Calcium in PDB 2zuy: Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx

The structure of Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx, PDB code: 2zuy was solved by A.Ochiai, T.Itoh, B.Mikami, W.Hashimoto, K.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.19 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.853, 88.070, 99.304, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.4

The binding sites of Calcium atom in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx (pdb code 2zuy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx, PDB code: 2zuy:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


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 Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca621 b:2.0 occ:1.00 OE1 A:GLU389 2.1 6.4 1.0 NE2 A:HIS330 2.1 4.4 1.0 OD2 A:ASP368 2.2 5.5 1.0 NE2 A:HIS366 2.2 5.9 1.0 O A:HOH766 2.2 6.6 1.0 O A:HOH767 2.2 8.5 1.0 CD2 A:HIS330 2.9 4.4 1.0 CD A:GLU389 3.1 7.3 1.0 CG A:ASP368 3.1 6.3 1.0 CE1 A:HIS366 3.1 4.7 1.0 CD2 A:HIS366 3.2 5.5 1.0 CE1 A:HIS330 3.2 4.8 1.0 OD1 A:ASP368 3.4 8.5 1.0 OE2 A:GLU389 3.4 8.4 1.0 O A:HOH835 4.0 8.9 1.0 OH A:TYR293 4.0 7.8 1.0 CG A:HIS330 4.1 3.8 1.0 ND1 A:HIS330 4.2 5.0 1.0 ND1 A:HIS366 4.3 3.8 1.0 O A:HOH779 4.3 14.6 1.0 CG A:HIS366 4.3 4.7 1.0 CG A:GLU389 4.4 7.1 1.0 CB A:ASP368 4.5 4.7 1.0 O A:GLY367 4.6 4.3 1.0 CB A:GLU389 4.6 6.8 1.0 C A:GLY367 4.7 4.4 1.0 CA A:ASP368 4.8 4.8 1.0 N A:ASP368 4.9 4.7 1.0 CE1 A:TYR293 5.0 7.9 1.0 CE2 A:TYR579 5.0 5.5 1.0 CZ A:TYR293 5.0 7.1 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


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 Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca622 b:6.3 occ:1.00 OD2 A:ASP472 2.3 7.4 1.0 O A:VAL476 2.3 6.0 1.0 OD2 A:ASP474 2.3 7.9 1.0 O A:HOH706 2.4 7.2 1.0 OE2 A:GLU478 2.5 6.6 1.0 OE1 A:GLU478 2.5 6.1 1.0 O A:ASP474 2.6 8.2 1.0 CD A:GLU478 2.9 6.2 1.0 CG A:ASP472 3.4 8.2 1.0 C A:VAL476 3.4 6.0 1.0 C A:ASP474 3.4 7.8 1.0 CG A:ASP474 3.5 8.7 1.0 N A:ASP474 3.8 7.6 1.0 NZ A:LYS495 3.9 10.0 1.0 CA A:ASP474 3.9 7.9 1.0 OD1 A:ASP472 4.0 10.5 1.0 N A:VAL476 4.0 7.1 1.0 O A:ASP472 4.1 6.7 1.0 CA A:VAL476 4.2 6.8 1.0 N A:ASP472 4.2 6.0 1.0 C A:ASP472 4.2 6.7 1.0 CB A:ASP474 4.3 8.3 1.0 OD1 A:ASP474 4.4 9.0 1.0 N A:LEU475 4.4 7.8 1.0 CG A:GLU478 4.4 5.1 1.0 N A:ARG477 4.4 5.2 1.0 C A:LEU475 4.4 7.8 1.0 CA A:ASP472 4.5 6.6 1.0 CB A:VAL476 4.5 7.2 1.0 CB A:ASP472 4.5 6.8 1.0 CA A:ARG477 4.6 5.1 1.0 N A:TRP471 4.7 5.5 1.0 N A:GLY473 4.7 7.0 1.0 N A:GLU478 4.7 5.0 1.0 CG1 A:VAL476 4.7 8.8 1.0 C A:GLY473 4.8 7.6 1.0 CA A:LEU475 4.8 8.1 1.0 CD1 A:TRP470 4.8 6.0 1.0 C A:ARG477 4.9 5.2 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


