Sodium in PDB 6xzz: Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide, PDB code: 6xzz was solved by T.Zacharchenko, S.C.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.22 / 1.39
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.014, 67.014, 152.016, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 20.6

The structure of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide (pdb code 6xzz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide, PDB code: 6xzz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


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 the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:31.1 occ:1.00 NE A:ARG28 2.8 33.8 0.5 O A:HOH372 2.9 20.1 1.0 NH1 A:ARG28 3.0 31.9 0.5 CZ A:ARG28 3.0 33.6 0.5 CD A:ARG28 3.5 29.3 0.5 CD A:ARG28 3.7 30.3 0.5 CB A:ARG24 3.9 17.4 1.0 CD2 A:LEU25 4.0 16.1 1.0 NH2 A:ARG28 4.1 36.1 0.5 C A:ARG24 4.1 13.7 1.0 O A:ARG24 4.1 14.8 1.0 NH1 A:ARG28 4.1 35.0 0.5 NE A:ARG28 4.1 33.1 0.5 CD1 A:ILE30 4.2 19.2 1.0 N A:LEU25 4.2 12.4 1.0 CZ A:ARG28 4.4 35.0 0.5 CA A:LEU25 4.5 12.9 1.0 CG A:ARG28 4.5 25.3 0.5 CG A:ARG28 4.5 24.6 0.5 CA A:ARG24 4.7 13.9 1.0 CG A:LEU25 4.9 12.8 1.0 CB A:ARG28 5.0 20.4 0.5 CB A:ARG28 5.0 21.1 0.5

Sodium binding site 2 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


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 the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:45.3 occ:1.00 N A:GLN64 2.9 21.2 1.0 O A:THR62 3.5 21.2 1.0 CB A:GLN64 3.5 30.8 1.0 CA A:ASP63 3.7 19.0 0.3 CA A:ASP63 3.8 17.4 0.7 O A:HOH305 3.8 31.8 1.0 CA A:GLN64 3.8 26.0 1.0 C A:ASP63 3.8 19.2 1.0 O A:HOH304 3.9 34.1 1.0 NA A:NA203 4.0 22.1 1.0 OD1 A:ASP63 4.2 25.9 0.3 O A:HOH387 4.2 30.4 1.0 C A:THR62 4.5 16.7 1.0 CG A:ASP63 4.6 23.4 0.3 N A:ASP63 4.6 16.9 1.0 CB A:ASP63 4.7 20.6 0.3 NH2 A:ARG67 4.7 32.7 0.5 CB A:ASP63 4.8 17.3 0.7 OD1 A:ASP63 4.9 20.1 0.7 CG A:GLN64 4.9 39.0 1.0 O A:ASP63 5.0 20.3 1.0

Sodium binding site 3 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:22.1 occ:1.00 OD1 A:ASP63 2.4 25.9 0.3 OD2 A:ASP63 2.8 23.1 0.3 CG A:ASP63 2.8 23.4 0.3 N A:LEU65 3.2 22.8 1.0 O A:HOH308 3.3 24.4 1.0 O A:HOH304 3.4 34.1 1.0 N A:GLN64 3.5 21.2 1.0 CB A:LEU65 3.7 25.6 1.0 NA A:NA202 4.0 45.3 1.0 CB A:GLN64 4.0 30.8 1.0 CG A:LEU65 4.0 28.4 1.0 CA A:GLN64 4.0 26.0 1.0 C A:ASP63 4.0 19.2 1.0 CA A:LEU65 4.1 25.5 1.0 C A:GLN64 4.1 25.1 1.0 CB A:ASP63 4.1 20.6 0.3 CB A:ASP63 4.2 17.3 0.7 CA A:ASP63 4.3 17.4 0.7 CA A:ASP63 4.3 19.0 0.3 CD1 A:LEU65 4.5 28.1 1.0 O A:ASP63 4.8 20.3 1.0 CG A:ASP63 4.9 19.1 0.7

