Calcium in PDB 2o04: Pectate Lyase Bound to Hexasaccharide Compound II

All present enzymatic activity of Pectate Lyase Bound to Hexasaccharide Compound II:
4.2.2.2;

The structure of Pectate Lyase Bound to Hexasaccharide Compound II, PDB code: 2o04 was solved by R.W.Pickersgill, A.Seyedarabi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.31 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.619, 68.879, 59.459, 90.00, 113.14, 90.00
R / Rfree (%)	16.6 / 20.1

The binding sites of Calcium atom in the Pectate Lyase Bound to Hexasaccharide Compound II (pdb code 2o04). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Pectate Lyase Bound to Hexasaccharide Compound II, PDB code: 2o04:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pectate Lyase Bound to Hexasaccharide Compound II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pectate Lyase Bound to Hexasaccharide Compound II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:28.9 occ:1.00 O6A A:ADA401 2.3 28.8 1.0 O A:HOH563 2.4 23.3 1.0 OD1 A:ASN180 2.6 14.4 1.0 O A:HOH564 2.6 42.2 1.0 OD2 A:ASP173 2.6 19.9 1.0 O3 A:ADA400 2.6 24.1 1.0 O5 A:ADA401 2.7 28.0 1.0 C6 A:ADA401 3.2 29.1 1.0 CG A:ASP173 3.4 19.7 1.0 CG A:ASN180 3.5 12.2 1.0 C5 A:ADA401 3.5 28.3 1.0 OD1 A:ASP173 3.6 20.1 1.0 C1 A:ADA401 3.8 27.4 1.0 ND2 A:ASN180 3.8 13.7 1.0 C3 A:ADA400 3.8 24.4 1.0 O4 A:ADA400 4.1 25.5 1.0 C2 A:ADA400 4.1 24.7 1.0 O2 A:ADA400 4.3 24.2 1.0 O6B A:ADA401 4.4 29.4 1.0 NZ A:LYS247 4.4 15.9 1.0 O A:HOH844 4.4 50.7 1.0 O A:HOH491 4.4 26.2 1.0 O A:HOH666 4.4 43.1 1.0 C4 A:ADA400 4.6 24.5 1.0 C4 A:ADA401 4.8 28.6 1.0 CB A:ASN180 4.8 10.1 1.0 O4 A:ADA401 4.8 28.3 1.0 CB A:ASP173 4.8 19.2 1.0

Calcium binding site 2 out of 3 in the Pectate Lyase Bound to Hexasaccharide Compound II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pectate Lyase Bound to Hexasaccharide Compound II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:14.5 occ:1.00 OD2 A:ASP223 2.3 15.1 1.0 OD2 A:ASP227 2.3 13.2 1.0 OD1 A:ASP184 2.3 13.5 1.0 O A:HOH882 2.4 26.2 1.0 O A:HOH454 2.4 18.1 1.0 O A:HOH936 2.5 34.1 1.0 OD2 A:ASP184 2.6 11.8 1.0 CG A:ASP184 2.8 10.1 1.0 CG A:ASP227 3.5 9.3 1.0 CG A:ASP223 3.6 12.7 1.0 CA A:CA404 3.9 24.2 1.0 CB A:ASP227 4.0 7.6 1.0 O A:HOH499 4.1 29.3 1.0 N A:GLY224 4.3 8.3 1.0 CB A:ASP184 4.3 8.1 1.0 CB A:ASP223 4.4 9.4 1.0 O A:HOH891 4.4 26.8 1.0 OD1 A:ASP223 4.4 20.1 1.0 OD1 A:ASP227 4.5 8.7 1.0 O A:HOH714 4.5 18.1 1.0 CA A:GLY224 4.6 8.1 1.0 O A:HOH523 4.7 38.0 1.0 OG1 A:THR187 4.9 9.3 1.0 N A:ASP184 5.0 7.5 1.0

Calcium binding site 3 out of 3 in the Pectate Lyase Bound to Hexasaccharide Compound II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pectate Lyase Bound to Hexasaccharide Compound II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:24.2 occ:1.00 OD1 A:ASP223 2.3 20.1 1.0 O6B A:ADA401 2.5 29.4 1.0 O A:HOH936 2.5 34.1 1.0 OD2 A:ASP223 2.6 15.1 1.0 O A:HOH666 2.7 43.1 1.0 CG A:ASP223 2.8 12.7 1.0 O A:HOH523 2.9 38.0 1.0 O A:HOH499 3.1 29.3 1.0 C6 A:ADA401 3.4 29.1 1.0 O4 A:ADA401 3.8 28.3 1.0 CA A:CA402 3.9 14.5 1.0 O6A A:ADA401 4.0 28.8 1.0 C4 A:ADA401 4.2 28.6 1.0 CB A:ASP223 4.3 9.4 1.0 O A:HOH891 4.4 26.8 1.0 C5 A:ADA401 4.4 28.3 1.0 O A:SER181 4.6 9.4 1.0 O A:HOH882 4.7 26.2 1.0 NZ A:LYS247 4.9 15.9 1.0 O A:HOH618 4.9 10.5 1.0

A.Seyedarabi, T.T.To, S.Ali, S.Hussain, M.Fries, R.Madsen, M.H.Clausen, S.Teixteira, K.Brocklehurst, R.W.Pickersgill. Structural Insights Into Substrate Specificity and the Anti Beta-Elimination Mechanism of Pectate Lyase. Biochemistry V. 49 539 2010.
ISSN: ISSN 0006-2960
PubMed: 20000851
DOI: 10.1021/BI901503G