Calcium in PDB 2zux: Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose

The structure of Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose, PDB code: 2zux 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)	50.00 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.282, 105.858, 100.967, 90.00, 94.82, 90.00
R / Rfree (%)	16.6 / 18

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose (pdb code 2zux). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 20 binding sites of Calcium where determined in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose, PDB code: 2zux:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca629 b:5.8 occ:1.00 OE1 A:GLU422 2.1 11.7 1.0 O A:HOH968 2.1 13.1 1.0 OD1 A:ASP401 2.1 9.7 1.0 NE2 A:HIS363 2.2 10.4 1.0 NE2 A:HIS399 2.2 10.5 1.0 O A:HOH785 2.2 11.1 1.0 CD2 A:HIS363 3.0 10.0 1.0 CD A:GLU422 3.1 11.6 1.0 CG A:ASP401 3.1 11.3 1.0 CD2 A:HIS399 3.1 10.4 1.0 CE1 A:HIS399 3.2 11.0 1.0 CE1 A:HIS363 3.2 10.4 1.0 OD2 A:ASP401 3.4 13.8 1.0 OE2 A:GLU422 3.4 12.0 1.0 O A:HOH820 4.0 13.8 1.0 OH A:TYR326 4.1 12.0 1.0 CG A:HIS363 4.2 8.8 1.0 O A:HOH1103 4.2 31.4 1.0 ND1 A:HIS363 4.2 9.9 1.0 ND1 A:HIS399 4.3 11.2 1.0 CG A:HIS399 4.3 10.2 1.0 O A:HOH1123 4.3 27.4 1.0 CG A:GLU422 4.4 11.3 1.0 O A:HOH1122 4.4 20.2 1.0 CB A:ASP401 4.5 10.2 1.0 O A:GLY400 4.6 9.4 1.0 C A:GLY400 4.7 9.5 1.0 CB A:GLU422 4.7 11.4 1.0 CA A:ASP401 4.8 9.6 1.0 N A:ASP401 4.9 9.4 1.0 CE1 A:TYR326 5.0 11.8 1.0 CZ A:TYR326 5.0 11.3 1.0

Calcium binding site 2 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca630 b:8.3 occ:1.00 O A:ASN592 2.3 9.1 1.0 O A:HOH763 2.3 9.5 1.0 OD2 A:ASP153 2.4 9.4 1.0 O A:ALA594 2.4 8.4 1.0 O A:HOH687 2.4 8.3 1.0 OD1 A:ASN596 2.4 9.3 1.0 CG A:ASP153 3.3 9.0 1.0 C A:ALA594 3.5 8.4 1.0 C A:ASN592 3.5 8.8 1.0 CG A:ASN596 3.5 8.8 1.0 OD1 A:ASP153 3.7 8.9 1.0 N A:ALA594 3.7 8.3 1.0 C A:ILE593 3.8 8.6 1.0 CA A:ALA594 3.9 8.1 1.0 ND2 A:ASN596 4.0 9.0 1.0 O A:ILE593 4.0 8.5 1.0 O A:HOH671 4.1 9.9 1.0 O A:HOH700 4.3 9.3 1.0 NZ A:LYS170 4.3 10.0 1.0 N A:ASN596 4.3 8.3 1.0 CA A:ASN592 4.3 8.3 1.0 O A:HOH771 4.4 11.5 1.0 N A:ILE593 4.4 8.8 1.0 CA A:ILE593 4.4 9.4 1.0 OD1 A:ASN532 4.4 12.1 1.0 O A:HOH678 4.5 11.6 1.0 CB A:ASP153 4.5 8.3 1.0 N A:TYR595 4.6 8.2 1.0 O A:ALA213 4.6 8.8 1.0 CB A:ASN596 4.8 8.6 1.0 CA A:TYR595 4.9 8.6 1.0 CA A:ASN596 4.9 8.0 1.0 CB A:ALA213 4.9 9.2 1.0 CB A:ASN592 5.0 8.3 1.0

