Caesium in PDB 8u8l: X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna

The structure of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna, PDB code: 8u8l was solved by J.Nandakumar, S.Padmanaban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.98 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.05, 116.48, 118.969, 90, 90, 90
R / Rfree (%)	20.1 / 21.9

The binding sites of Caesium atom in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna (pdb code 8u8l). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 8 binding sites of Caesium where determined in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna, PDB code: 8u8l:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Caesium binding site 1 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cs501 b:92.9 occ:0.75 O A:LYS437 3.0 27.1 1.0 O A:ILE439 3.2 37.1 1.0 O A:LEU436 3.2 26.1 1.0 O A:HOH673 3.2 53.4 1.0 OD1 A:ASN466 3.3 41.2 1.0 O A:HOH607 3.5 33.4 1.0 O A:HOH650 3.5 53.1 1.0 C A:LYS437 3.6 37.8 1.0 CB A:ASN466 3.8 35.5 1.0 C A:ILE439 3.9 37.5 1.0 O A:LEU467 3.9 42.2 1.0 CG A:ASN466 4.0 38.3 1.0 CA A:LYS437 4.1 35.5 1.0 N A:ILE439 4.3 35.3 1.0 C A:LEU436 4.3 33.6 1.0 N A:ASN438 4.4 36.1 1.0 N A:LEU467 4.4 34.4 1.0 N A:GLY440 4.5 34.7 1.0 CA A:GLY440 4.6 30.9 1.0 N A:LYS437 4.7 32.0 1.0 CA A:ASN466 4.7 35.5 1.0 CA A:ILE439 4.8 35.5 1.0 N A:ILE441 4.8 31.4 1.0 CA A:ASN438 4.8 35.6 1.0 C A:ASN438 4.8 35.7 1.0 C A:ASN466 4.8 37.4 1.0 C A:LEU467 4.9 35.1 1.0

Caesium binding site 2 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Cs101 b:126.9 occ:0.75 O D:HOH231 3.1 83.6 1.0 O2 D:DT2 3.2 82.9 1.0 C2 C:DA19 3.6 79.8 1.0 O4' D:DG3 3.7 74.3 1.0 O2 D:DC1 3.8 99.8 1.0 N3 D:DG3 3.8 55.6 1.0 N3 C:DA19 3.9 80.2 1.0 C2 D:DC1 4.1 99.0 1.0 N3 D:DC1 4.2 90.5 1.0 C4 D:DG3 4.2 58.3 1.0 C2 D:DG3 4.3 58.0 1.0 N9 D:DG3 4.4 61.4 1.0 C2 D:DT2 4.4 82.5 1.0 C1' D:DG3 4.4 64.0 1.0 N1 C:DA19 4.7 79.6 1.0 N2 D:DG3 4.7 61.5 1.0 C4' D:DG3 4.9 72.7 1.0 C5 D:DG3 4.9 59.5 1.0

Caesium binding site 3 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Cs102 b:131.9 occ:0.75 O D:HOH240 3.2 67.5 1.0 O2 D:DT4 3.4 44.6 1.0 O4' D:DT5 3.5 42.2 1.0 O2 D:DT5 3.6 38.5 1.0 C4' D:DT5 3.9 45.5 1.0 C2 C:DA17 4.0 52.9 1.0 C1' D:DT5 4.2 39.8 1.0 N3 C:DA17 4.3 61.0 1.0 C2 D:DT5 4.5 41.0 1.0 C2 D:DT4 4.5 45.8 1.0 O D:HOH224 4.6 53.4 1.0 C5' D:DT5 4.6 46.3 1.0 N1 D:DT5 4.8 41.2 1.0 O4' D:DA6 4.8 50.5 1.0 O2 C:DC18 4.9 77.4 1.0 N1 C:DA17 5.0 50.6 1.0

Caesium binding site 4 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Cs103 b:128.3 occ:0.75 O D:HOH238 3.1 57.9 1.0 O D:HOH234 3.1 47.8 1.0 N3 D:DG14 3.5 32.5 1.0 O2 C:DC8 3.7 29.1 1.0 N2 D:DG14 3.8 30.9 1.0 O4' C:DT9 3.9 33.9 1.0 C2 D:DG14 4.0 32.9 1.0 N2 D:DG13 4.0 31.4 1.0 O4' D:DC15 4.3 39.9 1.0 C4 D:DG14 4.4 33.8 1.0 C1' D:DG14 4.5 37.6 1.0 O4' D:DG14 4.5 38.1 1.0 C4' C:DT9 4.5 34.1 1.0 C5' D:DC15 4.7 38.1 1.0 C4' D:DC15 4.8 43.8 1.0 N9 D:DG14 4.8 34.3 1.0 C2 C:DC8 4.9 31.6 1.0 C1' C:DC8 4.9 38.2 1.0 C1' C:DT9 4.9 32.6 1.0

