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

The structure of Structure of Alistipes Sp. 3-Keto-Beta-Glucopyranoside-1,2-Lyase AL1, PDB code: 8tcd 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)	46.39 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.574, 112.608, 209.335, 90, 90, 90
R / Rfree (%)	19.1 / 22.8

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

Cobalt binding site 1 out of 4 in the Structure of 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 Alistipes Sp. 3-Keto-Beta-Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:57.4 occ:0.84 OD2 B:ASP211 2.4 25.2 1.0 ND1 B:HIS237 2.6 15.1 1.0 NE2 B:HIS178 2.6 15.1 1.0 O B:HOH527 3.0 28.7 1.0 CG B:ASP211 3.5 21.0 1.0 CG B:HIS237 3.5 15.5 1.0 CE1 B:HIS178 3.6 17.1 1.0 CE1 B:HIS237 3.6 16.0 1.0 CD2 B:HIS178 3.6 15.0 1.0 CB B:HIS237 3.7 15.5 1.0 O3 B:GOL402 3.8 36.6 1.0 CG B:GLU270 3.9 26.6 1.0 CB B:ASP211 4.0 17.6 1.0 CD B:GLU270 4.0 30.6 1.0 C3 B:GOL402 4.1 38.2 1.0 CB B:GLU270 4.1 21.7 1.0 CD B:LYS239 4.3 21.7 1.0 OE1 B:GLU270 4.3 30.9 1.0 OE2 B:GLU270 4.4 33.0 1.0 CD1 B:TRP214 4.4 20.5 1.0 OD1 B:ASP211 4.6 17.9 1.0 NE1 B:TRP214 4.6 23.0 1.0 NE2 B:HIS237 4.7 15.5 1.0 ND1 B:HIS178 4.7 17.3 1.0 CD2 B:HIS237 4.7 14.4 1.0 OE2 B:GLU272 4.7 31.3 1.0 CG B:HIS178 4.7 14.9 1.0 CB B:LYS239 4.9 17.7 1.0

Cobalt binding site 2 out of 4 in the Structure of 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 Alistipes Sp. 3-Keto-Beta-Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co401 b:51.4 occ:0.80 OD2 C:ASP211 2.4 17.1 1.0 ND1 C:HIS237 2.5 15.4 1.0 NE2 C:HIS178 2.6 15.9 1.0 O C:HOH549 2.9 19.8 1.0 CE1 C:HIS178 3.5 15.7 1.0 CG C:HIS237 3.5 14.8 1.0 CD2 C:HIS178 3.5 17.3 1.0 CG C:ASP211 3.5 16.8 1.0 CE1 C:HIS237 3.5 16.5 1.0 CB C:HIS237 3.7 15.3 1.0 CD C:GLU270 3.7 25.8 1.0 O1 C:GOL402 3.8 24.4 1.0 CG C:GLU270 3.9 22.4 1.0 CB C:ASP211 3.9 17.0 1.0 OE1 C:GLU270 3.9 22.9 1.0 C1 C:GOL402 4.0 26.6 1.0 OE2 C:GLU270 4.0 22.2 1.0 CB C:GLU270 4.0 20.6 1.0 CD C:LYS239 4.2 14.3 1.0 NE1 C:TRP214 4.3 18.8 1.0 CD1 C:TRP214 4.4 19.5 1.0 ND1 C:HIS178 4.6 15.7 1.0 CD2 C:HIS237 4.6 15.2 1.0 NE2 C:HIS237 4.6 16.6 1.0 OD1 C:ASP211 4.6 15.3 1.0 CG C:HIS178 4.6 15.0 1.0 OE2 C:GLU272 4.8 21.2 1.0 CB C:LYS239 4.8 15.8 1.0

Cobalt binding site 3 out of 4 in the Structure of 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 Alistipes Sp. 3-Keto-Beta-Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co401 b:52.2 occ:0.83 OD2 D:ASP211 2.3 20.2 1.0 NE2 D:HIS178 2.5 16.5 1.0 ND1 D:HIS237 2.6 15.1 1.0 O D:HOH598 2.6 21.4 1.0 CE1 D:HIS178 3.3 17.8 1.0 CG D:ASP211 3.4 17.0 1.0 CD2 D:HIS178 3.5 17.9 1.0 CG D:HIS237 3.5 15.8 1.0 CE1 D:HIS237 3.6 16.1 1.0 CB D:HIS237 3.7 16.5 1.0 CD D:GLU270 3.7 22.4 1.0 CG D:GLU270 3.8 21.2 1.0 CB D:ASP211 3.9 15.1 1.0 O3 D:GOL402 3.9 27.5 1.0 OE1 D:GLU270 4.0 21.3 1.0 OE2 D:GLU270 4.0 22.0 1.0 CB D:GLU270 4.1 19.2 1.0 CD D:LYS239 4.1 18.8 1.0 C3 D:GOL402 4.2 27.9 1.0 NE1 D:TRP214 4.3 20.7 1.0 CD1 D:TRP214 4.3 19.1 1.0 ND1 D:HIS178 4.5 17.0 1.0 OD1 D:ASP211 4.5 15.6 1.0 CG D:HIS178 4.6 16.1 1.0 CD2 D:HIS237 4.7 15.6 1.0 NE2 D:HIS237 4.7 15.3 1.0 CB D:LYS239 4.7 16.0 1.0 OE2 D:GLU272 4.9 23.1 1.0 CG D:LYS239 5.0 17.4 1.0 CA D:ASP211 5.0 15.4 1.0

Cobalt binding site 4 out of 4 in the Structure of 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 Alistipes Sp. 3-Keto-Beta-Glucopyranoside-1,2-Lyase AL1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:62.4 occ:0.85 OD2 A:ASP211 2.4 20.5 1.0 ND1 A:HIS237 2.6 15.3 1.0 O A:HOH611 2.7 32.7 1.0 NE2 A:HIS178 3.0 19.2 1.0 CE1 A:HIS237 3.5 15.5 1.0 CD A:GLU270 3.5 26.8 1.0 C3 A:GOL402 3.5 43.8 1.0 CG A:ASP211 3.6 18.1 1.0 CG A:HIS237 3.6 15.7 1.0 CG A:GLU270 3.7 23.5 1.0 O3 A:GOL402 3.7 46.3 1.0 CE1 A:HIS178 3.7 20.1 1.0 OE2 A:GLU270 3.8 29.9 1.0 CD A:LYS239 3.8 23.4 1.0 OE1 A:GLU270 3.8 25.9 1.0 CB A:GLU270 3.8 21.8 1.0 CB A:HIS237 3.9 16.2 1.0 CD2 A:HIS178 4.0 18.2 1.0 OD1 A:ASP211 4.4 19.0 1.0 O A:HOH551 4.4 32.3 1.0 CE A:LYS239 4.5 25.7 1.0 CB A:LYS239 4.5 19.4 1.0 CB A:ASP211 4.5 16.3 1.0 CG A:LYS239 4.6 21.2 1.0 NE2 A:HIS237 4.6 14.9 1.0 CD1 A:TRP214 4.7 19.0 1.0 CD2 A:HIS237 4.7 14.4 1.0 NE1 A:TRP214 4.8 19.7 1.0 OE2 A:GLU272 4.8 33.9 1.0 C2 A:GOL402 4.9 45.2 1.0 ND1 A:HIS178 4.9 20.5 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.
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