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Calcium in PDB 7drq: Crystal Structure of Polysaccharide Lyase ULY1

Protein crystallography data

The structure of Crystal Structure of Polysaccharide Lyase ULY1, PDB code: 7drq was solved by X.L.Chen, H.Y.Cao, F.Xu, F.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.11 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.993, 99.998, 95.304, 90, 90.94, 90
R / Rfree (%) 15.7 / 18.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Polysaccharide Lyase ULY1 (pdb code 7drq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Polysaccharide Lyase ULY1, PDB code: 7drq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 7drq

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Calcium binding site 1 out of 5 in the Crystal Structure of Polysaccharide Lyase ULY1


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 Polysaccharide Lyase ULY1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:24.8
occ:1.00
 O A:LYS205 2.4 12.6 1.0
OD2 A:ASP193 2.4 11.5 1.0
O A:HOH971 2.5 11.9 1.0
OD2 A:ASP203 2.5 14.0 1.0
O A:HOH1005 2.5 11.6 1.0
O A:HOH840 2.5 11.8 1.0
OD1 A:ASP203 2.5 10.9 1.0
CG A:ASP203 2.8 18.2 1.0
CG A:ASP193 3.4 17.8 1.0
C A:LYS205 3.5 16.1 1.0
O A:HOH739 3.6 29.3 1.0
CB A:ASP193 3.7 16.0 1.0
CB A:LYS205 4.1 12.9 1.0
O A:HOH787 4.1 12.2 1.0
CA A:LYS205 4.2 11.9 1.0
N A:LYS205 4.3 10.4 1.0
CB A:ASP203 4.4 16.1 1.0
O A:LYS165 4.5 13.7 1.0
OD1 A:ASP193 4.5 16.2 1.0
N A:HIS206 4.6 11.0 1.0
OE2 A:GLU199 4.6 23.8 1.0
O A:ASN197 4.6 17.4 1.0
CG A:GLU199 4.7 20.6 1.0
O A:HOH972 4.7 22.5 1.0
N A:GLU199 4.7 17.1 1.0
O A:HOH1042 4.7 20.6 1.0
OD1 A:ASP166 4.8 16.9 1.0
CD A:GLU199 4.8 28.1 1.0
CA A:SER198 4.8 17.6 1.0
CA A:HIS206 4.9 13.4 1.0

Calcium binding site 2 out of 5 in 7drq

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Calcium binding site 2 out of 5 in the Crystal Structure of Polysaccharide Lyase ULY1


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 Polysaccharide Lyase ULY1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:24.8
occ:1.00
 OD2 B:ASP91 2.3 13.4 1.0
O A:HOH1234 2.4 13.5 1.0
O B:HOH891 2.4 11.5 1.0
OD1 A:ASN376 2.5 10.8 1.0
O B:HOH1208 2.5 15.7 1.0
O A:HOH1060 2.5 19.2 1.0
O A:HOH1221 2.6 13.7 1.0
CG A:ASN376 3.5 15.5 1.0
CG B:ASP91 3.5 14.0 1.0
O B:GLY87 4.0 11.0 1.0
NE B:ARG86 4.0 13.4 1.0
CB B:ASP91 4.0 11.8 1.0
CB A:ASN376 4.3 12.2 1.0
ND2 A:ASN376 4.3 13.9 1.0
O B:HOH1209 4.3 21.1 1.0
O A:HOH804 4.4 22.7 1.0
CZ B:ARG86 4.4 17.0 1.0
O A:HOH1271 4.5 40.0 1.0
OD1 B:ASP91 4.5 11.1 1.0
CA A:ASN376 4.5 9.1 1.0
NH2 B:ARG86 4.5 12.9 1.0
CD B:ARG86 4.5 12.6 1.0
O A:GLU375 4.6 12.4 1.0
O B:HOH1320 4.6 41.5 1.0
O A:HOH994 4.6 14.5 1.0
O B:HOH1181 4.7 30.4 1.0
OE1 B:GLN33 4.8 10.7 1.0
CG B:ARG86 4.9 11.9 1.0

Calcium binding site 3 out of 5 in 7drq

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Calcium binding site 3 out of 5 in the Crystal Structure of Polysaccharide Lyase ULY1


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 Polysaccharide Lyase ULY1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:30.0
occ:1.00
 O A:HOH1142 2.3 16.4 1.0
O A:LEU303 2.3 13.7 1.0
O A:PHE307 2.3 11.8 1.0
O A:HOH954 2.5 13.9 1.0
OD1 A:ASP305 2.5 14.3 1.0
O A:HOH1063 2.5 14.5 1.0
O A:HOH839 2.5 16.3 1.0
CG A:ASP305 3.4 13.7 1.0
C A:LEU303 3.5 17.6 1.0
C A:PHE307 3.5 12.3 1.0
N A:LEU303 3.7 14.3 1.0
OD2 A:ASP305 3.9 15.0 1.0
N A:ASP305 4.1 15.1 1.0
C A:ASN302 4.1 13.9 1.0
CA A:LEU303 4.2 12.5 1.0
CA A:ASN302 4.2 11.9 1.0
CB A:PHE307 4.2 15.3 1.0
CA A:PHE307 4.2 11.7 1.0
N A:PHE307 4.3 13.7 1.0
O A:HOH844 4.3 15.5 1.0
N A:ASN302 4.4 11.8 1.0
O A:ASP305 4.5 15.5 1.0
N A:PRO304 4.6 14.4 1.0
N A:ARG308 4.6 14.2 1.0
C A:ARG308 4.6 13.9 1.0
O A:HOH784 4.6 15.9 1.0
O A:ARG308 4.6 13.7 1.0
CB A:ASP305 4.6 13.4 1.0
OD1 A:ASP361 4.7 20.5 1.0
O A:ALA309 4.7 12.5 1.0
CA A:ASP305 4.7 14.1 1.0
CA A:PRO304 4.7 17.9 1.0
CB A:LEU303 4.7 10.3 1.0
C A:ASP305 4.7 15.6 1.0
CA A:ARG308 4.8 14.4 1.0
C A:PRO304 4.9 19.1 1.0
O A:HOH989 4.9 26.4 1.0
N A:ALA309 5.0 15.3 1.0
O A:ASN302 5.0 14.1 1.0