Calcium binding site 3 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca631 b:9.8 occ:1.00 O A:LEU545 2.3 11.4 1.0 O A:ARG549 2.3 9.6 1.0 O A:ASP547 2.3 10.7 1.0 OD1 A:ASP543 2.4 10.6 1.0 O A:HOH717 2.4 10.6 1.0 OE2 A:GLU551 2.5 10.2 1.0 OE1 A:GLU551 2.6 9.8 1.0 CD A:GLU551 2.9 9.5 1.0 CG A:ASP543 3.4 10.1 1.0 C A:ARG549 3.5 9.1 1.0 C A:LEU545 3.5 11.8 1.0 C A:ASP547 3.5 11.1 1.0 C A:GLY546 3.8 10.6 1.0 N A:ASP547 3.9 10.7 1.0 N A:ARG549 4.0 9.4 1.0 O A:GLY546 4.1 10.4 1.0 CA A:ASP543 4.1 9.6 1.0 CB A:ASP543 4.2 10.0 1.0 CA A:GLY546 4.2 11.1 1.0 N A:LEU545 4.2 12.0 1.0 O A:HOH800 4.2 13.9 1.0 OD2 A:ASP543 4.3 10.4 1.0 CA A:ARG549 4.3 9.7 1.0 N A:GLY546 4.3 11.5 1.0 C A:TRP548 4.3 10.2 1.0 CA A:ASP547 4.3 10.9 1.0 O A:HOH1214 4.4 10.7 1.0 CG A:GLU551 4.4 9.6 1.0 N A:GLU550 4.5 9.3 1.0 OD1 A:ASP547 4.5 11.2 1.0 N A:TRP548 4.5 10.9 1.0 CA A:LEU545 4.5 12.4 1.0 C A:ASP543 4.5 10.6 1.0 N A:LEU544 4.5 10.8 1.0 N A:GLU551 4.6 9.2 1.0 CA A:GLU550 4.6 9.4 1.0 OG1 A:THR566 4.6 11.0 1.0 O A:HOH704 4.7 10.8 1.0 CA A:TRP548 4.7 10.4 1.0 C A:GLU550 4.8 9.7 1.0 O A:TRP548 4.8 10.3 1.0 CB A:ARG549 4.9 9.6 1.0 O A:HOH651 5.0 11.2 1.0

Calcium binding site 4 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca632 b:10.7 occ:1.00 OD1 A:ASP496 2.3 11.7 1.0 O A:LEU500 2.3 10.6 1.0 OD1 A:ASP498 2.4 11.5 1.0 OE2 A:GLU502 2.4 11.8 1.0 O A:HOH673 2.5 11.0 1.0 O A:ASP498 2.5 11.4 1.0 OE1 A:GLU502 2.5 10.4 1.0 CD A:GLU502 2.8 10.8 1.0 C A:ASP498 3.3 11.7 1.0 CG A:ASP496 3.3 12.3 1.0 C A:LEU500 3.4 10.4 1.0 CG A:ASP498 3.5 12.4 1.0 N A:ASP498 3.8 12.2 1.0 N A:LEU500 3.9 11.1 1.0 CA A:ASP498 3.9 12.1 1.0 OD2 A:ASP496 3.9 13.8 1.0 O A:ASP496 4.1 11.3 1.0 NZ A:LYS511 4.1 16.0 1.0 CA A:LEU500 4.1 11.0 1.0 N A:ASP496 4.2 11.0 1.0 C A:ASP496 4.2 11.6 1.0 N A:LEU499 4.3 11.5 1.0 CB A:ASP498 4.3 12.1 1.0 OD2 A:ASP498 4.3 14.6 1.0 N A:ARG501 4.3 10.3 1.0 C A:LEU499 4.3 11.2 1.0 CG A:GLU502 4.4 11.5 1.0 CA A:ASP496 4.5 11.6 1.0 CB A:ASP496 4.5 12.0 1.0 CA A:ARG501 4.5 10.3 1.0 CB A:LEU500 4.5 11.2 1.0 N A:TRP495 4.6 9.8 1.0 CA A:LEU499 4.6 11.5 1.0 CD1 A:TRP494 4.7 9.7 1.0 N A:GLU502 4.7 10.2 1.0 N A:GLY497 4.7 11.8 1.0 C A:GLY497 4.8 12.3 1.0 C A:ARG501 4.8 10.2 1.0

