Zinc in PDB 5uam: Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase.

The structure of Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase., PDB code: 5uam was solved by T.S.Ulaganathan, M.T.Boniecki, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.20 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	174.260, 72.110, 109.510, 90.00, 122.50, 90.00
R / Rfree (%)	13.4 / 14.3

The structure of Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase. also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase. (pdb code 5uam). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase., PDB code: 5uam:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:20.8 occ:1.00 NE2 A:HIS264 2.0 18.1 1.0 NE2 A:HIS278 2.1 23.7 1.0 ND1 A:HIS208 2.1 19.1 1.0 SG A:CYS266 2.3 22.0 1.0 CE1 A:HIS208 3.0 18.5 1.0 CD2 A:HIS264 3.0 17.9 1.0 CD2 A:HIS278 3.0 24.4 1.0 HA A:CYS266 3.0 27.0 1.0 HE1 A:HIS208 3.1 22.2 1.0 CE1 A:HIS278 3.1 22.8 1.0 CE1 A:HIS264 3.1 19.9 1.0 HD2 A:HIS264 3.1 21.5 1.0 HB2 A:CYS266 3.1 25.5 1.0 HB3 A:HIS208 3.1 22.9 1.0 CG A:HIS208 3.1 20.5 1.0 HD2 A:HIS278 3.2 29.4 1.0 CB A:CYS266 3.2 21.2 1.0 HE1 A:HIS278 3.3 27.4 1.0 HE1 A:HIS264 3.3 24.0 1.0 H12 A:EDO507 3.5 59.3 1.0 CB A:HIS208 3.5 19.0 1.0 CA A:CYS266 3.6 22.5 1.0 HB2 A:HIS208 3.7 22.9 1.0 O2 A:EDO507 3.9 42.7 1.0 HB3 A:CYS266 4.1 25.5 1.0 NE2 A:HIS208 4.1 21.7 1.0 CG A:HIS264 4.1 17.9 1.0 ND1 A:HIS264 4.2 18.4 1.0 CG A:HIS278 4.2 25.4 1.0 ND1 A:HIS278 4.2 24.3 1.0 CD2 A:HIS208 4.2 19.8 1.0 H22 A:EDO507 4.3 55.0 1.0 HO2 A:EDO507 4.3 51.2 1.0 C1 A:EDO507 4.3 49.4 1.0 O A:HOH639 4.4 25.1 1.0 C2 A:EDO507 4.4 45.8 1.0 O A:THR279 4.5 24.3 1.0 C A:CYS266 4.5 24.7 1.0 H A:TRP267 4.6 27.4 1.0 HE A:ARG209 4.7 28.1 1.0 N A:CYS266 4.8 21.6 1.0 O1 A:EDO507 4.8 50.5 1.0 HE2 A:HIS208 4.9 26.0 1.0 N A:TRP267 4.9 22.8 1.0 HB3 A:SER244 5.0 20.2 1.0 HD1 A:HIS264 5.0 22.1 1.0 HD1 A:HIS278 5.0 29.1 1.0 HG3 A:ARG209 5.0 24.5 1.0 CA A:HIS208 5.0 16.2 1.0

Zinc binding site 2 out of 2 in the Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A New Family of Polysaccharide Lyase PL25-Ulvanlyase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:20.4 occ:1.00 NE2 B:HIS264 2.0 21.1 1.0 NE2 B:HIS278 2.0 21.8 1.0 ND1 B:HIS208 2.1 22.4 1.0 SG B:CYS266 2.3 21.2 1.0 CE1 B:HIS208 3.0 20.3 1.0 CD2 B:HIS264 3.0 21.5 1.0 CD2 B:HIS278 3.0 23.3 1.0 CE1 B:HIS278 3.0 26.8 1.0 HA B:CYS266 3.0 26.7 1.0 HE1 B:HIS208 3.1 24.4 1.0 CE1 B:HIS264 3.1 20.5 1.0 HD2 B:HIS264 3.1 25.8 1.0 HB3 B:HIS208 3.1 23.1 1.0 HB2 B:CYS266 3.2 28.4 1.0 CG B:HIS208 3.2 19.5 1.0 HD2 B:HIS278 3.2 27.9 1.0 CB B:CYS266 3.2 23.6 1.0 HE1 B:HIS278 3.2 32.2 1.0 HE1 B:HIS264 3.3 24.7 1.0 CB B:HIS208 3.6 19.3 1.0 CA B:CYS266 3.6 22.2 1.0 O B:HOH1030 3.7 36.5 1.0 HB2 B:HIS208 3.7 23.1 1.0 HB3 B:CYS266 4.1 28.4 1.0 NE2 B:HIS208 4.1 22.2 1.0 CG B:HIS264 4.1 17.6 1.0 ND1 B:HIS278 4.1 26.3 1.0 ND1 B:HIS264 4.1 18.2 1.0 CG B:HIS278 4.2 27.6 1.0 CD2 B:HIS208 4.2 20.8 1.0 O B:HOH640 4.5 25.2 1.0 O B:THR279 4.5 23.6 1.0 C B:CYS266 4.5 26.2 1.0 H B:TRP267 4.7 29.7 1.0 HE B:ARG209 4.7 27.1 1.0 N B:CYS266 4.7 22.8 1.0 HE2 B:HIS208 4.9 26.7 1.0 HB3 B:SER244 4.9 21.0 1.0 N B:TRP267 4.9 24.7 1.0 HD1 B:HIS278 4.9 31.5 1.0 HD1 B:HIS264 4.9 21.9 1.0 HG3 B:ARG209 5.0 23.8 1.0 OG B:SER244 5.0 17.1 1.0

T.Ulaganathan, M.T.Boniecki, E.Foran, V.Buravenkov, N.Mizrachi, E.Banin, W.Helbert, M.Cygler. New Ulvan-Degrading Polysaccharide Lyase Family: Structure and Catalytic Mechanism Suggests Convergent Evolution of Active Site Architecture. Acs Chem. Biol. V. 12 1269 2017.
ISSN: ESSN 1554-8937
PubMed: 28290654
DOI: 10.1021/ACSCHEMBIO.7B00126