Calcium in PDB 7czh: PL24 Ulvan Lyase-ULY1
Protein crystallography data
The structure of PL24 Ulvan Lyase-ULY1, PDB code: 7czh
was solved by
Y.Z.Zhang,
X.L.Chen,
F.Dong,
F.Xu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.50 /
2.10
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.1,
99.444,
94.996,
90,
90.55,
90
|
|
R / Rfree (%)
|
15.6 /
19.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the PL24 Ulvan Lyase-ULY1
(pdb code 7czh). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
PL24 Ulvan Lyase-ULY1, PDB code: 7czh:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 1 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca601
b:23.0
occ:1.00
|
O
|
A:LYS205
|
2.3
|
19.4
|
1.0
|
|
OD2
|
A:ASP193
|
2.4
|
24.4
|
1.0
|
|
O
|
A:HOH944
|
2.5
|
19.4
|
1.0
|
|
OD2
|
A:ASP203
|
2.5
|
25.3
|
1.0
|
|
O
|
A:HOH876
|
2.6
|
29.0
|
1.0
|
|
OD1
|
A:ASP203
|
2.7
|
21.3
|
1.0
|
|
O
|
A:HOH751
|
2.7
|
20.3
|
1.0
|
|
CG
|
A:ASP203
|
2.9
|
26.3
|
1.0
|
|
CG
|
A:ASP193
|
3.4
|
25.3
|
1.0
|
|
C
|
A:LYS205
|
3.5
|
21.6
|
1.0
|
|
CB
|
A:ASP193
|
3.7
|
23.4
|
1.0
|
|
O
|
A:HOH972
|
3.9
|
21.2
|
1.0
|
|
CB
|
A:LYS205
|
4.2
|
22.4
|
1.0
|
|
CA
|
A:LYS205
|
4.2
|
19.0
|
1.0
|
|
N
|
A:LYS205
|
4.3
|
18.6
|
1.0
|
|
CB
|
A:ASP203
|
4.4
|
25.6
|
1.0
|
|
N
|
A:HIS206
|
4.5
|
16.9
|
1.0
|
|
O
|
A:LYS165
|
4.5
|
22.5
|
1.0
|
|
OD1
|
A:ASP193
|
4.6
|
23.8
|
1.0
|
|
O
|
A:ASN197
|
4.6
|
26.2
|
1.0
|
|
CG
|
A:GLU199
|
4.7
|
37.1
|
1.0
|
|
OE2
|
A:GLU199
|
4.7
|
47.2
|
1.0
|
|
CA
|
A:HIS206
|
4.8
|
18.3
|
1.0
|
|
O
|
A:HOH1031
|
4.8
|
28.4
|
1.0
|
|
N
|
A:GLU199
|
4.8
|
24.9
|
1.0
|
|
OD1
|
A:ASP166
|
4.8
|
30.2
|
1.0
|
|
CA
|
A:SER198
|
4.8
|
22.1
|
1.0
|
|
O
|
A:HOH789
|
4.9
|
31.5
|
1.0
|
|
CD
|
A:GLU199
|
4.9
|
45.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 2 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca602
b:22.8
occ:1.00
|
O
|
A:HOH997
|
2.3
|
19.0
|
1.0
|
|
O
|
A:PHE307
|
2.3
|
19.5
|
1.0
|
|
O
|
A:LEU303
|
2.4
|
26.6
|
1.0
|
|
O
|
A:HOH921
|
2.4
|
17.1
|
1.0
|
|
OD1
|
A:ASP305
|
2.6
|
23.3
|
1.0
|
|
O
|
A:HOH752
|
2.7
|
25.3
|
1.0
|
|
O
|
A:HOH849
|
2.7
|
17.3
|
1.0
|
|
C
|
A:PHE307
|
3.4
|
20.0
|
1.0
|
|
C
|
A:LEU303
|
3.6
|
27.3
|
1.0
|
|
CG
|
A:ASP305
|
3.6
|
25.6
|
1.0
|
|
N
|
A:LEU303
|
3.7
|
23.1
|
1.0
|
|
OD2
|
A:ASP305
|
4.1
|
22.9
|
1.0
|
|
N
|
A:ASP305
|
4.1