Calcium binding site 5 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca633 b:11.9 occ:1.00 OD1 A:ASP226 2.3 13.7 1.0 O A:LYS228 2.3 12.3 1.0 OD1 A:ASP224 2.3 13.8 1.0 OD1 A:ASP222 2.4 10.8 1.0 O A:HOH962 2.4 23.7 1.0 OE2 A:GLU230 2.5 13.2 1.0 OE1 A:GLU230 2.5 12.9 1.0 CD A:GLU230 2.8 12.5 1.0 CG A:ASP226 3.3 15.7 1.0 CG A:ASP224 3.3 15.5 1.0 C A:LYS228 3.5 12.2 1.0 CG A:ASP222 3.5 10.9 1.0 OD2 A:ASP224 3.8 17.7 1.0 OD2 A:ASP226 3.8 17.1 1.0 N A:LYS228 4.0 12.8 1.0 CA A:ASP222 4.1 10.7 1.0 CA A:LYS228 4.2 12.8 1.0 N A:ASP226 4.2 14.9 1.0 N A:ASP224 4.2 13.2 1.0 CB A:ASP222 4.3 10.6 1.0 CG A:GLU230 4.4 13.2 1.0 CB A:ASP226 4.4 15.2 1.0 OD2 A:ASP222 4.4 11.4 1.0 CB A:LYS228 4.4 13.2 1.0 N A:GLY225 4.4 14.4 1.0 O A:HOH679 4.5 14.9 1.0 N A:LEU223 4.5 11.4 1.0 C A:ASP222 4.5 10.8 1.0 N A:ALA229 4.5 11.5 1.0 CB A:ASP224 4.6 14.5 1.0 C A:ALA229 4.7 11.4 1.0 N A:GLU230 4.7 11.3 1.0 CA A:ASP226 4.7 15.3 1.0 CA A:ASP224 4.7 14.2 1.0 CA A:ALA229 4.7 11.6 1.0 N A:GLY227 4.8 14.4 1.0 C A:ASP224 4.9 14.7 1.0

Calcium binding site 6 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca634 b:11.8 occ:1.00 OD1 A:ASP160 2.3 14.1 1.0 O A:GLN164 2.3 11.7 1.0 OD1 A:ASP162 2.3 13.8 1.0 O A:HOH946 2.4 18.8 1.0 OD1 A:ASP158 2.4 11.2 1.0 OE2 A:GLU166 2.5 12.8 1.0 OE1 A:GLU166 2.5 11.6 1.0 CD A:GLU166 2.9 11.8 1.0 CG A:ASP162 3.4 15.0 1.0 CG A:ASP160 3.4 15.9 1.0 C A:GLN164 3.5 11.9 1.0 CG A:ASP158 3.5 11.4 1.0 OD2 A:ASP162 3.8 16.6 1.0 OD2 A:ASP160 3.9 20.0 1.0 N A:GLN164 4.1 12.7 1.0 CA A:GLN164 4.2 12.7 1.0 NZ A:LYS194 4.2 25.0 1.0 CA A:ASP158 4.2 10.8 1.0 CB A:GLN164 4.3 12.8 1.0 OD2 A:ASP158 4.3 12.5 1.0 N A:ASP160 4.3 13.6 1.0 CB A:ASP158 4.3 10.9 1.0 N A:ASP162 4.4 15.2 1.0 CG A:GLU166 4.4 11.1 1.0 N A:VAL159 4.4 12.1 1.0 O A:HOH822 4.5 12.1 1.0 N A:TYR165 4.5 11.1 1.0 C A:ASP158 4.6 11.1 1.0 CB A:ASP162 4.6 15.0 1.0 C A:TYR165 4.6 10.7 1.0 N A:GLY161 4.6 15.1 1.0 N A:GLU166 4.6 10.4 1.0 CB A:ASP160 4.7 14.7 1.0 CA A:TYR165 4.8 11.0 1.0 N A:GLY163 4.8 13.5 1.0 CA A:ASP160 4.9 14.5 1.0 CA A:ASP162 4.9 14.8 1.0 CG A:GLN164 5.0 13.6 1.0 O A:TYR165 5.0 10.7 1.0