Calcium binding site 4 out of 5 in 7drq

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Calcium binding site 4 out of 5 in the Crystal Structure of Polysaccharide Lyase ULY1


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 Polysaccharide Lyase ULY1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:24.8
occ:1.00
 O B:HOH810 2.4 11.1 1.0
OD2 B:ASP193 2.4 14.9 1.0
OD2 B:ASP203 2.4 11.7 1.0
O B:LYS205 2.4 12.2 1.0
O B:HOH730 2.5 15.2 1.0
O B:HOH919 2.5 13.0 1.0
OD1 B:ASP203 2.6 12.9 1.0
CG B:ASP203 2.9 17.4 1.0
CG B:ASP193 3.4 20.5 1.0
C B:LYS205 3.6 16.0 1.0
CB B:ASP193 3.7 16.4 1.0
O B:HOH805 4.1 13.9 1.0
CB B:LYS205 4.1 12.8 1.0
CA B:LYS205 4.3 12.9 1.0
OE2 B:GLU199 4.3 30.8 1.0
CB B:ASP203 4.4 15.0 1.0
N B:LYS205 4.4 9.8 1.0
O B:LYS165 4.5 11.9 1.0
OD1 B:ASP193 4.5 16.4 1.0
O B:ASN197 4.6 18.1 1.0
CD B:GLU199 4.6 29.7 1.0
N B:HIS206 4.6 14.1 1.0
O B:HOH725 4.7 21.5 1.0
OD1 B:ASP166 4.7 14.7 1.0
CG B:GLU199 4.7 18.8 1.0
O B:HOH1079 4.7 17.2 1.0
N B:GLU199 4.7 15.9 1.0
CA B:SER198 4.8 16.6 1.0
CA B:HIS206 4.9 16.3 1.0

Calcium binding site 5 out of 5 in 7drq

Go back to Calcium Binding Sites List in 7drq
Calcium binding site 5 out of 5 in the Crystal Structure of Polysaccharide Lyase ULY1


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 Polysaccharide Lyase ULY1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:30.0
occ:1.00
 O B:PHE307 2.3 11.3 1.0
O B:LEU303 2.4 13.1 1.0
O B:HOH801 2.4 13.3 1.0
OD1 B:ASP305 2.4 13.4 1.0
O B:HOH1180 2.5 15.3 1.0
O B:HOH885 2.5 16.7 1.0
O B:HOH992 2.5 15.6 1.0
CG B:ASP305 3.4 17.7 1.0
C B:PHE307 3.4 14.0 1.0
C B:LEU303 3.5 15.7 1.0
N B:LEU303 3.8 13.1 1.0
OD2 B:ASP305 3.8 15.4 1.0
N B:ASP305 4.0 14.3 1.0
CA B:PHE307 4.2 15.1 1.0
CB B:PHE307 4.2 12.6 1.0
CA B:LEU303 4.2 15.8 1.0
C B:ASN302 4.3 14.4 1.0
N B:PHE307 4.3 14.6 1.0
O B:HOH1237 4.3 20.9 1.0
CA B:ASN302 4.3 13.6 1.0
O B:HOH879 4.4 15.8 1.0
O B:ASP305 4.5 14.8 1.0
N B:ARG308 4.5 13.1 1.0
N B:ASN302 4.5 12.6 1.0
C B:ARG308 4.5 12.8 1.0
O B:ARG308 4.5 14.5 1.0
N B:PRO304 4.6 14.1 1.0
CB B:ASP305 4.6 12.1 1.0
O B:HOH777 4.6 16.6 1.0
OD1 B:ASP361 4.6 15.9 1.0
CA B:ASP305 4.6 11.9 1.0
C B:ASP305 4.7 14.7 1.0
CA B:ARG308 4.7 14.1 1.0
O B:ALA309 4.7 14.9 1.0
CA B:PRO304 4.7 14.0 1.0
CB B:LEU303 4.8 15.3 1.0
C B:PRO304 4.8 15.3 1.0
N B:ALA309 5.0 12.3 1.0
O B:HOH814 5.0 26.4 1.0

Reference:

X.L.Chen, H.Y.Cao, F.Xu, F.Dong. Crystal Structure of Polysaccharide Lyase ULY1 To Be Published.
Page generated: Fri Jul 19 00:09:35 2024

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