|
25.9
|
1.0
|
|
CA
|
A:PHE307
|
4.2
|
22.5
|
1.0
|
|
C
|
A:ASN302
|
4.2
|
20.1
|
1.0
|
|
CA
|
A:LEU303
|
4.2
|
26.4
|
1.0
|
|
CB
|
A:PHE307
|
4.2
|
18.5
|
1.0
|
|
CA
|
A:ASN302
|
4.2
|
21.4
|
1.0
|
|
O
|
A:HOH738
|
4.3
|
22.8
|
1.0
|
|
N
|
A:PHE307
|
4.4
|
21.6
|
1.0
|
|
OD1
|
A:ASP361
|
4.4
|
32.3
|
1.0
|
|
N
|
A:ARG308
|
4.5
|
22.7
|
1.0
|
|
N
|
A:ASN302
|
4.5
|
21.7
|
1.0
|
|
O
|
A:ASP305
|
4.5
|
21.6
|
1.0
|
|
C
|
A:ARG308
|
4.6
|
24.9
|
1.0
|
|
O
|
A:ARG308
|
4.6
|
20.6
|
1.0
|
|
N
|
A:PRO304
|
4.7
|
25.0
|
1.0
|
|
CA
|
A:ARG308
|
4.7
|
20.2
|
1.0
|
|
O
|
A:HOH756
|
4.7
|
19.6
|
1.0
|
|
CB
|
A:ASP305
|
4.8
|
19.4
|
1.0
|
|
C
|
A:ASP305
|
4.8
|
20.2
|
1.0
|
|
CA
|
A:ASP305
|
4.8
|
23.6
|
1.0
|
|
CB
|
A:LEU303
|
4.8
|
22.6
|
1.0
|
|
CA
|
A:PRO304
|
4.8
|
25.3
|
1.0
|
|
O
|
A:ALA309
|
4.9
|
18.2
|
1.0
|
|
C
|
A:PRO304
|
5.0
|
27.5
|
1.0
|
|
N
|
A:ALA309
|
5.0
|
19.6
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 3 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca603
b:25.2
occ:1.00
|
N
|
A:GLY351
|
3.1
|
20.9
|
1.0
|
|
O
|
A:HOH1179
|
3.2
|
31.8
|
1.0
|
|
N
|
A:GLY312
|
3.3
|
15.1
|
1.0
|
|
O
|
A:HOH723
|
3.3
|
15.4
|
1.0
|
|
CB
|
A:ARG349
|
3.4
|
22.0
|
1.0
|
|
CD
|
A:PRO350
|
3.5
|
20.3
|
1.0
|
|
CA
|
A:ARG349
|
3.5
|
19.4
|
1.0
|
|
N
|
A:PRO350
|
3.5
|
20.6
|
1.0
|
|
CZ
|
A:PHE307
|
3.6
|
21.9
|
1.0
|
|
C
|
A:ARG349
|
3.6
|
23.9
|
1.0
|
|
CA
|
A:GLY312
|
3.7
|
20.4
|
1.0
|
|
CD
|
A:ARG349
|
3.8
|
22.7
|
1.0
|
|
CE1
|
A:PHE307
|
3.8
|
22.9
|
1.0
|
|
CA
|
A:GLY351
|
3.8
|
23.2
|
1.0
|
|
C
|
A:PRO350
|
4.1
|
21.2
|
1.0
|
|
CG
|
A:ARG349
|
4.2
|
24.9
|
1.0
|
|
CA
|
A:PRO350
|
4.3
|
22.5
|
1.0
|
|
C
|
A:ASP311
|
4.3
|
19.3
|
1.0
|
|
O
|
A:ARG349
|
4.3
|
20.9
|
1.0
|
|
CB
|
A:ASP311
|
4.4
|
17.5
|
1.0
|
|
CA
|
A:ASP311
|
4.5
|
20.0
|
1.0
|
|
CG
|
A:PRO350
|
4.5
|
26.0
|
1.0
|
|
CE2
|
A:PHE307
|
4.6
|
22.1
|
1.0
|
|
CB
|
A:PRO350
|
4.6
|
19.0
|
1.0
|
|
OD1
|
A:ASP311
|
4.8
|
24.4
|
1.0
|
|
N
|
A:ARG349
|
4.9
|
20.1
|
1.0
|
|
CD1
|
A:PHE307
|
4.9
|
17.1
|
1.0
|
|
C
|
A:GLY312
|
4.9
|
16.7
|
1.0
|
|
C
|
A:GLY351
|
5.0
|
24.8
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 4 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:21.7
occ:1.00
|
OD2
|
B:ASP193
|
2.3
|
24.6
|
1.0
|
|
OD2
|
B:ASP203
|
2.3
|
24.1
|
1.0
|
|
O
|
B:LYS205
|
2.4
|
24.3
|
1.0
|
|
O
|
