Chlorine in PDB 3vdh: Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14

The structure of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, PDB code: 3vdh was solved by P.J.Stogios, E.Evdokimova, O.Egorova, V.Yim, A.Joachimiak, A.M.Edwards, A.Savchenko, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.35 / 1.62
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.908, 85.254, 74.556, 90.00, 109.15, 90.00
R / Rfree (%)	15.1 / 19.9

The binding sites of Chlorine atom in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14 (pdb code 3vdh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14, PDB code: 3vdh:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:26.7 occ:1.00 O A:HOH960 2.4 22.5 1.0 O A:HOH954 2.4 24.6 1.0 O A:HOH962 2.4 26.4 1.0 O A:HOH955 2.4 18.1 1.0 O A:HOH959 2.5 21.9 1.0 O A:HOH976 2.6 38.0 1.0 O A:HOH975 3.0 45.1 1.0 O A:HOH958 3.6 36.3 1.0 O A:HOH794 4.0 55.5 1.0 O A:HOH555 4.1 19.6 1.0 O A:HOH510 4.1 15.2 1.0 O A:HOH565 4.2 18.4 1.0 OE1 A:GLU162 4.3 13.8 1.0 OE1 A:GLU280 4.5 15.1 1.0 OD1 A:ASP288 4.5 31.5 1.0 O A:HOH735 4.6 16.2 1.0 OE2 A:GLU162 4.7 15.3 1.0 OH A:TYR240 4.7 14.5 1.0 O A:HOH836 4.8 45.2 1.0 CD A:GLU162 4.9 15.3 1.0 O A:HOH595 5.0 20.1 1.0 CZ A:TYR240 5.0 15.8 1.0 CE1 A:TYR240 5.0 12.0 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:28.2 occ:1.00 O A:HOH830 2.3 25.9 1.0 O A:HOH832 2.4 38.0 1.0 O B:HOH807 2.4 21.6 1.0 O A:HOH831 2.5 41.6 1.0 O A:HOH873 2.5 39.4 1.0 OG A:SER119 2.5 29.3 1.0 O B:HOH812 3.0 56.6 1.0 CB A:SER119 3.7 24.6 1.0 O A:HOH698 4.0 26.0 1.0 N A:SER119 4.2 16.9 1.0 O A:HOH612 4.2 31.9 1.0 O A:HOH779 4.4 47.3 1.0 CA A:SER119 4.5 19.5 1.0 CA A:GLY34 4.5 21.7 1.0 O A:SER119 4.5 32.8 1.0 OE1 B:GLU286 4.6 21.0 1.0 OD1 A:ASN33 4.7 22.9 1.0 OE2 B:GLU286 4.8 25.5 1.0 C A:SER119 4.9 19.0 1.0 O B:HOH630 4.9 23.6 1.0 O A:ASN33 5.0 20.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of PBGH5A, A Glycoside Hydrolase Family 5 Enzyme From Prevotella Bryantii B14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:30.5 occ:1.00 O B:HOH918 2.3 29.2 1.0 O B:HOH921 2.3 29.1 1.0 O B:HOH916 2.4 20.1 1.0 O B:HOH920 2.4 23.4 1.0 O B:HOH917 2.4 23.5 1.0 O B:HOH919 2.7 41.5 1.0 O B:HOH563 3.7 39.0 1.0 O B:HOH907 3.8 42.7 1.0 O B:HOH685 4.1 23.9 1.0 O B:HOH582 4.2 18.1 1.0 O B:HOH552 4.3 18.3 1.0 OE1 B:GLU162 4.3 17.0 1.0 OD1 B:ASP288 4.5 32.2 1.0 OE1 B:GLU280 4.5 14.7 1.0 O B:HOH684 4.6 46.5 1.0 O B:HOH601 4.7 18.2 1.0 OE2 B:GLU162 4.7 16.4 1.0 O B:HOH799 4.8 26.2 0.5 OH B:TYR240 4.8 16.1 1.0 CE1 B:TYR240 4.9 14.3 1.0 CD B:GLU162 4.9 19.3 1.0 O A:HOH909 5.0 47.3 1.0 CZ B:TYR240 5.0 14.5 1.0

N.Mcgregor, M.Morar, T.H.Fenger, P.Stogios, N.Lenfant, V.Yin, X.Xu, E.Evdokimova, H.Cui, B.Henrissat, A.Savchenko, H.Brumer. Structure-Function Analysis of A Mixed-Linkage Beta-Glucanase/Xyloglucanase From the Key Ruminal Bacteroidetes Prevotella Bryantii B14. J.Biol.Chem. V. 291 1175 2016.
ISSN: ISSN 0021-9258
PubMed: 26507654
DOI: 10.1074/JBC.M115.691659