Sodium in PDB 7p0w: Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion)

All present enzymatic activity of Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion):
4.2.99.18;

The structure of Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion), PDB code: 7p0w was solved by F.Coste, S.Goffinont, D.Flament, B.Castaing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.65 / 1.12
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	59.776, 71.578, 138.691, 90, 90, 90
R / Rfree (%)	12.4 / 14.3

The binding sites of Sodium atom in the Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion) (pdb code 7p0w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion), PDB code: 7p0w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:20.5 occ:1.00 O A:HOH633 2.8 23.3 1.0 O A:HOH623 2.8 24.6 1.0 HB3 A:ALA132 2.8 13.4 1.0 O A:GLY129 2.9 11.4 1.0 HA2 A:GLY129 2.9 12.7 1.0 O A:HOH548 2.9 18.0 1.0 HD3 A:LYS139 3.3 17.1 1.0 HB2 A:ARG133 3.5 14.1 1.0 HB3 A:LYS139 3.5 14.5 1.0 CA A:GLY129 3.5 10.6 1.0 HH22 A:ARG133 3.6 21.3 1.0 C A:GLY129 3.6 10.4 1.0 NH2 A:ARG133 3.6 17.8 1.0 HA3 A:GLY129 3.6 12.7 1.0 CB A:ALA132 3.7 11.2 1.0 H A:ARG133 3.7 12.9 1.0 HH21 A:ARG133 3.7 21.3 1.0 HB1 A:ALA132 3.7 13.4 1.0 N A:ARG133 3.9 10.7 1.0 O A:HOH502 4.0 27.3 1.0 CZ A:ARG133 4.1 15.8 1.0 CD A:LYS139 4.2 14.3 1.0 HB2 A:ALA132 4.2 13.4 1.0 CB A:ARG133 4.3 11.8 1.0 O A:HOH504 4.3 24.8 1.0 HA A:ARG133 4.3 13.5 1.0 H A:LYS139 4.4 13.8 1.0 HH12 A:ARG133 4.4 19.7 1.0 CB A:LYS139 4.4 12.1 1.0 C A:ALA132 4.5 10.8 1.0 CA A:ARG133 4.5 11.3 1.0 O A:HOH671 4.5 23.2 1.0 NH1 A:ARG133 4.5 16.4 1.0 HZ3 A:LYS139 4.6 22.4 1.0 HG2 A:LYS139 4.6 15.0 1.0 CA A:ALA132 4.6 10.4 1.0 HD2 A:LYS139 4.6 17.1 1.0 NE A:ARG133 4.7 15.7 1.0 CG A:LYS139 4.7 12.5 1.0 O A:HOH406 4.7 41.6 1.0 H A:ALA132 4.7 11.7 1.0 HE A:ARG133 4.8 18.9 1.0 HB3 A:ARG133 4.8 14.1 1.0 O A:VAL137 4.8 12.0 1.0 N A:GLY129 4.9 9.9 1.0 N A:SER130 4.9 10.8 1.0 O A:TRP128 5.0 10.5 1.0 N A:LYS139 5.0 11.5 1.0 HB2 A:LYS139 5.0 14.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:16.7 occ:1.00 H A:GLN97 2.5 14.1 1.0 HD2 A:PRO96 2.7 16.9 1.0 HA A:LEU94 2.8 13.7 1.0 H2'' I:DA5 2.8 19.7 1.0 O I:HOH628 2.8 43.4 1.0 O I:HOH638 3.0 40.6 1.0 HB2 A:GLN97 3.0 14.1 1.0 HB2 A:PRO96 3.1 17.4 1.0 O I:HOH608 3.1 41.8 1.0 N A:GLN97 3.3 11.7 1.0 HB3 A:GLN97 3.5 14.1 1.0 CD A:PRO96 3.5 14.1 1.0 CA A:LEU94 3.6 11.4 1.0 H1' I:DA5 3.6 19.7 1.0 CB A:GLN97 3.6 11.7 1.0 C A:LEU94 3.6 11.7 1.0 H5' I:DT6 3.6 20.3 1.0 HB3 A:LEU94 3.7 13.9 1.0 C2' I:DA5 3.7 16.4 1.0 CB A:PRO96 3.8 14.5 1.0 N A:PRO96 3.8 12.8 1.0 O A:LEU94 3.8 11.5 1.0 HG2 A:PRO96 3.9 18.6 1.0 HD22 A:LEU94 4.0 15.4 1.0 CG A:PRO96 4.0 15.5 1.0 H4' I:DA5 4.0 20.3 1.0 CA A:GLN97 4.0 11.4 1.0 C A:PRO96 4.2 12.5 1.0 CA A:PRO96 4.2 13.5 1.0 CB A:LEU94 4.2 11.6 1.0 C1' I:DA5 4.2 16.4 1.0 N A:ILE95 4.2 12.0 1.0 HD3 A:PRO96 4.3 16.9 1.0 HD23 A:LEU94 4.3 15.4 1.0 H2' I:DA5 4.3 19.7 1.0 H A:ILE95 4.4 14.4 1.0 O I:HOH629 4.4 41.3 1.0 O3' I:DA5 4.5 16.7 1.0 HA A:GLN97 4.5 13.7 1.0 CD2 A:LEU94 4.5 12.8 1.0 C3' I:DA5 4.5 16.1 1.0 C A:ILE95 4.6 12.3 1.0 C4' I:DA5 4.6 16.9 1.0 C5' I:DT6 4.6 16.9 1.0 HB3 A:PRO96 4.6 17.4 1.0 H A:LEU94 4.7 13.9 1.0 N A:LEU94 4.7 11.6 1.0 O I:HOH607 4.7 45.5 1.0 O4' I:DA5 4.8 17.9 1.0 H A:LYS98 4.8 12.5 1.0 HB2 A:LEU94 4.9 13.9 1.0 H5'' I:DT6 4.9 20.3 1.0 HG3 A:PRO96 4.9 18.6 1.0 CG A:GLN97 5.0 12.0 1.0

F.Coste, S.Goffinont, D.Flament, B.Castaing. Crystal Structure of A Trapped Pab-Agog/Double-Standed Dna Covalent Intermediate (Dna Containing Thymine Opposite to Lesion) To Be Published.