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

The structure of Structure of Glucose Bound Alistipes Sp. 3-Keto-Beta-Glucopyranoside- 1,2-Lyase AL1, PDB code: 8tcr 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)	47.40 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.517, 113.679, 208.58, 90, 90, 90
R / Rfree (%)	18.2 / 22.9

The binding sites of Cobalt atom in the Structure of Glucose Bound Alistipes Sp. 3-Keto-Beta-Glucopyranoside- 1,2-Lyase AL1 (pdb code 8tcr). 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 Glucose Bound Alistipes Sp. 3-Keto-Beta-Glucopyranoside- 1,2-Lyase AL1, PDB code: 8tcr:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Structure of Glucose 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 Glucose Bound Alistipes Sp. 3-Keto-Beta-Glucopyranoside- 1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co404 b:108.0 occ:1.00 ND1 C:HIS237 2.6 30.4 1.0 OD2 C:ASP211 2.7 32.8 1.0 NE2 C:HIS178 3.0 28.7 1.0 O6 C:MLI401 3.1 58.6 1.0 CE1 C:HIS237 3.3 30.6 1.0 CG C:GLU270 3.6 33.4 1.0 CD C:GLU270 3.6 39.5 1.0 O9 C:MLI401 3.6 60.6 1.0 CE1 C:HIS178 3.6 28.8 1.0 CG C:HIS237 3.7 26.6 1.0 OE1 C:GLU270 3.8 42.0 1.0 CG C:ASP211 3.9 31.4 1.0 CB C:GLU270 3.9 29.0 1.0 CD2 C:HIS178 4.0 28.8 1.0 CD C:LYS239 4.0 29.9 1.0 OE2 C:GLU270 4.1 42.2 1.0 CB C:HIS237 4.1 25.5 1.0 C2 C:MLI401 4.3 54.5 1.0 NE2 C:HIS237 4.5 27.4 1.0 C3 C:MLI401 4.6 56.4 1.0 OD1 C:ASP211 4.7 27.2 1.0 CB C:ASP211 4.7 30.2 1.0 CD2 C:HIS237 4.7 28.8 1.0 ND1 C:HIS178 4.7 31.9 1.0 OE1 C:GLU272 4.8 44.5 1.0 CE C:LYS239 4.8 33.8 1.0 CB C:LYS239 4.9 26.1 1.0 C1 C:MLI401 4.9 53.3 1.0 CG C:HIS178 4.9 29.1 1.0 CD1 C:TRP214 4.9 28.8 1.0 CG C:LYS239 5.0 28.8 1.0

Cobalt binding site 2 out of 4 in the Structure of Glucose 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 Glucose 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:96.7 occ:1.00 ND1 B:HIS237 2.6 24.4 1.0 OD2 B:ASP211 2.6 31.6 1.0 NE2 B:HIS178 3.0 30.2 1.0 O3 B:GLC402 3.1 35.3 1.0 CE1 B:HIS237 3.3 27.2 1.0 CG B:GLU270 3.5 36.8 1.0 CD B:GLU270 3.6 40.6 1.0 O4 B:GLC402 3.6 35.1 1.0 CE1 B:HIS178 3.6 30.8 1.0 CG B:HIS237 3.7 26.2 1.0 CG B:ASP211 3.8 27.7 1.0 OE1 B:GLU270 3.8 36.7 1.0 CB B:GLU270 3.9 31.9 1.0 CD2 B:HIS178 3.9 28.2 1.0 CD B:LYS239 4.0 27.3 1.0 OE2 B:GLU270 4.0 37.1 1.0 O B:HOH528 4.0 46.2 1.0 C3 B:GLC402 4.0 39.4 1.0 CB B:HIS237 4.1 25.1 1.0 C4 B:GLC402 4.3 39.5 1.0 OE1 B:GLU272 4.5 37.5 1.0 CB B:ASP211 4.6 26.9 1.0 NE2 B:HIS237 4.6 26.7 1.0 OD1 B:ASP211 4.7 23.3 1.0 ND1 B:HIS178 4.7 30.1 1.0 CD2 B:HIS237 4.8 24.9 1.0 CB B:LYS239 4.8 28.0 1.0 CE B:LYS239 4.8 28.4 1.0 CD1 B:TRP214 4.8 30.4 1.0 CG B:HIS178 4.9 27.7 1.0 CG B:LYS239 4.9 26.8 1.0 NE1 B:TRP214 5.0 28.2 1.0