Sodium binding site 4 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:25.7 occ:1.00 O A:HOH410 2.9 50.6 1.0 N A:SER70 3.1 17.7 1.0 N A:VAL71 3.5 14.3 1.0 CA A:SER70 3.9 19.4 1.0 CB A:SER70 4.0 22.6 1.0 CA A:LEU69 4.0 22.6 1.0 C A:LEU69 4.0 20.4 1.0 CD2 A:LEU69 4.0 25.8 1.0 C A:SER70 4.1 15.7 1.0 O A:VAL71 4.3 17.7 1.0 CB A:VAL71 4.3 18.6 1.0 CB A:LEU69 4.4 22.1 1.0 CA A:VAL71 4.4 15.2 1.0 CG2 A:VAL71 4.5 19.5 1.0 OG A:SER70 4.5 28.4 1.0 C A:VAL71 4.8 15.9 1.0 CG A:LEU69 4.9 24.8 1.0 O A:ASN68 5.0 33.4 1.0

Sodium binding site 5 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:35.0 occ:1.00 ND2 A:ASN101 3.0 15.8 1.0 O A:HOH400 3.5 38.6 1.0 CB A:ASN101 3.8 16.5 1.0 CD1 A:ILE85 3.8 18.8 1.0 CG A:ASN101 3.9 16.0 1.0 CG A:GLU81 4.4 32.4 1.0 O A:HOH384 4.5 39.6 1.0 ND2 A:ASN96 4.6 25.2 1.0 O A:HOH392 4.8 37.2 1.0 CG1 A:ILE85 4.9 15.3 1.0 OE1 A:GLU81 4.9 43.7 1.0

Sodium binding site 6 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:31.8 occ:1.00 O A:HOH359 2.8 26.6 1.0 O A:HOH338 2.9 14.6 1.0 ND2 A:ASN23 3.0 16.5 1.0 CD1 A:LEU20 3.3 28.4 1.0 CB A:ASN23 3.8 12.3 1.0 CG A:ASN23 3.9 13.3 1.0 CG2 A:THR92 3.9 14.4 1.0 CA A:LEU20 4.5 13.9 1.0 O A:HOH389 4.5 31.4 1.0 CG A:LEU20 4.6 25.4 1.0 NH2 A:ARG94 4.6 31.7 1.0 O A:TYR91 4.7 13.3 1.0 O A:LEU20 4.7 14.2 1.0 O A:HOH348 4.8 49.3 1.0 CB A:THR92 4.8 13.0 1.0 CB A:LEU20 4.8 19.1 1.0

Sodium binding site 7 out of 7 in the Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the BCL6 Btb Domain in Complex with the NCOR1 BBD2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:44.9 occ:0.79 O A:ILE78 2.4 20.4 1.0 O A:PRO76 2.4 19.0 1.0 OG A:SER39 2.8 27.2 0.8 C A:ILE78 3.4 17.2 1.0 C A:GLU77 3.5 18.5 1.0 C A:PRO76 3.5 17.4 1.0 O A:GLU77 3.6 20.2 1.0 OG A:SER39 3.6 19.6 0.2 N A:ILE78 3.8 17.4 1.0 CA A:GLU77 3.8 19.1 1.0 CB A:SER39 3.8 19.6 0.2 CB A:SER39 3.9 24.1 0.8 CD A:PRO80 4.0 16.7 1.0 N A:GLU77 4.1 17.0 1.0 N A:ASN79 4.2 15.4 1.0 CA A:ILE78 4.2 18.2 1.0 CA A:ASN79 4.3 15.7 1.0 CA A:PRO76 4.6 16.0 1.0 CG A:PRO80 4.6 19.7 1.0 CG1 A:VAL38 4.8 24.4 1.0 N A:PRO80 4.8 14.3 1.0

T.Zacharchenko, S.C.Wright. Crystal Structure of An NCOR1BBD2-BCL6BTB Chimera To Be Published.