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 Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca623 b:7.6 occ:1.00 OD2 A:ASP129 2.3 10.0 1.0 OD1 A:ASP127 2.3 9.2 1.0 O A:GLU131 2.4 7.5 1.0 OD1 A:ASP125 2.4 5.5 1.0 OE1 A:GLU133 2.4 10.5 1.0 O A:HOH930 2.5 18.4 1.0 OE2 A:GLU133 2.5 6.6 1.0 CD A:GLU133 2.8 7.4 1.0 CG A:ASP129 3.3 11.0 1.0 CG A:ASP125 3.5 5.6 1.0 CG A:ASP127 3.5 10.6 1.0 C A:GLU131 3.5 7.6 1.0 OD1 A:ASP129 3.8 13.0 1.0 NZ A:LYS161 3.9 8.8 0.5 OD2 A:ASP127 4.0 13.4 1.0 N A:GLU131 4.1 7.7 1.0 CA A:GLU131 4.2 8.1 1.0 CA A:ASP125 4.2 5.4 1.0 OD2 A:ASP125 4.2 6.8 1.0 CB A:GLU131 4.2 8.9 1.0 N A:ASP127 4.3 7.9 1.0 N A:ILE126 4.3 5.9 1.0 CB A:ASP125 4.3 5.3 1.0 N A:ASP129 4.3 9.9 1.0 CG A:GLU133 4.3 6.4 1.0 CB A:ASP129 4.5 10.2 1.0 C A:ASP125 4.5 5.5 1.0 N A:TYR132 4.6 7.0 1.0 N A:GLY128 4.6 9.2 1.0 C A:TYR132 4.7 6.3 1.0 N A:GLU133 4.7 5.8 1.0 CB A:ASP127 4.7 9.3 1.0 CA A:TYR132 4.8 6.3 1.0 CA A:ASP129 4.8 10.0 1.0 CA A:ASP127 4.8 9.0 1.0 O A:HOH829 4.9 9.9 1.0 N A:GLY130 4.9 9.0 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


