Sodium in PDB 4ao5: B. Subtilis Prophage Dutpase Yoss in Complex with Dump

All present enzymatic activity of B. Subtilis Prophage Dutpase Yoss in Complex with Dump:
3.6.1.23;

The structure of B. Subtilis Prophage Dutpase Yoss in Complex with Dump, PDB code: 4ao5 was solved by J.Garcia-Nafria, C.Harrison, J.P.Turkenburg, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.65 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.820, 100.010, 99.510, 90.00, 90.00, 90.00
R / Rfree (%)	15.03 / 21.365

The binding sites of Sodium atom in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump (pdb code 4ao5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump, PDB code: 4ao5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of B. Subtilis Prophage Dutpase Yoss in Complex with Dump within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1130 b:25.4 occ:1.00 O A:ASP25 2.8 17.6 1.0 O A:HOH2042 2.9 19.9 1.0 NH2 A:ARG27 2.9 17.7 1.0 OD1 A:ASN16 3.0 47.4 1.0 N A:ASN16 3.2 32.0 1.0 N A:ASP25 3.4 14.4 1.0 CG A:ASN16 3.6 37.8 1.0 CG2 A:ILE24 3.6 18.0 1.0 CB A:ASN16 3.6 36.5 1.0 C A:ASP25 3.7 13.9 1.0 NE A:ARG27 3.7 17.8 1.0 CB A:ILE15 3.8 27.1 1.0 CZ A:ARG27 3.8 17.2 1.0 CA A:ASP25 3.8 14.8 1.0 CB A:ASP25 3.8 14.7 1.0 CA A:ASN16 4.0 34.1 1.0 CA A:ILE15 4.0 29.2 1.0 C A:ILE15 4.1 32.4 1.0 C A:ILE24 4.3 14.1 1.0 CG2 A:ILE15 4.3 28.9 1.0 NH1 A:ARG107 4.4 15.3 1.0 O A:HOH2041 4.5 40.0 1.0 CA A:ILE24 4.7 15.8 1.0 ND2 A:ASN16 4.7 43.9 1.0 CB A:ILE24 4.8 19.0 1.0 CG A:ASP25 4.8 15.8 1.0 CZ A:ARG107 4.8 18.2 1.0 CG1 A:ILE15 4.9 28.6 1.0 N A:LEU26 4.9 15.3 1.0

Sodium binding site 2 out of 5 in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of B. Subtilis Prophage Dutpase Yoss in Complex with Dump within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1130 b:15.8 occ:1.00 OG1 B:THR13 3.0 18.7 1.0 O B:HOH2034 3.2 27.3 1.0 O B:HOH2036 3.2 19.2 1.0 NE F:ARG107 3.3 18.7 1.0 NH2 F:ARG107 3.3 20.4 1.0 CA B:GLY105 3.6 16.7 1.0 O B:HOH2026 3.6 23.3 1.0 CZ F:ARG107 3.8 18.4 1.0 NH1 F:ARG27 3.9 18.2 1.0 N B:GLY105 4.0 15.0 1.0 CB B:THR13 4.0 17.7 1.0 CG B:LYS104 4.1 16.0 1.0 O B:THR11 4.1 21.0 1.0 O B:LYS104 4.2 14.9 1.0 C B:LYS104 4.2 15.3 1.0 N B:THR13 4.3 18.5 1.0 CD F:ARG107 4.4 18.2 1.0 CE B:LYS104 4.6 22.1 1.0 CD B:LYS104 4.7 20.6 1.0 CG F:ARG107 4.7 15.6 1.0 CA B:THR13 4.8 17.3 1.0 CZ F:ARG27 4.8 18.2 1.0 O B:HOH2037 4.9 20.7 1.0 NH2 F:ARG27 4.9 19.4 1.0 C B:GLY105 4.9 16.4 1.0 CB B:LYS104 5.0 14.6 1.0

