Zinc in PDB 8a0c: Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp

The structure of Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp, PDB code: 8a0c was solved by J.O.Cifuente, J.Schulze, A.Bethe, V.Didomenico, C.Litschko, I.Budde, L.Eidenberger, H.Thiesler, I.Ramon-Roth, M.Berger, H.Claus, C.Dangelo, A.Marina, R.Gerardy-Schahn, M.Schubert, M.E.Guerin, T.Fiebig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.40 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.97, 164.78, 302.567, 90, 90, 90
R / Rfree (%)	19.7 / 25.6

The binding sites of Zinc atom in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp (pdb code 8a0c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp, PDB code: 8a0c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1209 b:58.4 occ:1.00 OD2 A:ASP386 2.0 35.5 1.0 OD1 A:ASP573 2.0 35.1 1.0 O A:HOH1375 2.1 43.6 1.0 O A:PHE388 2.2 24.3 1.0 O4 A:PO41203 2.3 31.6 1.0 O A:HOH1488 2.3 34.5 1.0 CG A:ASP386 2.9 31.6 1.0 CG A:ASP573 3.1 31.6 1.0 OD1 A:ASP386 3.1 40.4 1.0 HB2 A:ASP389 3.4 35.5 1.0 C A:PHE388 3.4 26.8 1.0 OD2 A:ASP573 3.5 32.1 1.0 HG1 A:THR390 3.5 39.3 1.0 P A:PO41203 3.7 36.1 1.0 HB2 A:PHE388 3.8 41.2 1.0 H A:ASP573 4.0 35.8 1.0 OG1 A:THR390 4.2 32.8 1.0 CA A:PHE388 4.2 30.3 1.0 CB A:ASP386 4.2 20.5 1.0 H A:PHE388 4.3 29.5 1.0 N A:PHE388 4.3 24.6 1.0 CB A:ASP389 4.3 29.6 1.0 OD2 A:ASP578 4.3 30.6 1.0 O A:HOH1439 4.3 30.5 1.0 O2 A:PO41203 4.3 31.7 1.0 O1 A:PO41203 4.3 24.8 1.0 HB3 A:ASP386 4.4 24.6 1.0 CB A:PHE388 4.4 34.3 1.0 CB A:ASP573 4.4 29.1 1.0 HB3 A:ASP573 4.4 34.9 1.0 N A:ASP389 4.4 37.0 1.0 HB3 A:PHE388 4.5 41.2 1.0 HB2 A:ASP386 4.6 24.6 1.0 C A:ASP389 4.6 31.6 1.0 HB A:THR390 4.7 33.3 1.0 CA A:ASP389 4.7 34.3 1.0 HZ1 A:LYS548 4.7 35.8 1.0 O3 A:PO41203 4.7 29.4 1.0 N A:ASP573 4.7 29.8 1.0 H A:ILE387 4.8 25.3 1.0 HB2 A:ASN574 4.8 40.1 1.0 H A:THR390 4.8 36.0 1.0 HB3 A:ASP389 4.8 35.5 1.0 N A:THR390 4.8 30.0 1.0 C A:ILE387 4.8 25.4 1.0 OD2 A:ASP389 4.9 44.1 1.0 CB A:THR390 5.0 27.8 1.0 O A:ASP389 5.0 33.5 1.0

Zinc binding site 2 out of 2 in the Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Capsular Polysaccharide Synthesis Multienzyme in Complex with Cmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1208 b:53.9 occ:1.00 OD2 B:ASP386 2.0 31.4 1.0 OD1 B:ASP573 2.0 42.3 1.0 O1 B:PO41203 2.2 40.3 1.0 O B:HOH1408 2.3 37.4 1.0 O B:PHE388 2.4 34.0 1.0 O B:HOH1386 2.5 36.6 1.0 CG B:ASP386 2.9 29.7 1.0 CG B:ASP573 3.0 34.2 1.0 OD1 B:ASP386 3.2 36.9 1.0 OD2 B:ASP573 3.4 34.1 1.0 P B:PO41203 3.5 37.0 1.0 C B:PHE388 3.5 37.3 1.0 HB2 B:PHE388 3.5 38.9 1.0 HB2 B:ASP389 3.6 64.2 1.0 HG1 B:THR390 3.7 52.6 1.0 O3 B:PO41203 3.8 28.3 1.0 H B:ASP573 4.0 37.7 1.0 H B:PHE388 4.1 40.2 1.0 O4 B:PO41203 4.1 36.3 1.0 OD2 B:ASP578 4.1 28.1 1.0 CA B:PHE388 4.2 36.3 1.0 CB B:PHE388 4.2 32.4 1.0 N B:PHE388 4.2 33.5 1.0 CB B:ASP386 4.3 23.8 1.0 CB B:ASP573 4.3 33.2 1.0 HB3 B:ASP573 4.3 39.8 1.0 HB3 B:ASP386 4.3 28.5 1.0 HB3 B:PHE388 4.4 38.9 1.0 HZ1 B:LYS548 4.4 39.7 1.0 H B:ASN574 4.4 39.5 1.0 OG1 B:THR390 4.4 43.9 1.0 CB B:ASP389 4.5 53.5 1.0 HB2 B:ASN574 4.6 37.0 1.0 N B:ASP389 4.6 40.2 1.0 H B:ILE387 4.6 42.5 1.0 HB2 B:ASP386 4.6 28.5 1.0 O2 B:PO41203 4.7 29.4 1.0 N B:ASP573 4.7 31.4 1.0 CA B:ASP389 4.9 39.6 1.0 HB2 B:ASP573 5.0 39.8 1.0 N B:ASN574 5.0 33.0 1.0 C B:ILE387 5.0 33.2 1.0

J.O.Cifuente, J.Schulze, A.Bethe, V.Didomenico, C.Litschko, I.Budde, L.Eidenberger, H.Thiesler, I.Ramon-Roth, M.Berger, H.Claus, C.Dangelo, A.Marina, R.Gerardy-Schahn, M.Schubert, M.E.Guerin, T.Fiebig. A Multi-Enzyme Machine Polymerizes the Haemophilus Influenzae Type B Capsule Nat.Chem.Biol. 2023.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-023-01324-3