Calcium in PDB 4peu: Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound

The structure of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound, PDB code: 4peu was solved by D.W.Close, S.D'angelo, A.R.M.Bradbury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.80 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.700, 123.429, 34.530, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 17.1

The binding sites of Calcium atom in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound (pdb code 4peu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound, PDB code: 4peu:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:15.0 occ:1.00 O A:HOH677 2.4 13.0 1.0 OD1 A:ASP247 2.4 15.6 1.0 OD2 A:ASP244 2.4 15.8 1.0 OD2 A:ASP243 2.4 23.8 1.0 O A:HOH701 2.4 21.6 1.0 OD1 A:ASP215 2.5 11.2 1.0 OD2 A:ASP215 2.5 15.7 1.0 CG A:ASP215 2.8 9.7 1.0 HZ2 A:LYS269 3.3 59.6 1.0 HB2 A:ASP247 3.4 12.9 1.0 CG A:ASP243 3.4 18.9 1.0 CG A:ASP247 3.4 16.1 1.0 HZ3 A:LYS218 3.5 36.6 1.0 CG A:ASP244 3.5 16.1 1.0 HB2 A:ASP244 3.6 14.9 1.0 H A:ASP244 3.7 11.9 1.0 HD2 A:LYS269 3.8 23.3 1.0 HB3 A:ASP243 3.8 15.7 1.0 CB A:ASP247 3.8 10.8 1.0 HB3 A:ASP247 4.1 12.9 1.0 CB A:ASP244 4.1 12.4 1.0 O A:HOH737 4.1 26.4 1.0 OD1 A:ASP243 4.2 19.6 1.0 NZ A:LYS269 4.2 49.6 1.0 CB A:ASP243 4.2 13.1 1.0 O A:HOH894 4.3 48.5 1.0 CB A:ASP215 4.3 10.4 1.0 NZ A:LYS218 4.3 30.5 1.0 N A:ASP244 4.4 9.9 1.0 OD1 A:ASP244 4.4 12.4 1.0 O A:HOH672 4.5 12.2 1.0 OD2 A:ASP247 4.5 15.9 1.0 HZ1 A:LYS218 4.6 36.6 1.0 HE3 A:LYS269 4.6 54.5 1.0 HZ3 A:LYS269 4.6 59.6 1.0 HZ1 A:LYS269 4.6 59.6 1.0 HZ2 A:LYS218 4.7 36.6 1.0 CD A:LYS269 4.7 19.4 1.0 HB3 A:ASP215 4.7 12.5 1.0 O A:HOH756 4.7 36.5 1.0 HB2 A:ASP215 4.7 12.5 1.0 HB2 A:ASP243 4.7 15.7 1.0 CE A:LYS269 4.8 45.4 1.0 HD2 A:LYS218 4.8 21.3 1.0 O A:HOH861 4.9 38.0 1.0 HB3 A:ASP244 4.9 14.9 1.0 CA A:ASP244 4.9 11.8 1.0

Calcium binding site 2 out of 3 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:19.4 occ:0.90 OD2 A:ASP178 2.4 15.9 1.0 OD2 A:ASP154 2.4 14.0 1.0 O A:HOH748 2.4 26.6 1.0 O A:HOH750 2.4 33.1 1.0 O A:HOH667 2.4 26.5 1.0 OD1 A:ASP154 2.6 11.2 1.0 O A:HOH768 2.7 34.6 1.0 CG A:ASP154 2.8 15.5 1.0 CG A:ASP178 3.5 14.1 1.0 HB2 A:ASP178 3.6 13.6 1.0 HB3 A:ASN177 3.6 13.0 1.0 HZ1 A:LYS227 3.7 23.0 1.0 HZ2 A:LYS227 3.8 23.0 1.0 H A:ASP178 4.1 12.3 1.0 CB A:ASP178 4.1 11.3 1.0 O A:HOH611 4.2 44.6 1.0 NZ A:LYS227 4.2 19.1 1.0 CB A:ASP154 4.3 12.1 1.0 O A:HOH814 4.4 29.7 1.0 O A:HOH684 4.4 18.6 1.0 OD1 A:ASP178 4.5 15.1 1.0 CB A:ASN177 4.5 10.8 1.0 O A:HOH687 4.5 17.2 1.0 HE3 A:LYS227 4.6 20.0 1.0 N A:ASP178 4.6 10.3 1.0 HB2 A:ASP154 4.7 14.5 1.0 O A:HOH774 4.7 27.7 1.0 HB3 A:ASP154 4.7 14.5 1.0 HB3 A:ASP178 4.8 13.6 1.0 HB2 A:ASN177 4.8 13.0 1.0 O A:HOH875 4.8 52.2 1.0 HZ3 A:LYS227 4.9 23.0 1.0 CG A:ASN177 4.9 23.3 1.0 H A:ASP154 5.0 11.9 1.0

Calcium binding site 3 out of 3 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Native Form with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:28.4 occ:0.71 O A:HOH548 2.5 24.6 1.0 OD1 A:ASP153 2.5 25.2 1.0 O A:HOH503 2.5 32.5 1.0 OD1 A:ASN177 2.6 24.7 1.0 O A:ARG152 2.6 15.9 1.0 HA A:ASP153 3.3 15.7 1.0 CG A:ASP153 3.4 27.3 1.0 CG A:ASN177 3.6 23.3 1.0 HD22 A:ASN177 3.7 22.8 1.0 C A:ARG152 3.7 13.8 1.0 HD3 A:LYS88 4.0 59.1 1.0 ND2 A:ASN177 4.0 19.0 1.0 HG A:SER176 4.1 28.1 1.0 OD2 A:ASP153 4.1 20.5 1.0 CA A:ASP153 4.1 13.1 1.0 HB3 A:ARG152 4.2 17.6 1.0 HZ1 A:LYS88 4.2 67.9 1.0 HD2 A:LYS88 4.2 59.1 1.0 OG A:SER176 4.3 23.4 1.0 CB A:ASP153 4.3 16.7 1.0 N A:ASP153 4.4 8.6 1.0 O A:HOH554 4.5 21.1 1.0 O A:HOH687 4.5 17.2 1.0 CD A:LYS88 4.6 49.2 1.0 O A:HOH550 4.6 32.9 1.0 O A:HOH611 4.7 44.6 1.0 HB3 A:ASP153 4.7 20.0 1.0 HB2 A:ASN177 4.8 13.0 1.0 HZ3 A:LYS88 4.8 67.9 1.0 CB A:ASN177 4.8 10.8 1.0 CA A:ARG152 4.8 8.9 1.0 CB A:ARG152 4.9 14.6 1.0 NZ A:LYS88 4.9 56.6 1.0 HD21 A:ASN177 4.9 22.8 1.0 HB2 A:ARG152 5.0 17.6 1.0

D.W.Close, S.D'angelo, A.R.Bradbury. A New Family of Beta-Helix Proteins with Similarities to the Polysaccharide Lyases. Acta Crystallogr.,Sect.D V. 70 2583 2014.
ISSN: ESSN 1399-0047
PubMed: 25286843
DOI: 10.1107/S1399004714015934