Calcium in PDB 2nzm: Hexasaccharide I Bound to Bacillus Subtilis Pectate Lyase

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

The structure of Hexasaccharide I Bound to Bacillus Subtilis Pectate Lyase, PDB code: 2nzm 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)	45.36 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.736, 68.919, 59.408, 90.00, 113.09, 90.00
R / Rfree (%)	15.5 / 18.5

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hexasaccharide I Bound to Bacillus Subtilis Pectate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:12.0 occ:1.00 OD1 A:ASP184 2.3 11.4 1.0 OD2 A:ASP227 2.3 11.1 1.0 OD2 A:ASP223 2.3 11.5 1.0 O A:HOH896 2.5 13.9 1.0 OD2 A:ASP184 2.5 9.4 1.0 O6A A:ADA402 2.5 15.5 1.0 O A:HOH457 2.6 15.0 1.0 CG A:ASP184 2.7 8.7 1.0 CG A:ASP227 3.5 7.4 1.0 C6 A:ADA402 3.5 18.2 1.0 CG A:ASP223 3.6 9.5 1.0 O A:HOH501 3.6 16.7 1.0 O6B A:ADA402 3.7 19.9 1.0 CA A:CA407 3.9 14.1 1.0 CB A:ASP227 4.0 5.5 1.0 CB A:ASP184 4.2 6.7 1.0 N A:GLY224 4.4 6.7 1.0 CB A:ASP223 4.4 7.2 1.0 O A:HOH524 4.4 19.9 1.0 O A:HOH721 4.4 24.0 1.0 O A:HOH621 4.5 24.2 1.0 OD1 A:ASP223 4.5 12.3 1.0 OD1 A:ASP227 4.5 7.8 1.0 O A:GLN182 4.5 7.7 1.0 CA A:GLY224 4.7 6.1 1.0 OG1 A:THR187 4.8 7.6 1.0 C5 A:ADA402 4.8 17.8 1.0 N A:ASP184 4.9 6.0 1.0 O5 A:ADA402 5.0 15.2 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hexasaccharide I Bound to Bacillus Subtilis Pectate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:10.0 occ:1.00 O6A A:ADA401 2.3 10.1 1.0 O A:HOH565 2.3 16.8 1.0 O A:HOH564 2.4 11.8 1.0 OD2 A:ASP173 2.4 11.5 1.0 OD1 A:ASN180 2.4 8.4 1.0 O3 A:ADA400 2.5 8.2 1.0 O5 A:ADA401 2.6 9.7 1.0 C6 A:ADA401 3.2 11.3 1.0 CG A:ASN180 3.4 7.8 1.0 CG A:ASP173 3.4 13.0 1.0 C5 A:ADA401 3.5 10.3 1.0 ND2 A:ASN180 3.6 8.3 1.0 OD1 A:ASP173 3.7 13.1 1.0 C1 A:ADA401 3.7 9.6 1.0 C3 A:ADA400 3.8 8.5 1.0 C2 A:ADA400 4.1 9.5 1.0 O4 A:ADA400 4.1 8.9 1.0 O A:HOH671 4.2 17.6 1.0 O2 A:ADA400 4.2 10.6 1.0 NZ A:LYS247 4.4 10.3 1.0 O6B A:ADA401 4.4 11.4 1.0 C4 A:ADA400 4.5 8.4 1.0 O A:HOH854 4.5 26.8 1.0 O A:HOH493 4.6 15.1 1.0 C1 A:ADA402 4.7 15.5 1.0 CB A:ASN180 4.7 7.1 1.0 C4 A:ADA401 4.7 11.1 1.0 O4 A:ADA401 4.8 12.2 1.0 CB A:ASP173 4.8 13.0 1.0 O2 A:ADA402 4.9 15.2 1.0 C2 A:ADA401 4.9 10.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Hexasaccharide I Bound to Bacillus Subtilis Pectate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:14.1 occ:1.00 OD1 A:ASP223 2.3 12.3 1.0 O5 A:ADA402 2.3 15.2 1.0 O6A A:ADA402 2.3 15.5 1.0 O A:HOH501 2.5 16.7 1.0 O6B A:ADA401 2.5 11.4 1.0 OD2 A:ASP223 2.6 11.5 1.0 O A:HOH524 2.6 19.9 1.0 O A:HOH671 2.7 17.6 1.0 CG A:ASP223 2.8 9.5 1.0 C6 A:ADA402 3.2 18.2 1.0 C1 A:ADA402 3.3 15.5 1.0 C5 A:ADA402 3.3 17.8 1.0 C6 A:ADA401 3.5 11.3 1.0 CA A:CA405 3.9 12.0 1.0 O4 A:ADA401 4.0 12.2 1.0 O6A A:ADA401 4.0 10.1 1.0 CB A:ASP223 4.3 7.2 1.0 C4 A:ADA401 4.3 11.1 1.0 O4 A:ADA402 4.4 22.4 1.0 O6B A:ADA402 4.4 19.9 1.0 C4 A:ADA402 4.4 18.2 1.0 C2 A:ADA402 4.5 16.0 1.0 C5 A:ADA401 4.5 10.3 1.0 O A:SER181 4.5 7.1 1.0 O A:HOH631 4.6 32.4 1.0 OD2 A:ASP227 4.7 11.1 1.0 NZ A:LYS247 4.8 10.3 1.0 O A:HOH620 4.8 8.0 1.0 O A:HOH896 4.8 13.9 1.0 CA A:ASP223 5.0 7.1 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