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Calcium in PDB 5xqg: Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose

Protein crystallography data

The structure of Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose, PDB code: 5xqg was solved by Y.Kunishige, M.Iwai, T.Tada, S.Nishimura, T.Sakamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 171.19 / 2.74
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 167.878, 171.935, 342.380, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose (pdb code 5xqg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose, PDB code: 5xqg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5xqg

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Calcium binding site 1 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1003

b:11.1
occ:1.00
 OD2 A:ASP562 2.0 21.5 1.0
OD2 A:ASP621 2.2 17.2 1.0
ND2 A:ASN585 2.2 20.7 1.0
OD1 A:ASP621 2.2 18.7 1.0
NE2 A:HIS616 2.3 19.3 1.0
ND1 A:HIS639 2.3 17.2 1.0
CG A:ASP621 2.5 18.0 1.0
CE1 A:HIS639 3.1 18.1 1.0
CD2 A:HIS616 3.1 19.7 1.0
CG A:ASN585 3.1 21.1 1.0
CG A:ASP562 3.2 20.7 1.0
CE1 A:HIS616 3.4 20.8 1.0
CG A:HIS639 3.4 18.2 1.0
OD1 A:ASN585 3.7 21.7 1.0
CB A:HIS639 3.8 18.1 1.0
CB A:ASP562 4.0 19.5 1.0
CB A:ASP621 4.0 18.7 1.0
CA A:ASN585 4.1 20.7 1.0
OD1 A:ASP562 4.1 21.8 1.0
CB A:ASN585 4.2 21.4 1.0
NE2 A:HIS639 4.2 18.4 1.0
N A:ASN585 4.3 20.7 1.0
CB A:TRP583 4.3 20.4 1.0
CG A:HIS616 4.3 20.3 1.0
CD2 A:HIS639 4.4 18.6 1.0
ND1 A:HIS616 4.4 21.6 1.0
CA A:HIS639 4.5 18.5 1.0
CA A:ASP621 4.8 19.3 1.0
CG A:TRP583 4.9 21.6 1.0
N A:ASP621 5.0 19.7 1.0

Calcium binding site 2 out of 8 in 5xqg

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Calcium binding site 2 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1003

b:11.3
occ:1.00
 OD2 B:ASP562 2.0 21.4 1.0
OD1 B:ASP621 2.1 22.2 1.0
OD2 B:ASP621 2.2 21.4 1.0
ND2 B:ASN585 2.3 20.2 1.0
ND1 B:HIS639 2.4 18.9 1.0
NE2 B:HIS616 2.4 18.6 1.0
CG B:ASP621 2.4 21.7 1.0
CE1 B:HIS639 3.1 19.6 1.0
CD2 B:HIS616 3.2 19.8 1.0
CG B:ASP562 3.2 19.7 1.0
CG B:ASN585 3.2 20.9 1.0
CG B:HIS639 3.5 18.9 1.0
CE1 B:HIS616 3.6 20.2 1.0
OD1 B:ASN585 3.8 21.7 1.0
CB B:HIS639 3.9 18.2 1.0
CB B:ASP562 3.9 18.7 1.0
CB B:ASP621 3.9 21.9 1.0
OD1 B:ASP562 4.0 20.4 1.0
CA B:ASN585 4.1 18.9 1.0
CB B:ASN585 4.2 20.6 1.0
N B:ASN585 4.3 18.6 1.0
NE2 B:HIS639 4.3 19.7 1.0
CB B:TRP583 4.4 23.3 1.0
CG B:HIS616 4.4 19.8 1.0
CD2 B:HIS639 4.5 20.0 1.0
ND1 B:HIS616 4.6 19.9 1.0
CA B:HIS639 4.6 18.3 1.0
CA B:ASP621 4.8 21.6 1.0
CG B:TRP583 5.0 23.4 1.0

Calcium binding site 3 out of 8 in 5xqg

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Calcium binding site 3 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1003

b:9.6
occ:1.00
 OD2 C:ASP562 2.0 22.4 1.0
OD1 C:ASP621 2.0 24.0 1.0
ND2 C:ASN585 2.2 21.2 1.0
ND1 C:HIS639 2.2 20.6 1.0
OD2 C:ASP621 2.3 22.3 1.0
NE2 C:HIS616 2.3 21.3 1.0
CG C:ASP621 2.4 23.2 1.0
CE1 C:HIS639 3.0 20.2 1.0
CG C:ASN585 3.1 23.0 1.0
CG C:ASP562 3.2 21.5 1.0
CD2 C:HIS616 3.2 22.6 1.0
CG C:HIS639 3.3 20.4 1.0
CE1 C:HIS616 3.3 23.4 1.0
OD1 C:ASN585 3.6 24.4 1.0
CB C:HIS639 3.7 20.5 1.0
CB C:ASP621 3.9 23.2 1.0
CB C:ASP562 4.0 21.6 1.0
OD1 C:ASP562 4.1 19.8 1.0
CA C:ASN585 4.1 24.4 1.0
NE2 C:HIS639 4.1 20.2 1.0
CB C:ASN585 4.2 23.8 1.0
CB C:TRP583 4.3 22.5 1.0
N C:ASN585 4.3 25.1 1.0
CD2 C:HIS639 4.3 20.4 1.0
CG C:HIS616 4.4 21.7 1.0
CA C:HIS639 4.4 20.6 1.0
ND1 C:HIS616 4.4 23.2 1.0
CA C:ASP621 4.8 23.2 1.0
CG C:TRP583 4.8 24.9 1.0
N C:ASP621 4.9 23.6 1.0

