Sodium in PDB 2b2n: Structure of Transcription-Repair Coupling Factor

The structure of Structure of Transcription-Repair Coupling Factor, PDB code: 2b2n was solved by N.Assenmacher, K.Wenig, A.Lammens, K.-P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.650, 112.650, 213.860, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 23.2

The binding sites of Sodium atom in the Structure of Transcription-Repair Coupling Factor (pdb code 2b2n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of Transcription-Repair Coupling Factor, PDB code: 2b2n:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structure of Transcription-Repair Coupling Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Transcription-Repair Coupling Factor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na345 b:26.5 occ:1.00 O A:HOH4176 2.2 32.4 1.0 O A:PHE62 2.3 19.9 1.0 O1 A:P4C4034 2.4 41.2 1.0 O10 A:P4C4034 2.6 36.9 1.0 O13 A:P4C4034 2.6 47.7 1.0 O4 A:P4C4034 2.7 36.7 1.0 O7 A:P4C4034 2.7 33.7 1.0 C A:PHE62 3.3 19.7 1.0 O16 A:P4C4034 3.3 54.1 1.0 C8 A:P4C4034 3.5 35.0 1.0 C9 A:P4C4034 3.5 34.2 1.0 C6 A:P4C4034 3.5 34.9 1.0 C11 A:P4C4034 3.5 40.8 1.0 C2 A:P4C4034 3.6 41.4 1.0 C15 A:P4C4034 3.6 51.4 1.0 C12 A:P4C4034 3.6 43.4 1.0 C14 A:P4C4034 3.6 49.3 1.0 C5 A:P4C4034 3.6 34.7 1.0 C3 A:P4C4034 3.6 40.2 1.0 O19 A:P4C4034 4.0 56.7 0.0 C17 A:P4C4034 4.1 55.8 1.0 CA A:PHE62 4.1 18.2 1.0 N A:THR63 4.1 18.0 1.0 CA A:THR63 4.2 15.1 1.0 CB A:PHE62 4.6 18.6 1.0 C18 A:P4C4034 4.6 56.1 0.0

Sodium binding site 2 out of 3 in the Structure of Transcription-Repair Coupling Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Transcription-Repair Coupling Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1001 b:15.2 occ:1.00 O A:SER60 2.2 14.2 1.0 O B:THR63 2.3 15.4 1.0 O B:SER60 2.3 19.7 1.0 O A:THR63 2.3 12.4 1.0 O B:HOH4853 2.5 15.2 1.0 C A:SER60 3.3 15.9 1.0 C B:SER60 3.4 20.4 1.0 C B:THR63 3.5 17.6 1.0 C A:THR63 3.5 14.7 1.0 CA A:SER60 4.0 15.7 1.0 CA B:SER60 4.1 20.1 1.0 N A:THR63 4.3 18.0 1.0 CG2 A:THR63 4.3 13.9 1.0 N B:THR63 4.3 18.9 1.0 CB A:SER60 4.3 16.2 1.0 N A:GLN61 4.3 14.3 1.0 CG2 B:THR63 4.4 16.7 1.0 N B:ASP64 4.4 15.0 1.0 CA B:ASP64 4.4 14.9 1.0 N A:ASP64 4.4 12.4 1.0 CA A:THR63 4.4 15.1 1.0 CA B:THR63 4.4 17.5 1.0 CA A:ASP64 4.5 12.5 1.0 N B:GLN61 4.5 19.7 1.0 O B:GLN65 4.6 12.9 1.0 CA A:GLN61 4.6 17.6 1.0 CB B:SER60 4.6 19.1 1.0 O A:GLN65 4.6 12.8 1.0 CA B:GLN61 4.8 21.1 1.0 C A:GLN61 4.9 17.9 1.0 C B:GLN61 4.9 21.3 1.0 C B:ASP64 5.0 14.5 1.0

Sodium binding site 3 out of 3 in the Structure of Transcription-Repair Coupling Factor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Transcription-Repair Coupling Factor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4850 b:45.8 occ:1.00 O B:PHE62 2.4 16.9 1.0 O7 B:P4C4035 2.7 56.5 1.0 O10 B:P4C4035 2.7 57.9 1.0 O13 B:P4C4035 2.8 62.0 1.0 O4 B:P4C4035 2.9 61.0 1.0 O1 B:P4C4035 3.1 64.1 1.0 C8 B:P4C4035 3.4 57.2 1.0 C B:PHE62 3.4 20.5 1.0 O16 B:P4C4035 3.4 64.9 1.0 C6 B:P4C4035 3.4 57.3 1.0 C9 B:P4C4035 3.6 57.9 1.0 C5 B:P4C4035 3.6 59.0 1.0 C15 B:P4C4035 3.6 64.7 1.0 C14 B:P4C4035 3.7 62.8 1.0 C11 B:P4C4035 3.8 59.5 1.0 C12 B:P4C4035 3.8 60.5 1.0 C3 B:P4C4035 3.9 62.1 1.0 C2 B:P4C4035 4.1 62.9 1.0 C17 B:P4C4035 4.1 64.2 0.0 N B:THR63 4.2 18.9 1.0 CA B:THR63 4.2 17.5 1.0 CA B:PHE62 4.3 22.0 1.0 C18 B:P4C4035 4.6 63.7 0.0 CB B:PHE62 4.7 27.9 1.0

N.Assenmacher, K.Wenig, A.Lammens, K.-P.Hopfner. Structural Basis For Transcription-Coupled Repair: the N Terminus of Mfd Resembles Uvrb with Degenerate Atpase Motifs J.Mol.Biol. V. 355 675 2006.
ISSN: ISSN 0022-2836
PubMed: 16309703
DOI: 10.1016/J.JMB.2005.10.033