Calcium in PDB 2o17: Pectate Lyase Bound to Hexasaccharide

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

The structure of Pectate Lyase Bound to Hexasaccharide, PDB code: 2o17 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)	45.88 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.254, 69.345, 59.826, 90.00, 113.69, 90.00
R / Rfree (%)	14.3 / 22.3

The binding sites of Calcium atom in the Pectate Lyase Bound to Hexasaccharide (pdb code 2o17). 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, PDB code: 2o17:
Jump to Calcium binding site number: 1; 2; 3;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:9.9 occ:1.00 OD1 A:ASP184 2.3 8.3 1.0 OD2 A:ASP227 2.3 9.0 1.0 OD2 A:ASP223 2.3 9.1 1.0 OD2 A:ASP184 2.5 8.3 1.0 O A:HOH458 2.6 5.5 1.0 O6A A:ADA402 2.6 12.0 1.0 CG A:ASP184 2.7 7.1 1.0 O A:HOH919 2.8 39.8 1.0 CG A:ASP227 3.4 6.8 1.0 C6 A:ADA402 3.5 13.0 1.0 CG A:ASP223 3.6 7.6 1.0 O6B A:ADA402 3.6 12.5 1.0 O A:HOH503 3.8 16.2 1.0 CB A:ASP227 3.8 5.9 1.0 CA A:CA407 4.0 11.8 1.0 CB A:ASP184 4.3 5.1 1.0 O A:HOH527 4.3 12.7 1.0 N A:GLY224 4.4 5.0 1.0 CB A:ASP223 4.4 5.7 1.0 OD1 A:ASP223 4.4 10.8 1.0 OD1 A:ASP227 4.5 8.1 1.0 O A:GLN182 4.5 4.2 1.0 O A:HOH728 4.7 22.0 1.0 O A:HOH625 4.8 19.5 1.0 CA A:GLY224 4.8 5.1 1.0 O A:HOH542 4.9 8.1 1.0 C5 A:ADA402 4.9 13.3 1.0 OG1 A:THR187 4.9 5.0 1.0 N A:ASP184 4.9 4.3 1.0 O2 A:ADA403 5.0 29.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:12.4 occ:1.00 O6A A:ADA401 2.3 11.5 1.0 OD1 A:ASN180 2.4 5.0 1.0 OD2 A:ASP173 2.5 13.8 1.0 O A:HOH567 2.5 10.4 1.0 O A:HOH568 2.6 12.4 1.0 O3 A:ADA400 2.7 12.5 1.0 O5 A:ADA401 2.7 11.8 1.0 C6 A:ADA401 3.2 11.6 1.0 CG A:ASN180 3.4 6.0 1.0 CG A:ASP173 3.4 13.5 1.0 C5 A:ADA401 3.5 11.8 1.0 OD1 A:ASP173 3.6 13.8 1.0 ND2 A:ASN180 3.7 3.8 1.0 C1 A:ADA401 3.8 12.2 1.0 C3 A:ADA400 4.0 12.2 1.0 O4 A:ADA400 4.1 12.2 1.0 C2 A:ADA400 4.2 12.3 1.0 O2 A:ADA400 4.2 12.4 1.0 O6B A:ADA401 4.4 11.7 1.0 NZ A:LYS247 4.4 10.2 1.0 O A:HOH677 4.4 11.9 1.0 O A:HOH495 4.7 2.0 1.0 C4 A:ADA400 4.7 13.2 1.0 CB A:ASN180 4.7 5.8 1.0 O A:HOH867 4.7 27.4 1.0 C1 A:ADA402 4.7 12.6 1.0 C4 A:ADA401 4.8 12.5 1.0 O4 A:ADA401 4.8 13.3 1.0 CB A:ASP173 4.8 12.7 1.0 CB A:ASN178 4.9 7.3 1.0 O2 A:ADA402 4.9 11.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:11.8 occ:1.00 OD1 A:ASP223 2.3 10.8 1.0 O5 A:ADA402 2.3 12.6 1.0 O6A A:ADA402 2.3 12.0 1.0 O A:HOH503 2.5 16.2 1.0 O6B A:ADA401 2.6 11.7 1.0 O A:HOH677 2.6 11.9 1.0 O A:HOH527 2.7 12.7 1.0 OD2 A:ASP223 2.8 9.1 1.0 CG A:ASP223 2.9 7.6 1.0 C6 A:ADA402 3.1 13.0 1.0 C5 A:ADA402 3.3 13.3 1.0 C1 A:ADA402 3.3 12.6 1.0 C6 A:ADA401 3.6 11.6 1.0 O4 A:ADA401 4.0 13.3 1.0 CA A:CA405 4.0 9.9 1.0 O6A A:ADA401 4.1 11.5 1.0 O6B A:ADA402 4.3 12.5 1.0 CB A:ASP223 4.4 5.7 1.0 C4 A:ADA401 4.4 12.5 1.0 C4 A:ADA402 4.4 14.5 1.0 O4 A:ADA402 4.5 17.9 1.0 C2 A:ADA402 4.5 12.7 1.0 C5 A:ADA401 4.6 11.8 1.0 OD2 A:ASP227 4.6 9.0 1.0 O A:SER181 4.6 5.4 1.0 O A:HOH624 4.6 8.1 1.0 O A:HOH919 4.7 39.8 1.0 O2 A:ADA403 4.9 29.8 1.0 CD1 A:ILE250 4.9 5.8 1.0 NZ A:LYS247 5.0 10.2 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