Calcium binding site 4 out of 8 in 5xqg

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Calcium binding site 4 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1003

b:12.0
occ:1.00
 OD2 D:ASP562 2.0 26.6 1.0
OD1 D:ASP621 2.2 24.7 1.0
ND2 D:ASN585 2.2 24.7 1.0
OD2 D:ASP621 2.2 23.5 1.0
NE2 D:HIS616 2.3 19.8 1.0
ND1 D:HIS639 2.4 25.6 1.0
CG D:ASP621 2.5 25.2 1.0
CG D:ASN585 3.1 26.5 1.0
CD2 D:HIS616 3.2 20.5 1.0
CE1 D:HIS639 3.2 26.4 1.0
CG D:ASP562 3.2 26.4 1.0
CE1 D:HIS616 3.3 21.9 1.0
CG D:HIS639 3.4 24.8 1.0
OD1 D:ASN585 3.5 28.8 1.0
CB D:HIS639 3.7 23.5 1.0
CB D:ASP621 4.0 25.2 1.0
CB D:ASP562 4.0 25.9 1.0
CA D:ASN585 4.1 26.3 1.0
CB D:ASN585 4.2 26.1 1.0
OD1 D:ASP562 4.2 25.9 1.0
CB D:TRP583 4.3 21.0 1.0
N D:ASN585 4.3 25.8 1.0
NE2 D:HIS639 4.4 26.9 1.0
CG D:HIS616 4.4 20.4 1.0
CA D:HIS639 4.4 22.9 1.0
ND1 D:HIS616 4.4 21.4 1.0
CD2 D:HIS639 4.4 26.6 1.0
CA D:ASP621 4.8 25.4 1.0
CG D:TRP583 4.9 21.8 1.0
N D:ASP621 5.0 25.5 1.0

Calcium binding site 5 out of 8 in 5xqg

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Calcium binding site 5 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1003

b:12.4
occ:1.00
 OD2 E:ASP562 2.1 22.9 1.0
ND2 E:ASN585 2.1 18.3 1.0
OD1 E:ASP621 2.2 21.6 1.0
ND1 E:HIS639 2.2 20.0 1.0
OD2 E:ASP621 2.3 22.3 1.0
NE2 E:HIS616 2.3 19.1 1.0
CG E:ASP621 2.5 21.9 1.0
CG E:ASN585 2.8 19.4 1.0
CE1 E:HIS639 2.9 20.6 1.0
OD1 E:ASN585 3.2 21.6 1.0
CG E:ASP562 3.2 21.6 1.0
CE1 E:HIS616 3.3 20.2 1.0
CD2 E:HIS616 3.3 20.3 1.0
CG E:HIS639 3.4 20.9 1.0
CB E:HIS639 3.9 20.1 1.0
CB E:ASN585 4.0 20.0 1.0
CB E:ASP621 4.0 21.8 1.0
CB E:ASP562 4.0 20.6 1.0
CA E:ASN585 4.1 20.0 1.0
OD1 E:ASP562 4.1 21.6 1.0
NE2 E:HIS639 4.1 21.2 1.0
N E:ASN585 4.3 19.9 1.0
CB E:TRP583 4.3 19.8 1.0
CD2 E:HIS639 4.4 21.4 1.0
ND1 E:HIS616 4.4 20.1 1.0
CG E:HIS616 4.5 20.1 1.0
CA E:HIS639 4.5 20.1 1.0
CA E:ASP621 4.8 21.8 1.0
CG E:TRP583 4.9 20.4 1.0
OG1 E:THR617 5.0 28.0 1.0

Calcium binding site 6 out of 8 in 5xqg

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Calcium binding site 6 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1003

