Cobalt in PDB 8u8m: X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer

The structure of X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer, PDB code: 8u8m 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)	49.58 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.842, 59.965, 151.966, 90, 101.82, 90
R / Rfree (%)	23.2 / 26.5

The binding sites of Cobalt atom in the X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer (pdb code 8u8m). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer, PDB code: 8u8m:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:97.4 occ:1.00 NE2 A:HIS216 2.2 95.5 1.0 NE2 A:HIS220 2.3 94.5 1.0 O A:HOH410 2.5 85.9 1.0 O A:HOH408 2.5 88.0 1.0 CE1 A:HIS216 2.9 91.6 1.0 CE1 A:HIS220 3.0 94.6 1.0 CD2 A:HIS216 3.3 87.3 1.0 CD2 A:HIS220 3.5 91.0 1.0 ND1 A:HIS216 4.1 88.1 1.0 ND1 A:HIS220 4.2 92.0 1.0 CG A:HIS216 4.3 84.0 1.0 CG A:HIS220 4.4 85.7 1.0

Cobalt binding site 2 out of 4 in the X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:104.3 occ:1.00 O B:HOH405 2.1 92.2 1.0 NE2 B:HIS216 2.1 94.4 1.0 O D:HOH405 2.5 97.7 1.0 NE2 B:HIS220 2.8 124.6 1.0 CE1 B:HIS216 3.1 92.2 1.0 CD2 B:HIS216 3.1 91.2 1.0 CD2 B:HIS220 3.4 113.7 1.0 CE1 B:HIS220 3.6 123.4 1.0 ND1 B:HIS216 4.2 87.8 1.0 CG B:HIS216 4.3 87.1 1.0 CG B:HIS220 4.4 112.8 1.0 ND1 B:HIS220 4.4 117.8 1.0

Cobalt binding site 3 out of 4 in the X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:147.1 occ:1.00 O C:HOH401 1.8 120.2 1.0 NE2 C:HIS220 2.4 140.5 1.0 CD2 C:HIS220 3.1 137.5 1.0 ND1 C:HIS216 3.3 137.0 1.0 CE1 C:HIS220 3.5 132.9 1.0 CE1 C:HIS216 3.9 140.7 1.0 CG C:HIS220 4.3 128.0 1.0 CG C:HIS216 4.5 132.0 1.0 ND1 C:HIS220 4.5 128.2 1.0 CB C:HIS216 4.9 127.3 1.0

Cobalt binding site 4 out of 4 in the X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of X-Ray Crystal Structure of Tebp-1 MCD2 Homodimer within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:94.2 occ:1.00 NE2 D:HIS216 2.0 100.7 1.0 O D:HOH401 2.0 97.6 1.0 O D:HOH407 2.3 96.7 1.0 NE2 D:HIS220 2.6 100.7 1.0 CD2 D:HIS216 2.9 97.8 1.0 O D:HOH408 3.0 85.5 1.0 CE1 D:HIS216 3.1 99.9 1.0 CD2 D:HIS220 3.3 95.7 1.0 CE1 D:HIS220 3.5 101.6 1.0 CG D:HIS216 4.1 95.1 1.0 ND1 D:HIS216 4.2 96.5 1.0 CG D:HIS220 4.4 94.2 1.0 ND1 D:HIS220 4.4 98.0 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