 | 3.72 |
| interactive model:
| Sodium binding site 4 out of 4 in 3mih
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Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Sodium in the PDB 3mih. 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: A: Cys126, A: Asp127, A: Gly129, A: Gly308, A: Azi3, | conact list:
| Atom | Atom | Distance (A) | | Na | O A:Cys126 | 2.74 | | Na | CB A:Cys126 | 4.45 | | Na | C A:Cys126 | 3.87 | | Na | CA A:Cys126 | 4.78 | | Na | N A:Asp127 | 4.71 | | Na | CA A:Asp127 | 4.82 | | Na | N A:Gly129 | 4.86 | | Na | CA A:Gly129 | 4.57 | | Na | O A:Gly308 | 4.84 | | Na | N1 A:Azi3 | 4.66 | | Na | N3 A:Azi3 | 2.93 | | Na | N2 A:Azi3 | 3.70 |
| interactive model:
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