Cobalt in PDB 8tcs: Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1

The structure of Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1, PDB code: 8tcs was solved by A.C.Lazarski, L.J.Worrall, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.34 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.994, 113.549, 212.442, 90, 90, 90
R / Rfree (%)	17.4 / 20.5

The binding sites of Cobalt atom in the Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1 (pdb code 8tcs). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1, PDB code: 8tcs:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co401 b:65.8 occ:1.00 OD2 D:ASP211 2.0 29.4 1.0 NE2 D:HIS178 2.0 23.8 1.0 ND1 D:HIS237 2.0 24.1 1.0 CE1 D:HIS178 2.9 24.3 1.0 CG D:HIS237 3.0 22.2 1.0 CD2 D:HIS178 3.0 22.1 1.0 CE1 D:HIS237 3.1 25.0 1.0 CG D:ASP211 3.2 25.6 1.0 O D:HOH568 3.2 40.2 1.0 CB D:HIS237 3.3 21.7 1.0 CB D:ASP211 3.7 20.0 1.0 ND1 D:HIS178 4.0 27.1 1.0 CG D:HIS178 4.1 20.8 1.0 NE2 D:HIS237 4.1 21.9 1.0 CD2 D:HIS237 4.1 22.9 1.0 OD1 D:ASP211 4.2 21.0 1.0 CA D:ASP211 4.6 18.0 1.0 CD D:LYS239 4.7 29.3 1.0 CB D:GLU270 4.7 23.9 1.0 CG D:GLU270 4.7 33.8 1.0 CA D:HIS237 4.8 18.6 1.0 CD1 D:TRP214 4.8 29.2 1.0 O D:ASN179 4.9 20.3 1.0 CD D:GLU270 5.0 45.6 1.0

Cobalt binding site 2 out of 4 in the Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:45.0 occ:1.00 O C:HOH673 1.9 42.6 1.0 OD2 C:ASP211 2.0 26.6 1.0 NE2 C:HIS178 2.1 21.9 1.0 ND1 C:HIS237 2.2 21.2 1.0 CE1 C:HIS178 3.0 22.4 1.0 CE1 C:HIS237 3.1 20.9 1.0 CD2 C:HIS178 3.1 20.1 1.0 CG C:ASP211 3.1 21.4 1.0 CG C:HIS237 3.2 19.1 1.0 CB C:HIS237 3.5 18.8 1.0 CB C:ASP211 3.7 18.4 1.0 O C:HOH683 4.1 40.2 1.0 ND1 C:HIS178 4.2 23.3 1.0 CG C:HIS178 4.2 19.2 1.0 OD1 C:ASP211 4.2 18.8 1.0 NE2 C:HIS237 4.3 19.5 1.0 CD2 C:HIS237 4.3 20.1 1.0 CG C:GLU270 4.4 29.7 1.0 CD C:LYS239 4.4 25.6 1.0 CD C:GLU270 4.4 32.9 1.0 CD1 C:TRP214 4.5 24.8 1.0 CB C:GLU270 4.6 24.1 1.0 CA C:ASP211 4.7 16.0 1.0 OE2 C:GLU270 4.7 33.4 1.0 OE1 C:GLU270 4.8 33.5 1.0 O C:ASN179 4.8 17.3 1.0 NE1 C:TRP214 4.9 26.1 1.0 O C:HOH523 4.9 42.1 1.0 CB C:LYS239 5.0 20.3 1.0

Cobalt binding site 3 out of 4 in the Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:42.6 occ:1.00 OD2 A:ASP211 2.0 27.4 1.0 O A:HOH689 2.1 31.5 1.0 NE2 A:HIS178 2.1 21.9 1.0 ND1 A:HIS237 2.2 20.5 1.0 CE1 A:HIS178 3.0 18.8 1.0 CE1 A:HIS237 3.2 22.8 1.0 CD2 A:HIS178 3.2 22.0 1.0 CG A:ASP211 3.2 24.0 1.0 CG A:HIS237 3.2 18.6 1.0 CB A:HIS237 3.6 19.7 1.0 CB A:ASP211 3.8 19.9 1.0 O A:HOH680 4.0 33.4 1.0 ND1 A:HIS178 4.2 20.6 1.0 CG A:HIS178 4.2 18.4 1.0 CG A:GLU270 4.3 29.2 1.0 NE2 A:HIS237 4.3 20.2 1.0 OD1 A:ASP211 4.3 20.2 1.0 CD2 A:HIS237 4.3 20.5 1.0 CD A:LYS239 4.4 22.8 1.0 CD A:GLU270 4.4 36.5 1.0 CD1 A:TRP214 4.4 22.2 1.0 CB A:GLU270 4.5 22.7 1.0 NE1 A:TRP214 4.5 24.8 1.0 OE1 A:GLU270 4.7 31.2 1.0 OE2 A:GLU270 4.7 37.4 1.0 CA A:ASP211 4.8 17.2 1.0 O A:ASN179 4.9 18.1 1.0 CB A:LYS239 5.0 19.4 1.0 O A:HOH506 5.0 40.1 1.0

Cobalt binding site 4 out of 4 in the Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Trehalose Bound Alistipes Sp. 3-Keto-Beta- Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:58.0 occ:1.00 O B:HOH514 1.9 74.2 1.0 OD2 B:ASP211 1.9 29.9 1.0 NE2 B:HIS178 2.0 24.8 1.0 ND1 B:HIS237 2.1 24.0 1.0 CE1 B:HIS178 2.9 22.8 1.0 CG B:HIS237 3.0 20.4 1.0 CD2 B:HIS178 3.1 22.0 1.0 CG B:ASP211 3.1 24.6 1.0 CE1 B:HIS237 3.1 24.3 1.0 CB B:HIS237 3.4 19.8 1.0 OE2 B:GLU270 3.4 64.6 1.0 CB B:ASP211 3.6 21.8 1.0 O B:HOH501 3.8 35.5 1.0 ND1 B:HIS178 4.1 25.7 1.0 CG B:HIS178 4.1 20.1 1.0 OD1 B:ASP211 4.2 20.6 1.0 CD2 B:HIS237 4.2 21.0 1.0 NE2 B:HIS237 4.2 21.0 1.0 CD B:GLU270 4.3 52.6 1.0 CB B:GLU270 4.6 25.3 1.0 CD B:LYS239 4.6 29.9 1.0 CA B:ASP211 4.6 19.9 1.0 CD1 B:TRP214 4.7 26.1 1.0 CG B:GLU270 4.8 34.9 1.0 O B:ASN179 4.8 19.8 1.0 CA B:HIS237 4.8 20.2 1.0 NE1 B:TRP214 5.0 28.1 1.0

S.A.Nasseri, A.C.Lazarski, I.L.Lemmer, C.Y.Zhang, E.Brencher, H.Chen, L.Sim, D.Panwar, L.Betschart, L.J.Worrall, H.Brumer, N.C.J.Strynadka, S.G.Withers. An Alternative Broad-Specificity Pathway For Glycan Breakdown in Bacteria Nature 2024.
ISSN: ESSN 1476-4687