Caesium binding site 5 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Cs101 b:121.8 occ:0.75 O2 C:DT15 3.0 51.2 1.0 O D:HOH237 3.0 57.9 1.0 O C:HOH235 3.1 76.3 1.0 O4' C:DA16 3.2 69.9 1.0 O D:HOH236 3.3 50.2 1.0 C4' C:DA16 3.6 70.8 1.0 O C:HOH208 3.6 55.2 1.0 C5' C:DA16 3.7 70.3 1.0 C2 C:DT15 4.1 46.4 1.0 C1' C:DT15 4.3 56.4 1.0 C1' C:DA16 4.5 64.8 1.0 N2 D:DG7 4.5 39.8 1.0 N1 C:DT15 4.8 50.9 1.0 C2 D:DA6 4.8 41.0 1.0 N3 D:DG7 4.9 40.8 1.0 O4' C:DT15 4.9 58.8 1.0 N9 C:DA16 4.9 58.9 1.0 O3' C:DT15 5.0 70.6 1.0

Caesium binding site 6 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Cs102 b:134.1 occ:0.75 O2 C:DT3 3.1 49.1 1.0 O C:HOH233 3.2 48.2 1.0 O C:HOH232 3.6 54.7 1.0 O D:HOH232 3.7 38.7 1.0 N3 D:DG19 3.7 42.3 1.0 O4' D:DG19 4.0 44.8 1.0 O4' C:DA4 4.0 39.5 1.0 O D:HOH243 4.1 43.9 1.0 C2 D:DA18 4.2 39.4 1.0 N2 D:DG19 4.2 40.9 1.0 C2 C:DT3 4.3 43.0 1.0 C2 D:DG19 4.3 41.8 1.0 C4' C:DA4 4.4 38.5 1.0 C1' D:DG19 4.4 45.2 1.0 C4 D:DG19 4.5 38.5 1.0 C5' C:DA4 4.6 39.0 1.0 N3 D:DA18 4.8 40.1 1.0 N9 D:DG19 4.8 37.1 1.0 O A:HOH633 4.8 34.8 1.0 C1' C:DT3 5.0 44.1 1.0 CE A:LYS359 5.0 52.9 1.0

Caesium binding site 7 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cs501 b:55.9 occ:0.75 O B:LYS437 2.9 43.1 1.0 O B:LEU467 3.3 38.5 1.0 O B:LEU436 3.3 35.4 1.0 O B:HOH619 3.4 32.3 1.0 N B:GLY440 3.4 38.0 1.0 CA B:GLY440 3.4 41.1 1.0 C B:LYS437 3.6 36.9 1.0 O B:HOH662 3.7 49.1 1.0 N B:LEU467 3.9 35.0 1.0 CA B:LYS437 4.0 38.9 1.0 C B:LEU467 4.2 37.3 1.0 CB B:ASN466 4.2 33.6 1.0 C B:LEU436 4.4 37.2 1.0 CA B:LEU467 4.4 35.7 1.0 ND2 B:ASN466 4.4 46.2 1.0 N B:ASN438 4.5 37.1 1.0 C B:ILE439 4.5 45.8 1.0 CB B:LEU467 4.5 35.2 1.0 N B:ILE439 4.6 42.5 1.0 C B:GLY440 4.6 42.9 1.0 C B:ASN466 4.7 35.9 1.0 N B:ILE441 4.7 40.4 1.0 CG B:ASN466 4.7 38.1 1.0 N B:LYS437 4.7 38.7 1.0 CA B:ASN466 4.8 31.0 1.0 CA B:ASN438 4.9 33.3 1.0 C B:ASN438 4.9 39.3 1.0

Caesium binding site 8 out of 8 in the X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of X-Ray Crystal Structure of Tebp-2 MCD3 with Ds Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cs502 b:203.7 occ:0.75 O B:THR401 3.5 62.4 1.0 O B:ARG402 3.6 69.0 1.0 O B:HOH651 3.7 66.4 1.0 C B:ARG402 4.2 64.3 1.0 CA B:SER403 4.3 54.6 1.0 N B:SER403 4.5 62.4 1.0 C B:THR401 4.7 54.6 1.0

S.Padmanaban, N.J.Lambacher, V.M.Tesmer, J.Zhang, H.Shibuya, J.Nandakumar. Caenorhabditis Elegans Telomere-Binding Proteins Tebp-1 and Tebp-2 Adapt the Myb Module to Dimerize and Bind Telomeric Dna Proc.Natl.Acad.Sci.Usa 2024.
ISSN: ESSN 1091-6490