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 Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca624 b:4.9 occ:1.00 OD1 A:ASP193 2.3 8.0 1.0 O A:LYS195 2.3 5.6 1.0 OD1 A:ASP191 2.3 6.0 1.0 OD1 A:ASP189 2.4 6.8 1.0 OE2 A:GLU197 2.5 5.6 1.0 OE1 A:GLU197 2.5 6.5 1.0 CD A:GLU197 2.9 6.7 1.0 CG A:ASP193 3.3 8.7 1.0 CG A:ASP191 3.4 7.8 1.0 CG A:ASP189 3.4 5.6 1.0 C A:LYS195 3.5 6.0 1.0 OD2 A:ASP191 3.8 8.2 1.0 OD2 A:ASP193 3.9 11.6 1.0 N A:LYS195 4.0 6.4 1.0 CA A:ASP189 4.1 4.3 1.0 N A:ASP193 4.1 7.5 1.0 CA A:LYS195 4.2 6.2 1.0 CB A:ASP189 4.2 4.7 1.0 N A:ASP191 4.3 5.8 1.0 CB A:ASP193 4.3 8.3 1.0 OD2 A:ASP189 4.3 5.9 1.0 N A:LEU190 4.4 4.2 1.0 CG A:GLU197 4.4 7.7 1.0 C A:ASP189 4.4 4.2 1.0 N A:GLY192 4.4 6.5 1.0 O A:HOH851 4.4 10.4 1.0 CB A:LYS195 4.5 6.6 1.0 N A:ALA196 4.5 5.3 1.0 CB A:ASP191 4.6 6.3 1.0 CA A:ASP193 4.7 7.9 1.0 C A:ALA196 4.7 5.8 1.0 CA A:ALA196 4.7 5.5 1.0 N A:GLY194 4.8 7.1 1.0 N A:GLU197 4.8 6.0 1.0 CA A:ASP191 4.8 6.2 1.0 C A:ASP191 4.9 6.5 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca625 b:8.3 occ:1.00 O A:ARG379 2.3 12.4 1.0 O A:GLY381 2.3 10.2 1.0 OD1 A:ASP374 2.4 8.8 1.0 O A:ASP376 2.4 8.2 1.0 OE2 A:GLU383 2.5 8.7 1.0 O A:HOH965 2.6 14.2 1.0 OE1 A:GLU383 2.7 8.5 1.0 CD A:GLU383 2.9 8.3 1.0 C A:ASP376 3.4 8.5 1.0 CG A:ASP374 3.4 6.9 1.0 C A:ARG379 3.5 12.8 1.0 C A:GLY381 3.5 9.7 1.0 OD2 A:ASP374 4.0 8.2 1.0 N A:GLY381 4.1 11.6 1.0 N A:PRO377 4.1 9.2 1.0 CA A:PRO377 4.1 9.8 1.0 N A:ASP376 4.2 8.0 1.0 C A:LYS380 4.2 12.5 1.0 CA A:ARG379 4.2 12.8 0.5 CB A:ARG379 4.2 12.8 0.5 CA A:ARG379 4.2 12.5 0.5 CA A:ASP376 4.3 8.4 1.0 N A:ARG379 4.3 12.7 1.0 CB A:ARG379 4.4 12.6 0.5 CA A:GLY381 4.4 10.8 1.0 N A:LEU382 4.5 8.6 1.0 CA A:ASP374 4.5 6.4 1.0 CG A:GLU383 4.5 6.4 1.0 CB A:ASP374 4.5 6.6 1.0 N A:LYS380 4.5 12.8 1.0 O A:LYS380 4.5 12.9 1.0 CA A:LEU382 4.5 7.5 1.0 C A:PRO377 4.6 10.8 1.0 CB A:ASP376 4.6 8.2 1.0 CA A:LYS380 4.7 12.8 0.5 CA A:LYS380 4.7 12.8 0.5 C A:LEU382 4.8 7.0 1.0 C A:ASP374 4.8 6.7 1.0 N A:LEU375 4.8 6.6 1.0 NE A:ARG379 4.8 11.8 0.5 O A:HOH1186 4.8 30.5 1.0 CG A:ARG379 4.9 11.9 0.5 O A:HOH1143 4.9 34.3 1.0 O A:PRO377 5.0 11.4 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca626 b:3.5 occ:1.00 O A:ASN576 2.3 3.4 1.0 O A:ALA578 2.3 4.0 1.0 O A:HOH800 2.3 4.0 1.0 OD1 A:ASN580 2.4 3.6 1.0 OD2 A:ASP120 2.4 4.7 1.0 O A:HOH674 2.4 5.0 1.0 CG A:ASP120 3.3 3.9 1.0 C A:ALA578 3.4 4.2 1.0 C A:ASN576 3.5 3.4 1.0 CG A:ASN580 3.5 3.5 1.0 OD1 A:ASP120 3.7 3.8 1.0 N A:ALA578 3.9 4.6 1.0 CA A:ALA578 4.0 4.2 1.0 ND2 A:ASN580 4.1 3.5 1.0 C A:THR577 4.1 4.4 1.0 NZ A:LYS137 4.2 3.6 1.0 CA A:ASN576 4.2 3.3 1.0 O A:HOH689 4.2 5.0 1.0 O A:HOH630 4.3 5.2 1.0 N A:ASN580 4.3 3.1 1.0 O A:THR577 4.3 4.5 1.0 N A:THR577 4.5 3.7 1.0 CB A:ASP120 4.5 3.5 1.0 ND2 A:ASN516 4.5 5.1 1.0 O A:HOH687 4.6 4.5 1.0 N A:TYR579 4.6 3.6 1.0 O A:ALA180 4.6 4.1 1.0 CA A:THR577 4.7 4.3 1.0 CB A:ASN580 4.7 3.2 1.0 O A:HOH635 4.8 5.2 1.0 CB A:ASN576 4.8 3.4 1.0 CA A:TYR579 4.9 3.5 1.0 CA A:ASN580 4.9 3.2 1.0 CB A:ALA180 5.0 4.3 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca627 