b:11.7
occ:1.00
 OD2 F:ASP562 2.1 23.2 1.0
OD1 F:ASP621 2.1 21.3 1.0
ND2 F:ASN585 2.1 17.8 1.0
OD2 F:ASP621 2.2 21.8 1.0
NE2 F:HIS616 2.3 20.0 1.0
ND1 F:HIS639 2.3 19.6 1.0
CG F:ASP621 2.5 21.6 1.0
CG F:ASN585 3.0 18.4 1.0
CE1 F:HIS639 3.0 20.8 1.0
CD2 F:HIS616 3.2 20.5 1.0
CG F:ASP562 3.2 22.0 1.0
CE1 F:HIS616 3.3 22.3 1.0
CG F:HIS639 3.4 20.7 1.0
OD1 F:ASN585 3.5 20.0 1.0
CB F:HIS639 3.9 20.3 1.0
CB F:ASP621 4.0 21.5 1.0
CB F:ASP562 4.0 21.8 1.0
OD1 F:ASP562 4.1 22.3 1.0
CA F:ASN585 4.1 18.8 1.0
CB F:ASN585 4.1 19.1 1.0
NE2 F:HIS639 4.2 20.8 1.0
N F:ASN585 4.3 18.9 1.0
CG F:HIS616 4.4 21.6 1.0
CB F:TRP583 4.4 20.2 1.0
ND1 F:HIS616 4.4 22.4 1.0
CD2 F:HIS639 4.4 21.4 1.0
CA F:HIS639 4.5 21.2 1.0
CA F:ASP621 4.9 20.9 1.0
CG F:TRP583 5.0 20.6 1.0

Calcium binding site 7 out of 8 in 5xqg

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Calcium binding site 7 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1003

b:18.6
occ:1.00
 OD2 G:ASP562 1.9 22.8 1.0
OD1 G:ASP621 2.0 20.3 1.0
ND2 G:ASN585 2.2 32.8 1.0
ND1 G:HIS639 2.2 23.2 1.0
OD2 G:ASP621 2.3 19.6 1.0
NE2 G:HIS616 2.4 22.8 1.0
CG G:ASP621 2.5 20.9 1.0
CE1 G:HIS639 3.0 23.0 1.0
CG G:ASP562 3.1 24.1 1.0
CG G:ASN585 3.1 31.0 1.0
CG G:HIS639 3.3 25.7 1.0
CE1 G:HIS616 3.4 23.6 1.0
CD2 G:HIS616 3.4 23.0 1.0
OD1 G:ASN585 3.5 31.6 1.0
CB G:HIS639 3.7 27.2 1.0
CB G:ASP562 3.9 23.9 1.0
CB G:ASP621 4.0 21.2 1.0
OD1 G:ASP562 4.0 23.7 1.0
NE2 G:HIS639 4.2 22.9 1.0
CB G:ASN585 4.3 28.7 1.0
CB G:TRP583 4.3 24.8 1.0
CA G:ASN585 4.3 28.9 1.0
CD2 G:HIS639 4.4 24.6 1.0
N G:ASN585 4.4 28.9 1.0
CA G:HIS639 4.4 27.7 1.0
ND1 G:HIS616 4.5 22.8 1.0
CG G:HIS616 4.5 23.9 1.0
CA G:ASP621 4.8 22.0 1.0
CG G:TRP583 4.8 24.2 1.0
N G:ASP621 4.9 21.9 1.0

Calcium binding site 8 out of 8 in 5xqg

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Calcium binding site 8 out of 8 in the Crystal Structure of A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl 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 A Pl 26 Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum Complexed with Unsaturated Galacturonosyl Rhamnose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1003

b:19.2
occ:1.00
 OD2 H:ASP562 2.0 22.8 1.0
OD1 H:ASP621 2.0 26.6 1.0
ND1 H:HIS639 2.2 22.7 1.0
OD2 H:ASP621 2.3 26.2 1.0
ND2 H:ASN585 2.3 26.2 1.0
NE2 H:HIS616 2.3 22.4 1.0
CG H:ASP621 2.4 27.3 1.0
CE1 H:HIS639 3.0 22.1 1.0
CG H:ASP562 3.1 24.5 1.0
CG H:ASN585 3.2 26.4 1.0
CD2 H:HIS616 3.2 21.7 1.0
CG H:HIS639 3.3 24.4 1.0
CE1 H:HIS616 3.4 22.9 1.0
OD1 H:ASN585 3.6 29.1 1.0
CB H:HIS639 3.7 25.1 1.0
CB H:ASP562 3.9 23.7 1.0
CB H:ASP621 4.0 25.9 1.0
OD1 H:ASP562 4.1 22.7 1.0
NE2 H:HIS639 4.1 22.7 1.0
CD2 H:HIS639 4.3 23.8 1.0
CB H:ASN585 4.3 25.5 1.0
CA H:ASN585 4.3 25.9 1.0
CG H:HIS616 4.4 22.4 1.0
CB H:TRP583 4.4 23.1 1.0
N H:ASN585 4.5 27.3 1.0
ND1 H:HIS616 4.5 22.6 1.0
CA H:HIS639 4.5 25.9 1.0
CA H:ASP621 4.8 26.2 1.0
N H:ASP621 4.9 26.2 1.0
CG H:TRP583 4.9 22.5 1.0

Reference:

Y.Kunishige, M.Iwai, M.Nakazawa, M.Ueda, T.Tada, S.Nishimura, T.Sakamoto. Crystal Structure of Exo-Rhamnogalacturonan Lyase From Penicillium Chrysogenum As A Member of Polysaccharide Lyase Family 26 Febs Lett. V. 592 1378 2018.
ISSN: ISSN 1873-3468
PubMed: 29574769
DOI: 10.1002/1873-3468.13034
Page generated: Wed Jul 9 11:44:49 2025

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