Sodium binding site 3 out of 5 in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of B. Subtilis Prophage Dutpase Yoss in Complex with Dump within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1130 b:17.1 occ:1.00 O C:HOH2138 3.2 19.2 1.0 NE C:ARG107 3.3 20.1 1.0 NH2 C:ARG107 3.4 21.7 1.0 CZ C:ARG107 3.8 18.0 1.0 NH1 C:ARG27 3.9 19.2 1.0 CD C:ARG107 4.4 18.2 1.0 CZ C:ARG27 4.8 19.2 1.0 CG C:ARG107 4.8 16.5 1.0 NH2 C:ARG27 4.8 18.7 1.0 O C:HOH2032 4.9 22.4 1.0

Sodium binding site 4 out of 5 in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of B. Subtilis Prophage Dutpase Yoss in Complex with Dump within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1130 b:31.1 occ:1.00 O D:HOH2042 2.3 35.1 1.0 O D:ARG14 2.7 22.9 1.0 NE D:ARG27 2.9 15.5 1.0 NH2 D:ARG27 3.0 18.0 1.0 CZ D:ARG27 3.4 14.3 1.0 ND2 D:ASN16 3.6 32.9 1.0 C D:ARG14 3.7 21.7 1.0 O D:HOH2064 3.7 30.5 1.0 CA D:ILE15 3.7 23.4 1.0 CG2 D:THR13 3.8 16.8 1.0 N D:ASN16 4.0 27.9 1.0 CD D:ARG27 4.1 14.7 1.0 N D:ILE15 4.1 21.9 1.0 CD1 D:ILE15 4.2 26.8 1.0 O D:HOH2038 4.2 28.0 1.0 O D:THR13 4.2 18.9 1.0 C D:ILE15 4.3 23.5 1.0 CG D:ASN16 4.6 31.6 1.0 C D:THR13 4.6 18.6 1.0 NH1 D:ARG27 4.7 16.0 1.0 CB D:THR13 4.8 16.2 1.0 CB D:ILE15 4.8 21.5 1.0 CG D:ARG27 4.8 14.3 1.0 N D:ARG14 4.9 19.4 1.0 CA D:ARG14 4.9 19.6 1.0 CB D:ASN16 4.9 29.2 1.0 CG1 D:ILE15 5.0 23.4 1.0

Sodium binding site 5 out of 5 in the B. Subtilis Prophage Dutpase Yoss in Complex with Dump


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of B. Subtilis Prophage Dutpase Yoss in Complex with Dump within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1130 b:16.6 occ:1.00 OG1 E:THR13 3.0 19.9 1.0 O E:HOH2026 3.2 31.4 1.0 CA E:GLY105 3.6 15.7 1.0 O E:HOH2021 3.7 24.3 1.0 N E:GLY105 3.9 15.8 1.0 CB E:THR13 4.0 18.4 1.0 CG E:LYS104 4.1 18.1 0.5 O E:THR11 4.1 24.7 1.0 CG E:LYS104 4.1 17.9 0.5 O E:LYS104 4.2 18.1 1.0 C E:LYS104 4.2 17.2 1.0 N E:THR13 4.3 19.0 1.0 CE E:LYS104 4.3 21.8 0.5 NZ E:LYS104 4.5 22.3 0.5 CE E:LYS104 4.6 22.9 0.5 CA E:THR13 4.7 17.8 1.0 CD E:LYS104 4.8 21.1 0.5 CD E:LYS104 4.8 21.2 0.5 C E:GLY105 4.9 16.0 1.0 CB E:LYS104 5.0 17.3 0.5 CB E:LYS104 5.0 17.2 0.5

J.Garcia-Nafria, J.Timm, C.Harrison, J.P.Turkenburg, K.S.Wilson. Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism Acta Crystallogr.,Sect.D V. 69 1367 2013.
ISSN: ISSN 0907-4449
PubMed: 23897460
DOI: 10.1107/S090744491300735X