The binding sites of Strontium atom in the structure of Dna Binding and Cleavage By the Hnh Homing Endonuclease I-Hmui (pdb code 1u3e). This binding sites where shown with 5.0 Angstroms radius around Strontium atom.
The 1u3e structure was solved by B.W.SHEN, M.LANDTHALER, D.A.SHUB, B.L.STODDARD, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
| Resolution (A) | 50.0-2.9 | | Space group | I222 | | a (A) | 45.000 | | b (A) | 108.300 | | c (A) | 248.100 | | alpha (°) | 90.00 | | beta (°) | 90.00 | | gamma (°) | 90.00 | | Rfactor (%) | 21.6 | | Rfree (%) | 24.7 |
|
Strontium binding site 1 out of 4 in 1u3e
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Strontium in the PDB 1u3e. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Dt26, A: Dc27, B: Dt14, B: Edo403, A: Hoh424, | conact list:
| Atom | Atom | Distance (A) | | Sr | O2 A:Dt26 | 4.43 | | Sr | O4' A:Dc27 | 4.55 | | Sr | C5' A:Dc27 | 4.16 | | Sr | C4' A:Dc27 | 4.22 | | Sr | O4' B:Dt14 | 4.63 | | Sr | C4' B:Dt14 | 4.72 | | Sr | O1 B:Edo403 | 4.05 | | Sr | O2 B:Edo403 | 3.51 | | Sr | C2 B:Edo403 | 3.99 | | Sr | C1 B:Edo403 | 4.70 | | Sr | O A:Hoh424 | 3.13 |
| interactive model:
| Strontium binding site 2 out of 4 in 1u3e
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Strontium in the PDB 1u3e. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: A: Dg36, A: Hoh418, B: Hoh405, | conact list:
| Atom | Atom | Distance (A) | | Sr | O6 A:Dg36 | 4.27 | | Sr | O A:Hoh418 | 3.37 | | Sr | O B:Hoh405 | 3.09 |
| interactive model:
| Strontium binding site 3 out of 4 in 1u3e
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Strontium in the PDB 1u3e. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: M: Ile117, M: Lys118, M: Asn119, M: Gln120, M: Sr418, M: Hoh425, | conact list:
| Atom | Atom | Distance (A) | | Sr | O M:Ile117 | 4.92 | | Sr | O M:Lys118 | 2.81 | | Sr | CB M:Lys118 | 4.91 | | Sr | C M:Lys118 | 3.66 | | Sr | CA M:Lys118 | 4.17 | | Sr | N M:Asn119 | 4.60 | | Sr | C M:Asn119 | 4.65 | | Sr | CA M:Asn119 | 4.81 | | Sr | O M:Gln120 | 3.01 | | Sr | N M:Gln120 | 4.48 | | Sr | C M:Gln120 | 4.16 | | Sr | CA M:Gln120 | 4.94 | | Sr | SR M:Sr418 | 3.18 | | Sr | O M:Hoh425 | 3.17 |
| interactive model:
| Strontium binding site 4 out of 4 in 1u3e
| 
Click to enlarge | 
Click to enlarge | Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Strontium in the PDB 1u3e. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Strontium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: B: Dc17, B: Dt18, M: Lys118, M: Asn119, M: Sr417, B: Hoh404, | conact list:
| Atom | Atom | Distance (A) | | Sr | O3' B:Dc17 | 4.52 | | Sr | OP1 B:Dt18 | 3.80 | | Sr | P B:Dt18 | 4.84 | | Sr | O M:Lys118 | 2.83 | | Sr | CB M:Lys118 | 4.97 | | Sr | C M:Lys118 | 4.04 | | Sr | CA M:Lys118 | 4.97 | | Sr | N M:Asn119 | 4.83 | | Sr | OD1 M:Asn119 | 4.93 | | Sr | CA M:Asn119 | 4.58 | | Sr | SR M:Sr417 | 3.18 | | Sr | O B:Hoh404 | 3.09 |
| interactive model:
|
|