Chlorine in PDB 4yzx: C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid

All present enzymatic activity of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid:
4.2.2.2;

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid, PDB code: 4yzx was solved by P.M.Alahuhta, V.V.Lunin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.58 / 1.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.334, 36.352, 100.106, 90.00, 132.67, 90.00
R / Rfree (%)	11 / 15.6

The structure of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Chlorine atom in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid (pdb code 4yzx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid, PDB code: 4yzx:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl210 b:16.4 occ:0.77 O A:HOH369 2.9 29.6 0.7 OG A:SER156 2.9 25.2 0.5 ND2 A:ASN107 3.1 15.3 1.0 NZ A:LYS130 3.2 17.1 1.0 O A:HOH341 3.2 34.2 0.8 CB A:SER156 3.5 17.4 0.5 CA A:GLY129 3.5 11.3 1.0 CB A:SER156 3.7 11.7 0.5 C A:GLY129 3.7 10.0 1.0 CG A:LYS130 3.8 12.7 1.0 CA A:ASN107 3.9 10.9 1.0 O A:GLY129 4.1 10.5 1.0 CG A:ASN107 4.1 14.6 1.0 N A:LYS130 4.1 9.5 1.0 CE A:LYS130 4.2 16.0 1.0 OG A:SER156 4.2 15.1 0.5 C A:ASN107 4.3 10.0 1.0 O A:ASN107 4.3 10.8 1.0 O A:ALA106 4.4 14.1 1.0 CD A:LYS130 4.4 13.7 1.0 CB A:ASN107 4.5 13.2 1.0 O A:HOH398 4.6 29.8 0.7 C1 A:ADA211 4.6 23.9 1.0 O5 A:ADA211 4.7 18.8 1.0 CB A:LYS130 4.8 11.8 1.0 O A:HOH383 4.8 16.9 0.9 N A:GLY129 4.8 9.7 1.0 CA A:SER156 4.8 13.1 0.5 O A:HOH400 4.9 21.0 0.7 O1 A:ADA211 4.9 27.3 1.0 N A:SER156 4.9 12.4 0.5 CA A:SER156 5.0 12.8 0.5

Chlorine binding site 2 out of 2 in the C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of C. Bescii Family 3 Pectate Lyase Double Mutant K108A/D107N in Complex with Trigalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl208 b:14.9 occ:0.97 OG B:SER156 3.0 20.1 0.5 O B:HOH344 3.0 19.7 0.5 ND2 B:ASN107 3.1 16.5 1.0 NZ B:LYS130 3.2 14.8 1.0 O B:HOH314 3.2 23.6 0.6 O B:HOH459 3.3 27.4 0.6 O1 B:GTR212 3.5 23.1 0.3 CB B:SER156 3.5 16.5 0.5 CA B:GLY129 3.6 9.2 1.0 CB B:SER156 3.6 10.9 0.5 C B:GLY129 3.7 9.5 1.0 CG B:LYS130 3.9 10.9 1.0 CA B:ASN107 3.9 10.3 1.0 O B:GLY129 4.1 10.7 1.0 N B:LYS130 4.1 8.6 1.0 OG B:SER156 4.1 15.8 0.5 CG B:ASN107 4.2 16.0 1.0 C B:ASN107 4.3 9.5 1.0 CE B:LYS130 4.3 13.7 1.0 O B:ASN107 4.3 10.6 1.0 O B:ALA106 4.4 12.4 1.0 CD B:LYS130 4.4 12.1 1.0 CB B:ASN107 4.5 12.3 1.0 C1 B:ADA209 4.5 14.1 0.7 O5 B:ADA209 4.6 14.8 0.7 C1 B:GTR212 4.7 25.8 0.3 O5 B:GTR212 4.7 28.1 0.3 CB B:LYS130 4.7 10.8 1.0 O1 B:ADA209 4.7 17.0 0.7 O B:HOH379 4.8 15.4 1.0 O B:HOH425 4.8 16.7 0.5 CA B:SER156 4.8 11.6 0.5 N B:GLY129 4.8 9.1 1.0 CA B:SER156 4.9 11.3 0.5 N B:SER156 4.9 10.2 0.5 N B:ASN107 4.9 10.3 1.0 O B:HOH418 5.0 28.3 1.0 CA B:LYS130 5.0 9.0 1.0

M.Alahuhta, L.E.Taylor, R.Brunecky, D.W.Sammond, W.Michener, M.W.Adams, M.E.Himmel, Y.J.Bomble, V.Lunin. The Catalytic Mechanism and Unique Low pH Optimum of Caldicellulosiruptor Bescii Family 3 Pectate Lyase. Acta Crystallogr.,Sect.D V. 71 1946 2015.
ISSN: ESSN 1399-0047
PubMed: 26327384
DOI: 10.1107/S1399004715013760