Calcium in PDB 2o1d: Pectate Lyase Bound to Trisaccharide

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

The structure of Pectate Lyase Bound to Trisaccharide, PDB code: 2o1d 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)	29.81 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.571, 69.023, 59.198, 90.00, 113.64, 90.00
R / Rfree (%)	14.7 / 19.9

The binding sites of Calcium atom in the Pectate Lyase Bound to Trisaccharide (pdb code 2o1d). 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 Trisaccharide, PDB code: 2o1d:
Jump to Calcium binding site number: 1; 2; 3;

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


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 Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:8.3 occ:1.00 OD1 A:ASP184 2.3 7.9 1.0 OD2 A:ASP227 2.3 7.7 1.0 OD2 A:ASP223 2.3 8.4 1.0 O A:HOH656 2.4 11.5 1.0 OD2 A:ASP184 2.5 5.7 1.0 O A:HOH496 2.5 7.4 1.0 O6A A:ADA402 2.6 9.1 1.0 CG A:ASP184 2.7 6.6 1.0 CG A:ASP227 3.4 6.5 1.0 CG A:ASP223 3.5 7.9 1.0 O A:HOH432 3.5 11.2 1.0 C6 A:ADA402 3.5 9.7 1.0 O6B A:ADA402 3.8 11.0 1.0 CB A:ASP227 3.8 6.3 1.0 CA A:CA405 3.9 9.5 1.0 O A:HOH467 4.1 12.7 1.0 CB A:ASP184 4.3 5.5 1.0 N A:GLY224 4.3 5.9 1.0 CB A:ASP223 4.3 6.2 1.0 O A:HOH697 4.4 30.2 1.0 OD1 A:ASP223 4.4 9.4 1.0 OD1 A:ASP227 4.5 5.3 1.0 O A:GLN182 4.6 8.6 1.0 OG1 A:THR187 4.7 5.8 1.0 CA A:GLY224 4.7 5.6 1.0 O A:HOH777 4.8 22.3 1.0 O A:HOH437 4.9 8.1 1.0 C5 A:ADA402 4.9 9.2 1.0 N A:ASP184 5.0 5.7 1.0

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


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 Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:10.5 occ:1.00 OD2 A:ASP173 2.3 11.1 1.0 O6A A:ADA401 2.3 10.4 1.0 O A:HOH508 2.4 12.5 1.0 O A:HOH450 2.5 11.4 1.0 OD1 A:ASN180 2.5 8.0 1.0 O3 A:ADA400 2.5 7.6 1.0 O5 A:ADA401 2.6 8.7 1.0 C6 A:ADA401 3.2 9.8 1.0 CG A:ASP173 3.3 13.0 1.0 CG A:ASN180 3.4 8.8 1.0 C5 A:ADA401 3.4 9.3 1.0 OD1 A:ASP173 3.5 12.9 1.0 ND2 A:ASN180 3.6 9.6 1.0 C1 A:ADA401 3.7 8.1 1.0 C3 A:ADA400 3.8 8.8 1.0 C2 A:ADA400 4.0 9.8 1.0 O4 A:ADA400 4.1 8.2 1.0 O2 A:ADA400 4.2 10.6 1.0 O A:HOH464 4.3 3.2 1.0 NZ A:LYS247 4.4 5.9 1.0 O6B A:ADA401 4.4 9.6 1.0 O A:HOH622 4.5 20.7 1.0 C4 A:ADA400 4.5 8.1 1.0 CB A:ASP173 4.7 13.7 1.0 O A:HOH475 4.7 9.3 1.0 C4 A:ADA401 4.7 8.9 1.0 C1 A:ADA402 4.7 9.2 1.0 CB A:ASN180 4.8 8.2 1.0 O4 A:ADA401 4.8 8.8 1.0 CB A:ASN178 4.9 10.2 1.0 O2 A:ADA402 4.9 10.2 1.0 C2 A:ADA401 4.9 7.9 1.0

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


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 Trisaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:9.5 occ:1.00 OD1 A:ASP223 2.3 9.4 1.0 O6A A:ADA402 2.3 9.1 1.0 O A:HOH432 2.4 11.2 1.0 O5 A:ADA402 2.4 8.8 1.0 O6B A:ADA401 2.5 9.6 1.0 O A:HOH467 2.6 12.7 1.0 O A:HOH464 2.6 3.2 1.0 OD2 A:ASP223 2.7 8.4 1.0 CG A:ASP223 2.8 7.9 1.0 C6 A:ADA402 3.2 9.7 1.0 C5 A:ADA402 3.4 9.2 1.0 C6 A:ADA401 3.4 9.8 1.0 C1 A:ADA402 3.5 9.2 1.0 CA A:CA403 3.9 8.3 1.0 O6A A:ADA401 4.0 10.4 1.0 O4 A:ADA402 4.2 7.7 1.0 O A:HOH609 4.2 22.9 1.0 O4 A:ADA401 4.3 8.8 1.0 CB A:ASP223 4.3 6.2 1.0 C4 A:ADA401 4.4 8.9 1.0 O6B A:ADA402 4.4 11.0 1.0 C4 A:ADA402 4.4 9.5 1.0 OD2 A:ASP227 4.4 7.7 1.0 C2 A:ADA402 4.5 10.3 1.0 C5 A:ADA401 4.5 9.3 1.0 NZ A:LYS247 4.5 5.9 1.0 O A:HOH479 4.6 4.2 1.0 O A:HOH656 4.7 11.5 1.0 O A:SER181 4.7 8.7 1.0 CE A:LYS247 4.9 7.9 1.0 CA A:ASP223 5.0 6.4 1.0 CD1 A:ILE250 5.0 6.2 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