Phosphorus in PDB 1a3t: Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate

All present enzymatic activity of Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate:
3.1.31.1;

The structure of Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate, PDB code: 1a3t was solved by R.Wynn, P.C.Harkins, F.M.Richards, R.O.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.10
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	48.400, 48.400, 63.300, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / n/a

The binding sites of Phosphorus atom in the Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate (pdb code 1a3t). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 2 binding sites of Phosphorus where determined in the Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate, PDB code: 1a3t:
Jump to Phosphorus binding site number: 1; 2;

Phosphorus binding site 1 out of 2 in the Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:P151 b:28.6 occ:1.00 P2 A:THP151 0.0 28.6 1.0 O6P A:THP151 1.5 26.8 1.0 O5P A:THP151 1.5 26.7 1.0 O4P A:THP151 1.5 33.9 1.0 O5' A:THP151 1.6 29.0 1.0 HE A:ARG35 2.6 0.0 1.0 H2 A:HOH257 2.6 0.0 1.0 C5' A:THP151 2.7 30.1 1.0 HH21 A:ARG35 2.8 0.0 1.0 H1 A:HOH220 3.0 0.0 1.0 HH22 A:ARG87 3.0 0.0 1.0 HH12 A:ARG87 3.1 0.0 1.0 O A:HOH257 3.3 25.3 1.0 NE A:ARG35 3.5 26.4 1.0 H1 A:HOH257 3.6 0.0 1.0 C4' A:THP151 3.7 31.9 1.0 NH2 A:ARG35 3.7 28.9 1.0 CA A:CA150 3.7 35.0 1.0 O A:HOH220 3.7 38.2 1.0 NH2 A:ARG87 4.0 15.4 1.0 NH1 A:ARG87 4.0 19.9 1.0 CZ A:ARG35 4.1 23.9 1.0 O4' A:THP151 4.3 33.3 1.0 H2 A:HOH220 4.4 0.0 1.0 CZ A:ARG87 4.5 19.0 1.0 OD1 A:ASP40 4.5 35.1 1.0 HH22 A:ARG35 4.5 0.0 1.0 CD A:ARG35 4.6 18.3 1.0 HH21 A:ARG87 4.7 0.0 1.0 O A:HOH205 4.8 45.8 1.0 HH11 A:ARG87 4.8 0.0 1.0 OH A:TYR113 4.8 25.3 1.0 OD2 A:ASP21 4.8 22.2 1.0 H2 A:HOH205 4.9 0.0 1.0 C3' A:THP151 5.0 30.7 1.0 CE2 A:TYR113 5.0 25.0 1.0

Phosphorus binding site 2 out of 2 in the Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Staphylococcal Nuclease, V23C Variant, Complex with 2-Fluoroethane Thiol and 3',5'-Thymidine Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:P151 b:38.2 occ:1.00 P1 A:THP151 0.0 38.2 1.0 O2P A:THP151 1.5 37.0 1.0 O1P A:THP151 1.5 47.0 1.0 O3P A:THP151 1.5 45.4 1.0 O3' A:THP151 1.6 39.8 1.0 C3' A:THP151 2.7 30.7 1.0 HZ2 A:LYS84 2.8 0.0 1.0 C4' A:THP151 3.5 31.9 1.0 NZ A:LYS84 3.7 44.8 1.0 OH A:TYR85 3.8 35.4 1.0 C2' A:THP151 3.9 25.3 1.0 HZ1 A:LYS84 4.1 0.0 1.0 CE A:LYS84 4.1 36.8 1.0 CE2 A:TYR85 4.4 34.0 1.0 O4' A:THP151 4.4 33.3 1.0 HZ3 A:LYS84 4.4 0.0 1.0 HH A:TYR85 4.5 0.0 1.0 C1' A:THP151 4.5 26.0 1.0 CZ A:TYR85 4.6 31.5 1.0 C5' A:THP151 4.6 30.1 1.0 HH A:TYR113 4.9 0.0 1.0

R.Wynn, P.C.Harkins, F.M.Richards, R.O.Fox. Comparison of Straight Chain and Cyclic Unnatural Amino Acids Embedded in the Core of Staphylococcal Nuclease. Protein Sci. V. 6 1621 1997.
ISSN: ISSN 0961-8368
PubMed: 9260275