Calcium in PDB 2ewe: Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid

All present enzymatic activity of Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid:
4.2.2.2;

The structure of Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid, PDB code: 2ewe was solved by R.D.Scavetta, F.Jurnak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.140, 78.320, 94.430, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 23.3

The binding sites of Calcium atom in the Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid (pdb code 2ewe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid, PDB code: 2ewe:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:8.0 occ:1.00 O A:HOH1204 2.2 2.2 1.0 OD1 A:ASP129 2.3 3.7 1.0 OD2 A:ASP131 2.3 5.7 1.0 OE1 A:GLU166 2.4 6.6 1.0 OD2 A:ASP170 2.5 5.0 1.0 O6A A:ADA904 2.5 4.6 0.8 OD1 A:ASP131 2.5 7.8 1.0 CG A:ASP131 2.8 4.6 1.0 CG A:ASP129 3.3 4.5 1.0 C6 A:ADA904 3.4 2.4 0.8 CG A:ASP170 3.6 5.7 1.0 CD A:GLU166 3.6 5.2 1.0 OD2 A:ASP129 3.7 4.9 1.0 O A:HOH1203 3.7 2.0 1.0 O6B A:ADA904 3.7 2.1 0.8 CA A:CA702 3.9 5.2 1.0 O A:HOH1074 3.9 13.6 1.0 CB A:ASP170 4.1 5.7 1.0 CB A:ASP131 4.3 4.4 1.0 OG A:SER167 4.3 7.8 1.0 CG A:GLU166 4.3 2.7 1.0 CB A:ASP129 4.5 4.4 1.0 NE A:ARG134 4.5 4.1 1.0 OE2 A:GLU166 4.6 6.0 1.0 CA A:ASP129 4.6 4.6 1.0 OD1 A:ASP170 4.6 6.5 1.0 CB A:GLU166 4.7 3.2 1.0 O A:ASP129 4.8 2.2 1.0 C5 A:ADA904 4.8 2.1 0.8 CB A:SER167 4.9 6.4 1.0 C A:ASP129 4.9 3.6 1.0 N A:SER167 5.0 4.6 1.0 O5 A:ADA904 5.0 2.0 0.8

Calcium binding site 2 out of 4 in the Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:5.2 occ:1.00 O5 A:ADA904 2.4 2.0 0.8 O6B A:ADA903 2.4 2.9 0.8 O A:HOH1076 2.4 9.8 1.0 O6A A:ADA904 2.4 4.6 0.8 O A:HOH1203 2.4 2.0 1.0 O A:HOH1074 2.5 13.6 1.0 OE2 A:GLU166 2.5 6.0 1.0 OE1 A:GLU166 2.5 6.6 1.0 CD A:GLU166 2.9 5.2 1.0 C6 A:ADA903 3.3 2.2 0.8 C6 A:ADA904 3.3 2.4 0.8 C1 A:ADA904 3.4 2.6 0.8 C5 A:ADA904 3.4 2.1 0.8 NZ A:LYS190 3.9 4.9 1.0 CA A:CA701 3.9 8.0 1.0 O6A A:ADA903 4.0 2.0 0.8 O4 A:ADA903 4.3 2.2 0.8 O4 A:ADA904 4.3 3.6 0.8 C4 A:ADA903 4.3 2.4 0.8 OD1 A:ASP129 4.3 3.7 1.0 C5 A:ADA903 4.3 2.0 0.8 OD2 A:ASP170 4.4 5.0 1.0 CG A:GLU166 4.4 2.7 1.0 CE A:LYS190 4.5 2.8 1.0 C4 A:ADA904 4.5 3.1 0.8 C2 A:ADA904 4.5 2.7 0.8 O6B A:ADA904 4.5 2.1 0.8 O A:HOH1075 4.6 9.1 1.0 CD1 A:LEU193 4.9 2.4 1.0 O A:HOH1077 5.0 5.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:8.7 occ:1.00 O A:HOH1078 2.2 15.2 1.0 O6A A:ADA903 2.3 2.0 0.8 OD2 A:ASP160 2.3 12.2 1.0 OD2 A:ASP162 2.4 6.4 1.0 O5 A:ADA903 2.5 3.1 0.8 O A:HOH1077 2.6 5.8 1.0 O3 A:ADA902 2.6 8.4 0.8 C6 A:ADA903 3.2 2.2 0.8 C5 A:ADA903 3.3 2.0 0.8 CG A:ASP162 3.4 8.7 1.0 C1 A:ADA903 3.4 5.0 0.8 CG A:ASP160 3.5 12.7 1.0 OD1 A:ASP162 3.7 9.5 1.0 C3 A:ADA902 3.7 7.2 0.8 C2 A:ADA902 3.9 8.1 0.8 O2 A:ADA902 3.9 7.3 0.8 O4 A:ADA902 4.0 6.2 0.8 O A:HOH1076 4.2 9.8 1.0 CB A:ASP160 4.2 10.3 1.0 O6B A:ADA903 4.4 2.9 0.8 OD1 A:ASP160 4.4 15.7 1.0 C4 A:ADA902 4.5 6.7 0.8 C1 A:ADA904 4.5 2.6 0.8 C4 A:ADA903 4.6 2.4 0.8 O2 A:ADA904 4.7 2.6 0.8 C2 A:ADA903 4.7 4.6 0.8 CB A:ASP162 4.7 9.4 1.0 O4 A:ADA903 4.8 2.2 0.8 NZ A:LYS190 4.8 4.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Pectate Lyase C R218K Mutant in Complex with Pentagalacturonic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:14.1 occ:0.50 O6A A:ADA902 2.6 4.9 0.8 NZ A:LYS218 2.7 20.1 1.0 O A:HOH1308 2.8 2.0 1.0 O6B A:ADA901 2.9 14.3 0.8 O5 A:ADA902 2.9 7.6 0.8 CE2 A:TYR268 3.6 2.9 1.0 C6 A:ADA902 3.6 4.1 0.8 CG A:LYS218 3.7 12.0 1.0 CD2 A:TYR268 3.8 4.3 1.0 C5 A:ADA902 3.8 5.1 0.8 C1 A:ADA902 3.9 8.4 0.8 CE A:LYS218 3.9 17.8 1.0 C6 A:ADA901 4.0 15.5 0.8 CB A:ALA217 4.1 4.8 1.0 CD1 A:LEU221 4.2 3.2 1.0 CD A:LYS218 4.2 15.2 1.0 C4 A:ADA901 4.2 13.2 0.8 O A:HOH1048 4.5 22.0 1.0 NH1 A:ARG245 4.5 4.1 1.0 O4 A:ADA901 4.6 10.0 0.8 O A:HOH1049 4.6 10.9 1.0 C5 A:ADA901 4.6 14.4 0.8 CZ A:TYR268 4.7 4.3 1.0 ND2 A:ASN243 4.7 6.6 1.0 CG A:LEU221 4.8 3.6 1.0 O A:HOH1307 4.8 2.1 1.0 O6B A:ADA902 4.8 4.6 0.8 N A:LYS218 4.9 6.7 1.0 OG A:SER240 5.0 8.0 1.0

R.D.Scavetta, S.R.Herron, A.T.Hotchkiss, N.Kita, N.T.Keen, J.A.Benen, H.C.Kester, J.Visser, F.Jurnak. Structure of A Plant Cell Wall Fragment Complexed to Pectate Lyase C Plant Cell V. 11 1081 1999.
ISSN: ISSN 1040-4651
PubMed: 10368179
DOI: 10.1105/TPC.11.6.1081