Cobalt binding site 3 out of 4 in the Structure of Glucose 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 Glucose 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:89.4 occ:1.00 OD2 A:ASP211 2.4 35.2 1.0 ND1 A:HIS237 2.7 30.6 1.0 O A:HOH502 2.8 36.2 1.0 NE2 A:HIS178 2.9 29.6 1.0 O3 A:GLC402 3.3 50.8 1.0 CE1 A:HIS237 3.5 30.6 1.0 CG A:ASP211 3.6 30.2 1.0 CE1 A:HIS178 3.7 28.6 1.0 CD A:GLU270 3.7 43.3 1.0 CG A:HIS237 3.7 27.6 1.0 CD2 A:HIS178 3.8 29.2 1.0 CG A:GLU270 3.8 38.0 1.0 CB A:GLU270 3.9 35.5 1.0 OE2 A:GLU270 3.9 45.1 1.0 CB A:HIS237 4.0 26.5 1.0 O4 A:GLC402 4.0 46.2 1.0 CD A:LYS239 4.0 26.5 1.0 OE1 A:GLU270 4.0 44.4 1.0 CB A:ASP211 4.2 29.8 1.0 C3 A:GLC402 4.4 51.8 1.0 CD1 A:TRP214 4.4 34.4 1.0 NE1 A:TRP214 4.5 33.5 1.0 OE1 A:GLU272 4.5 38.8 1.0 OD1 A:ASP211 4.6 27.8 1.0 C4 A:GLC402 4.6 50.1 1.0 NE2 A:HIS237 4.7 30.6 1.0 CB A:LYS239 4.7 26.8 1.0 ND1 A:HIS178 4.8 29.6 1.0 CD2 A:HIS237 4.8 28.7 1.0 CG A:LYS239 4.8 27.3 1.0 CG A:HIS178 4.8 28.5 1.0 CE A:LYS239 4.9 27.3 1.0

Cobalt binding site 4 out of 4 in the Structure of Glucose 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 Glucose 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:100.2 occ:1.00 OD2 D:ASP211 2.5 42.5 1.0 ND1 D:HIS237 2.7 26.9 1.0 NE2 D:HIS178 2.8 28.3 1.0 O3 D:GLC402 3.2 53.0 1.0 CE1 D:HIS237 3.6 27.1 1.0 CE1 D:HIS178 3.6 30.1 1.0 CG D:ASP211 3.6 34.7 1.0 O4 D:GLC402 3.7 45.7 1.0 CD D:GLU270 3.8 41.1 1.0 CG D:HIS237 3.8 27.0 1.0 CD2 D:HIS178 3.8 28.2 1.0 CG D:GLU270 3.9 35.8 1.0 CD D:LYS239 4.0 30.6 1.0 CB D:HIS237 4.0 26.9 1.0 OE1 D:GLU270 4.0 40.2 1.0 CB D:GLU270 4.1 31.3 1.0 OE2 D:GLU270 4.1 36.0 1.0 C3 D:GLC402 4.2 51.3 1.0 CB D:ASP211 4.3 28.8 1.0 C4 D:GLC402 4.4 52.0 1.0 CD1 D:TRP214 4.6 34.7 1.0 OD1 D:ASP211 4.6 31.5 1.0 OE1 D:GLU272 4.7 41.5 1.0 NE1 D:TRP214 4.7 31.7 1.0 ND1 D:HIS178 4.7 31.5 1.0 NE2 D:HIS237 4.7 28.5 1.0 CE D:LYS239 4.8 33.0 1.0 CG D:HIS178 4.8 28.9 1.0 CB D:LYS239 4.9 26.6 1.0 CD2 D:HIS237 4.9 29.5 1.0 CG D:LYS239 4.9 28.0 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