Calcium binding site 7 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca635 b:10.8 occ:1.00 O A:TYR462 2.3 12.1 1.0 OD1 A:ASP457 2.3 10.1 1.0 O A:GLY464 2.4 11.2 1.0 O A:ASP459 2.4 11.9 1.0 O A:HOH1125 2.4 12.3 1.0 OE2 A:GLU466 2.4 10.3 1.0 OE1 A:GLU466 2.7 10.5 1.0 CD A:GLU466 2.9 10.7 1.0 CG A:ASP457 3.3 9.9 1.0 C A:ASP459 3.4 11.8 1.0 C A:TYR462 3.5 12.4 1.0 C A:GLY464 3.6 11.0 1.0 OD2 A:ASP457 3.9 11.2 1.0 N A:GLY464 3.9 11.7 1.0 N A:ASP459 4.0 11.5 1.0 C A:PRO463 4.1 12.5 1.0 O A:HOH1128 4.2 13.4 1.0 CA A:ASP459 4.3 11.9 1.0 CB A:ASP457 4.3 10.2 1.0 CA A:ASP457 4.3 10.0 1.0 N A:PRO460 4.3 12.1 1.0 CA A:PRO460 4.3 12.3 1.0 CA A:GLY464 4.3 11.6 1.0 CA A:TYR462 4.4 12.2 1.0 O A:PRO463 4.4 13.5 1.0 N A:TYR462 4.4 12.3 1.0 CG A:GLU466 4.4 10.5 1.0 CA A:PRO463 4.5 12.4 1.0 N A:PRO463 4.5 12.1 1.0 CB A:TYR462 4.5 12.2 1.0 N A:GLN465 4.6 10.9 1.0 N A:GLU466 4.6 10.2 1.0 N A:ILE458 4.6 10.6 1.0 CB A:ASP459 4.7 12.0 1.0 CA A:GLN465 4.7 10.7 1.0 C A:ASP457 4.7 10.3 1.0 C A:PRO460 4.8 12.6 1.0 O A:HOH1127 4.9 15.2 1.0 C A:GLN465 4.9 10.4 1.0

Calcium binding site 8 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca636 b:11.6 occ:1.00 O A:ARG412 2.3 15.3 1.0 O A:ASP409 2.3 12.0 1.0 O A:GLY414 2.3 13.5 1.0 OD1 A:ASP407 2.4 12.1 1.0 OE2 A:GLU416 2.4 12.6 1.0 O A:HOH1144 2.4 14.0 1.0 OE1 A:GLU416 2.7 11.3 1.0 CD A:GLU416 3.0 11.5 1.0 C A:ASP409 3.4 12.5 1.0 CG A:ASP407 3.4 11.4 1.0 C A:ARG412 3.5 15.9 1.0 C A:GLY414 3.5 13.5 1.0 OD2 A:ASP407 3.9 13.8 1.0 N A:GLY414 4.0 15.2 1.0 N A:PRO410 4.2 13.1 1.0 CA A:PRO410 4.2 13.8 1.0 N A:ASP409 4.2 11.8 1.0 C A:PRO413 4.2 15.7 1.0 CA A:ASP409 4.2 12.1 1.0 CA A:ARG412 4.3 16.0 1.0 N A:ARG412 4.3 16.0 1.0 CA A:GLY414 4.4 14.3 1.0 CB A:ARG412 4.4 16.4 1.0 N A:LEU415 4.5 13.0 1.0 CG A:GLU416 4.5 11.3 1.0 N A:PRO413 4.5 15.8 1.0 CA A:LEU415 4.5 11.9 1.0 CB A:ASP409 4.5 12.3 1.0 CA A:ASP407 4.5 10.8 1.0 CB A:ASP407 4.5 11.4 1.0 CA A:PRO413 4.6 15.9 1.0 C A:PRO410 4.6 14.6 1.0 O A:PRO413 4.7 16.0 1.0 NE A:ARG412 4.8 18.2 1.0 N A:LEU408 4.8 10.6 1.0 C A:LEU415 4.8 11.6 1.0 C A:ASP407 4.9 10.9 1.0 O A:PRO410 5.0 16.1 1.0