b:8.2 occ:1.00 OE1 A:GLU344 2.3 6.7 1.0 OD2 A:ASP340 2.3 10.5 1.0 O A:HOH794 2.4 9.7 1.0 OD2 A:ASP338 2.4 9.9 1.0 OD1 A:ASP353 2.4 6.9 1.0 ND1 A:HIS354 2.6 9.2 1.0 CG A:ASP338 3.2 9.2 1.0 CE1 A:HIS354 3.2 9.3 1.0 OD1 A:ASP338 3.3 7.8 1.0 CG A:ASP340 3.3 10.5 1.0 CD A:GLU344 3.3 6.9 1.0 CG A:ASP353 3.5 7.0 1.0 OD1 A:ASP340 3.6 9.4 1.0 CA A:CA628 3.6 12.9 1.0 CG A:HIS354 3.7 8.3 1.0 OD2 A:ASP353 3.8 9.3 1.0 CG A:GLU344 4.0 5.9 1.0 CB A:HIS354 4.2 7.3 1.0 N A:HIS354 4.2 6.7 1.0 OE2 A:GLU344 4.2 6.0 1.0 O A:HOH1092 4.3 24.3 1.0 NE2 A:HIS354 4.5 9.6 1.0 O A:HOH839 4.5 13.6 1.0 CB A:ASP340 4.6 10.1 1.0 CB A:ASP338 4.6 9.6 1.0 CD2 A:HIS354 4.7 9.1 1.0 CB A:ASP353 4.8 6.4 1.0 CA A:HIS354 4.9 6.9 1.0 O A:LYS342 5.0 6.5 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca628 b:12.9 occ:1.00 O A:LYS342 2.2 6.5 1.0 OD1 A:ASP340 2.2 9.4 1.0 OD1 A:ASP338 2.3 7.8 1.0 OD1 A:ASP336 2.3 9.0 1.0 OE1 A:GLU344 2.4 6.7 1.0 OE2 A:GLU344 2.5 6.0 1.0 CD A:GLU344 2.8 6.9 1.0 CG A:ASP340 3.1 10.5 1.0 CG A:ASP336 3.2 7.5 1.0 C A:LYS342 3.3 6.6 1.0 CG A:ASP338 3.3 9.2 1.0 OD2 A:ASP340 3.6 10.5 1.0 CA A:CA627 3.6 8.2 1.0 N A:LYS342 3.7 8.0 1.0 CA A:ASP336 3.8 6.3 1.0 OD2 A:ASP338 3.9 9.9 1.0 CB A:ASP336 3.9 6.0 1.0 N A:ASP340 3.9 10.4 1.0 CA A:LYS342 3.9 7.2 1.0 N A:ASP338 4.0 8.9 1.0 N A:VAL337 4.0 6.6 1.0 OD2 A:ASP336 4.1 8.8 1.0 C A:ASP336 4.2 6.3 1.0 CB A:LYS342 4.2 7.3 1.0 CG A:GLU344 4.3 5.9 1.0 N A:GLY341 4.3 9.3 1.0 N A:GLY339 4.3 10.7 1.0 CB A:ASP340 4.3 10.1 1.0 N A:ASP343 4.4 6.3 1.0 CA A:ASP340 4.4 10.1 1.0 CB A:ASP338 4.5 9.6 1.0 CA A:ASP338 4.5 9.8 1.0 C A:ASP340 4.5 9.9 1.0 C A:ASP338 4.6 10.6 1.0 N A:GLU344 4.6 5.5 1.0 C A:GLY341 4.7 8.8 1.0 C A:ASP343 4.7 5.8 1.0 CA A:ASP343 4.7 5.8 1.0 C A:GLY339 4.9 11.2 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Exotype Rhamnogalacturonan Lyase Yesx within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca629 b:15.7 occ:1.00 O A:PHE529 2.4 4.7 1.0 O A:HOH827 2.4 8.4 1.0 O A:ARG533 2.4 5.0 1.0 OE2 A:GLU535 2.4 6.0 1.0 O A:ASP531 2.5 5.1 1.0 OE1 A:GLU535 3.0 5.3 1.0 OD1 A:ASN527 3.0 12.5 1.0 CD A:GLU535 3.1 6.0 1.0 C A:ARG533 3.5 4.8 1.0 C A:ASP531 3.6 5.2 1.0 C A:PHE529 3.6 5.0 1.0 N A:ASP531 3.7 5.2 1.0 C A:GLY530 3.8 5.0 1.0 N A:ARG533 4.0 5.0 1.0 CA A:GLY530 4.0 5.1 1.0 O A:HOH653 4.1 4.8 1.0 CG A:ASN527 4.2 8.7 1.0 CA A:ARG533 4.2 4.8 1.0 OD1 A:ASP531 4.2 6.1 1.0 CA A:ASP531 4.2 5.0 1.0 O A:GLY530 4.2 5.6 1.0 N A:GLY530 4.3 4.9 1.0 OG1 A:THR550 4.4 5.6 1.0 CB A:ARG533 4.5 4.8 1.0 C A:TRP532 4.5 5.2 1.0 N A:GLU534 4.5 4.2 1.0 N A:PHE529 4.5 5.5 1.0 CG A:GLU535 4.6 4.9 1.0 N A:TRP532 4.6 5.2 1.0 O A:HOH805 4.6 6.7 1.0 CA A:PHE529 4.7 4.9 1.0 N A:GLU535 4.8 4.5 1.0 CA A:GLU534 4.8 4.2 1.0 CA A:ASN527 4.9 6.3 1.0 C A:GLU534 4.9 4.4 1.0 CA A:TRP532 4.9 5.4 1.0 CB A:ASN527 5.0 6.8 1.0

A.Ochiai, T.Itoh, B.Mikami, W.Hashimoto, K.Murata. Structural Determinants Responsible For Substrate Recognition and Mode of Action in Family 11 Polysaccharide Lyases J.Biol.Chem. V. 284 10181 2009.
ISSN: ISSN 0021-9258
PubMed: 19193638
DOI: 10.1074/JBC.M807799200