Zinc in PDB 4b9p: Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome

The structure of Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome, PDB code: 4b9p was solved by O.Yaniv, L.J.W.Shimon, E.A.Bayer, R.Lamed, F.Frolow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.978 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.736, 62.289, 79.274, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 14.99

The structure of Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome (pdb code 4b9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome, PDB code: 4b9p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1168 b:34.0 occ:0.76 NE2 A:HIS14 2.0 25.2 1.0 O A:HOH2024 2.1 49.6 1.0 O A:HOH2023 2.1 56.8 1.0 CE1 A:HIS14 2.9 25.2 1.0 CD2 A:HIS14 3.0 23.8 1.0 ND1 A:HIS14 4.0 24.8 1.0 CG A:HIS14 4.1 21.9 1.0 NH1 A:ARG26 4.3 33.3 1.0 NH2 A:ARG26 4.7 29.2 1.0 CZ A:ARG26 4.8 28.8 1.0

Zinc binding site 2 out of 3 in the Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1169 b:38.6 occ:0.53 NZ A:LYS81 1.9 29.7 0.6 OXT A:PRO166 2.2 30.3 1.0 O A:PRO166 2.7 30.6 1.0 C A:PRO166 2.8 27.9 1.0 CE A:LYS81 3.3 31.7 0.6 CD A:LYS81 3.8 29.6 0.6 CG A:LYS81 4.2 27.1 0.6 CD A:LYS81 4.2 20.7 0.4 CE A:LYS81 4.2 20.4 0.4 CA A:PRO166 4.3 22.1 1.0 O A:GLU165 4.5 25.3 1.0 CG A:LYS81 4.6 20.8 0.4 O A:HOH2214 4.7 53.4 1.0 O A:HOH2212 4.7 49.0 1.0 O A:HOH2188 4.7 46.2 1.0 N A:PRO166 4.8 21.8 1.0 C A:GLU165 4.9 23.6 1.0 CB A:LYS81 5.0 24.0 0.6

Zinc binding site 3 out of 3 in the Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Biomass Sensoring Module From Putative RSGI2 Protein of Clostridium Thermocellum Resemble Family 3 Carbohydrate- Binding Module of Cellulosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1170 b:53.2 occ:0.75 OE2 A:GLU126 1.9 34.6 1.0 O A:HOH2044 2.0 49.8 1.0 OE1 A:GLU19 2.0 36.0 1.0 CD A:GLU19 2.8 36.7 1.0 OE2 A:GLU19 2.9 42.3 1.0 CD A:GLU126 2.9 30.7 1.0 OE1 A:GLU126 3.2 34.5 1.0 O A:HOH2174 3.2 42.3 1.0 O A:HOH2043 3.9 50.5 1.0 CG A:GLU126 4.3 30.0 1.0 CG A:GLU19 4.3 30.9 1.0 CE A:MET130 4.3 22.3 0.6 O A:HOH2176 4.5 45.2 1.0 CG A:MET130 4.6 17.9 0.6 CE A:MET130 4.7 26.0 0.4 CB A:GLU19 4.8 24.3 1.0

O.Yaniv, G.Fichman, I.Borovok, Y.Shoham, E.A.Bayer, R.Lamed, L.J.W.Shimon, F.Frolow. Fine-Structural Variance of Family 3 Carbohydrate-Binding Modules As Extracellular Biomass-Sensing Components of Clostridium Thermocellum Anti-Sigma(I) Factors. Acta Crystallogr.,Sect.D V. 70 522 2014.
ISSN: ISSN 0907-4449
PubMed: 24531486
DOI: 10.1107/S139900471302926X