Calcium in PDB 2o0w: Pectate Lyase Bound to Hexasaccharide Compound IV

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

The structure of Pectate Lyase Bound to Hexasaccharide Compound IV, PDB code: 2o0w 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)	45.27 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.725, 68.956, 59.482, 90.00, 112.70, 90.00
R / Rfree (%)	15.4 / 19.8

The binding sites of Calcium atom in the Pectate Lyase Bound to Hexasaccharide Compound IV (pdb code 2o0w). 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 IV, PDB code: 2o0w:
Jump to Calcium binding site number: 1; 2; 3;

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


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 IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca400 b:15.6 occ:1.00 OD2 A:ASP227 2.3 15.0 1.0 OD2 A:ASP223 2.3 17.3 1.0 OD1 A:ASP184 2.3 13.6 1.0 O A:HOH844 2.3 19.9 1.0 OD2 A:ASP184 2.4 12.7 1.0 CG A:ASP184 2.7 10.3 1.0 O A:HOH451 2.8 17.1 1.0 CG A:ASP227 2.8 10.4 1.0 O A:HOH828 2.8 14.5 1.0 CG A:ASP223 2.8 13.1 1.0 OD1 A:ASP227 2.9 13.8 1.0 OD1 A:ASP223 3.0 18.6 1.0 CA A:CA402 3.4 21.7 1.0 O A:HOH495 3.5 27.4 1.0 CB A:ASP227 3.9 7.4 1.0 N A:GLY224 3.9 7.4 1.0 CB A:ASP223 4.1 9.1 1.0 CB A:ASP184 4.3 8.0 1.0 O A:HOH837 4.3 26.8 1.0 CA A:GLY224 4.3 6.7 1.0 O A:HOH518 4.4 31.0 1.0 O A:HOH695 4.7 25.4 1.0 O A:HOH964 4.7 27.4 1.0 O A:HOH524 4.8 13.6 1.0 C A:ASP223 4.9 7.9 1.0 O A:GLN182 5.0 9.4 1.0

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


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 IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:32.9 occ:1.00 O A:HOH905 2.3 34.7 1.0 O A:HOH555 2.5 24.4 1.0 OD1 A:ASN180 2.5 16.9 1.0 OD2 A:ASP173 2.5 22.1 1.0 O A:HOH556 2.6 37.2 1.0 O A:HOH852 2.6 22.2 1.0 O A:HOH880 2.7 33.6 1.0 CG A:ASN180 3.5 13.9 1.0 CG A:ASP173 3.5 21.8 1.0 OD1 A:ASP173 3.7 22.0 1.0 ND2 A:ASN180 3.7 16.8 1.0 O A:HOH868 4.2 38.0 1.0 O A:HOH861 4.2 41.6 1.0 O A:HOH907 4.3 35.3 1.0 O A:HOH652 4.3 39.6 1.0 NZ A:LYS247 4.5 16.2 1.0 O A:HOH799 4.5 37.3 1.0 O A:HOH900 4.6 29.2 1.0 O A:HOH487 4.7 21.5 1.0 O A:HOH897 4.8 30.8 1.0 CB A:ASN180 4.8 11.1 1.0 CB A:ASP173 4.9 21.4 1.0

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


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 IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:21.7 occ:1.00 O A:HOH844 2.2 19.9 1.0 O A:HOH964 2.2 27.4 1.0 OD1 A:ASP223 2.3 18.6 1.0 OD2 A:ASP223 2.5 17.3 1.0 O A:HOH518 2.6 31.0 1.0 O A:HOH495 2.8 27.4 1.0 CG A:ASP223 2.9 13.1 1.0 O A:HOH652 2.9 39.6 1.0 O A:HOH868 3.0 38.0 1.0 CA A:CA400 3.4 15.6 1.0 O A:HOH900 4.2 29.2 1.0 O A:HOH837 4.2 26.8 1.0 CB A:ASP223 4.3 9.1 1.0 O A:HOH828 4.4 14.5 1.0 O A:HOH905 4.4 34.7 1.0 O A:SER181 4.7 9.0 1.0 O A:HOH975 4.8 41.9 1.0 CE A:LYS247 4.9 13.9 1.0 CA A:ASP223 4.9 8.5 1.0 NZ A:LYS247 4.9 16.2 1.0 OD1 A:ASP184 4.9 13.6 1.0 OD1 A:ASP227 4.9 13.8 1.0 CD1 A:ILE250 5.0 7.7 1.0

A.Seyedarabi, S.Hussain, M.Fries, A.Macdoughall, N.Cummings, D.Smith, K.Worboys, K.Brocklehurst, R.W.Pickersgill. Structural and Thermodynamic Insights Into the Mechanism of Pectate Lyase To Be Published.