Calcium binding site 9 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


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 Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca637 b:16.3 occ:1.00 OD1 A:ASP386 2.4 13.3 1.0 OE2 A:GLU377 2.4 15.1 1.0 OD2 A:ASP373 2.4 18.0 1.0 OD2 A:ASP371 2.4 18.5 1.0 ND1 A:HIS387 2.6 14.6 1.0 CE1 A:HIS387 3.3 15.3 1.0 CG A:ASP371 3.3 18.1 1.0 CD A:GLU377 3.4 14.0 1.0 CG A:ASP386 3.4 13.7 1.0 CG A:ASP373 3.4 18.1 1.0 OD1 A:ASP371 3.5 16.7 1.0 CA A:CA638 3.6 16.5 1.0 OD1 A:ASP373 3.7 16.4 1.0 OD2 A:ASP386 3.7 15.4 1.0 CG A:HIS387 3.8 13.4 1.0 CG A:GLU377 4.0 13.0 1.0 N A:HIS387 4.2 11.5 1.0 OE1 A:GLU377 4.2 12.7 1.0 CB A:HIS387 4.3 12.3 1.0 NE2 A:HIS387 4.5 15.3 1.0 CB A:ASP373 4.7 17.5 1.0 CB A:ASP386 4.7 12.2 1.0 CB A:ASP371 4.7 17.5 1.0 CD2 A:HIS387 4.8 14.8 1.0 O A:LYS375 4.8 13.3 1.0 CB A:LYS375 4.9 13.2 1.0 CA A:HIS387 4.9 12.1 1.0

Calcium binding site 10 out of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Rhamnose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca638 b:16.5 occ:1.00 OD1 A:ASP373 2.1 16.4 1.0 OD1 A:ASP371 2.1 16.7 1.0 O A:LYS375 2.2 13.3 1.0 OE2 A:GLU377 2.3 15.1 1.0 OD1 A:ASP369 2.3 14.2 1.0 OE1 A:GLU377 2.4 12.7 1.0 CD A:GLU377 2.6 14.0 1.0 CG A:ASP373 3.0 18.1 1.0 CG A:ASP371 3.2 18.1 1.0 CG A:ASP369 3.3 13.6 1.0 C A:LYS375 3.3 12.9 1.0 OD2 A:ASP373 3.4 18.0 1.0 CA A:CA637 3.6 16.3 1.0 OD2 A:ASP371 3.6 18.5 1.0 N A:LYS375 3.7 13.4 1.0 N A:ASP373 3.9 18.0 1.0 CA A:ASP369 3.9 12.2 1.0 CA A:LYS375 3.9 13.0 1.0 N A:ASP371 4.0 16.2 1.0 CB A:ASP369 4.0 12.2 1.0 N A:VAL370 4.1 12.9 1.0 OD2 A:ASP369 4.2 16.1 1.0 CG A:GLU377 4.2 13.0 1.0 CB A:LYS375 4.2 13.2 1.0 N A:GLY372 4.2 18.2 1.0 CB A:ASP373 4.2 17.5 1.0 C A:ASP369 4.3 12.7 1.0 N A:GLY374 4.4 16.0 1.0 CB A:ASP371 4.4 17.5 1.0 N A:ASP376 4.4 11.4 1.0 CA A:ASP373 4.4 17.4 1.0 CA A:ASP371 4.5 17.3 1.0 C A:ASP371 4.6 18.0 1.0 C A:ASP373 4.6 17.0 1.0 N A:GLU377 4.7 11.1 1.0 CA A:ASP376 4.7 11.3 1.0 C A:ASP376 4.7 11.2 1.0 C A:GLY374 4.7 14.3 1.0 C A:GLY372 4.9 18.6 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