Chlorine in PDB 6f2p: Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution

All present enzymatic activity of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution:
4.2.2.12;

The structure of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution, PDB code: 6f2p was solved by L.Lo Leggio, A.Kadziola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.05 / 2.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.610, 100.610, 324.830, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.3

The structure of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution also contains other interesting chemical elements:

Calcium

(Ca)

9 atoms

The binding sites of Chlorine atom in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution (pdb code 6f2p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution, PDB code: 6f2p:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1110 b:24.2 occ:1.00 O6 A:BTB1114 3.4 54.0 1.0 NZ A:LYS50 3.4 19.7 1.0 O A:HOH1397 3.5 34.8 1.0 CD A:LYS50 3.7 20.2 1.0 O A:HOH1281 3.9 32.1 1.0 CG A:LYS50 3.9 18.0 1.0 CE A:LYS50 4.0 28.0 1.0 CB A:LYS50 4.1 19.2 1.0 O A:MET48 4.3 17.6 1.0 N A:LYS50 4.8 18.9 1.0 C6 A:BTB1114 4.8 56.5 1.0

Chlorine binding site 2 out of 4 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1111 b:39.6 occ:1.00 O A:HOH1543 2.9 25.2 1.0 CE A:LYS794 3.6 33.0 1.0 CG1 A:VAL784 3.6 25.6 1.0 NZ A:LYS794 3.6 30.7 1.0 CD A:LYS794 3.6 30.2 1.0 CB A:VAL784 4.0 26.1 1.0 CG2 A:VAL784 4.3 26.7 1.0 CG A:LYS794 4.9 31.1 1.0

Chlorine binding site 3 out of 4 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1112 b:27.9 occ:1.00 N A:ASP60 3.2 22.3 1.0 O A:HOH1335 3.2 17.1 1.0 O A:HOH1638 3.3 32.1 1.0 N A:ASN59 3.3 24.5 1.0 CB A:ASP60 3.6 21.9 1.0 CG A:ASP60 3.7 23.1 1.0 OD1 A:ASP60 3.8 26.3 1.0 CA A:ASN59 3.9 24.4 1.0 CB A:ASN59 3.9 22.1 1.0 CB A:TRP58 3.9 19.9 1.0 O A:HOH1410 3.9 35.9 1.0 C A:ASN59 3.9 25.6 1.0 CA A:ASP60 4.0 22.0 1.0 CD1 A:TRP58 4.1 19.9 1.0 C A:TRP58 4.1 24.3 1.0 OD2 A:ASP60 4.2 29.6 1.0 CA A:TRP58 4.3 20.4 1.0 CB A:SER47 4.4 19.2 1.0 CG A:TRP58 4.4 20.3 1.0 OG A:SER47 4.6 25.2 1.0 O A:SER47 4.6 21.8 1.0

Chlorine binding site 4 out of 4 in the Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Paenibacillus Xanthan Lyase to 2.6 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1113 b:67.9 occ:1.00 O A:HOH1618 3.2 26.0 1.0 N A:ALA169 3.6 19.7 1.0 O A:HOH1505 3.6 35.8 1.0 O A:THR167 3.9 20.9 1.0 N A:ASN170 3.9 19.5 1.0 ND2 A:ASN170 4.1 23.8 1.0 CB A:ALA169 4.2 20.5 1.0 CG A:ASN170 4.2 23.9 1.0 CA A:ALA169 4.3 24.3 1.0 C A:GLY168 4.3 19.3 1.0 CA A:GLY168 4.4 20.4 1.0 OD1 A:ASN170 4.5 27.2 1.0 C A:ALA169 4.6 25.3 1.0 C A:THR167 4.7 22.8 1.0 CB A:ASN170 4.7 21.9 1.0 N A:GLY168 4.9 21.7 1.0 CE1 A:TYR229 4.9 39.2 1.0 O A:HOH1560 4.9 14.7 1.0 CA A:ASN170 5.0 20.9 1.0 OG1 A:THR167 5.0 23.6 1.0

P.F.Jensen, A.Kadziola, G.Comamala, D.R.Segura, L.Anderson, J.N.Poulsen, K.K.Rasmussen, S.Agarwal, R.K.Sainathan, R.N.Monrad, A.Svendsen, J.E.Nielsen, L.Lo Leggio, K.D.Rand. Structure and Dynamics of A Promiscuous Xanthan Lyase From Paenibacillus Nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol V. 26 191 2019.
ISSN: ESSN 2451-9448
PubMed: 30503284
DOI: 10.1016/J.CHEMBIOL.2018.10.016