B:HOH773
|
2.4
|
22.0
|
1.0
|
|
O
|
B:HOH950
|
2.5
|
26.0
|
1.0
|
|
O
|
B:HOH946
|
2.6
|
24.6
|
1.0
|
|
OD1
|
B:ASP203
|
2.6
|
23.2
|
1.0
|
|
CG
|
B:ASP203
|
2.8
|
27.2
|
1.0
|
|
CG
|
B:ASP193
|
3.3
|
26.4
|
1.0
|
|
C
|
B:LYS205
|
3.6
|
22.1
|
1.0
|
|
CB
|
B:ASP193
|
3.6
|
22.8
|
1.0
|
|
CB
|
B:LYS205
|
4.2
|
25.5
|
1.0
|
|
O
|
B:HOH726
|
4.2
|
32.8
|
1.0
|
|
CA
|
B:LYS205
|
4.3
|
21.4
|
1.0
|
|
CB
|
B:ASP203
|
4.3
|
22.9
|
1.0
|
|
OD1
|
B:ASP193
|
4.4
|
22.2
|
1.0
|
|
N
|
B:LYS205
|
4.5
|
19.6
|
1.0
|
|
O
|
B:ASN197
|
4.5
|
28.0
|
1.0
|
|
O
|
B:LYS165
|
4.5
|
25.8
|
1.0
|
|
O
|
B:HOH1036
|
4.6
|
28.1
|
1.0
|
|
N
|
B:HIS206
|
4.6
|
22.6
|
1.0
|
|
CA
|
B:SER198
|
4.7
|
25.6
|
1.0
|
|
N
|
B:GLU199
|
4.8
|
29.0
|
1.0
|
|
CD
|
B:GLU199
|
4.8
|
47.5
|
1.0
|
|
OD1
|
B:ASP166
|
4.8
|
29.1
|
1.0
|
|
CA
|
B:HIS206
|
4.8
|
24.4
|
1.0
|
|
OE1
|
B:GLU199
|
4.9
|
45.3
|
1.0
|
|
O
|
B:HOH767
|
4.9
|
30.4
|
1.0
|
|
CG
|
B:GLU199
|
5.0
|
35.4
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 5 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca602
b:23.5
occ:1.00
|
O
|
B:LEU303
|
2.3
|
19.8
|
1.0
|
|
O
|
B:PHE307
|
2.3
|
25.3
|
1.0
|
|
OD1
|
B:ASP305
|
2.4
|
24.0
|
1.0
|
|
O
|
B:HOH867
|
2.6
|
22.7
|
1.0
|
|
O
|
B:HOH839
|
2.6
|
26.5
|
1.0
|
|
O
|
B:HOH982
|
2.6
|
21.3
|
1.0
|
|
O
|
B:HOH758
|
2.6
|
19.7
|
1.0
|
|
CG
|
B:ASP305
|
3.3
|
27.3
|
1.0
|
|
C
|
B:LEU303
|
3.5
|
22.6
|
1.0
|
|
C
|
B:PHE307
|
3.5
|
21.4
|
1.0
|
|
OD2
|
B:ASP305
|
3.7
|
28.8
|
1.0
|
|
N
|
B:LEU303
|
3.8
|
20.5
|
1.0
|
|
N
|
B:ASP305
|
4.1
|
24.8
|
1.0
|
|
CB
|
B:PHE307
|
4.2
|
22.7
|
1.0
|
|
CA
|
B:LEU303
|
4.2
|
20.2
|
1.0
|
|
CA
|
B:PHE307
|
4.2
|
22.1
|
1.0
|
|
C
|
B:ASN302
|
4.3
|
24.6
|
1.0
|
|
O
|
B:HOH787
|
4.4
|
23.9
|
1.0
|
|
N
|
B:PHE307
|
4.4
|
22.3
|
1.0
|
|
CA
|
B:ASN302
|
4.4
|
22.2
|
1.0
|
|
O
|
B:ASP305
|
4.5
|
26.4
|
1.0
|
|
N
|
B:ARG308
|
4.5
|
23.2
|
1.0
|
|
N
|
B:PRO304
|
4.5
|
25.5
|
1.0
|
|
CB
|
B:ASP305
|
4.6
|
24.2
|
1.0
|
|
C
|
B:ARG308
|
4.6
|
24.3
|
1.0
|
|
N
|
B:ASN302
|
4.6
|
20.0
|
1.0
|
|
OD1
|
B:ASP361
|
4.6
|
31.9
|
1.0
|
|
O
|
B:ARG308
|
4.6
|
26.9
|
1.0
|
|
CA
|
B:ASP305
|
4.7
|
23.3
|
1.0
|
|
CA
|
B:PRO304
|
4.7
|
27.0
|
1.0
|
|
C
|
B:ASP305
|
4.7
|
25.2
|
1.0
|
|
CA
|
B:ARG308
|
4.7
|
24.8
|
1.0
|
|
CB
|
B:LEU303
|
4.8
|
23.4
|
1.0
|
|
O
|
B:HOH711
|
4.8
|
20.9
|
1.0
|
|
C
|
B:PRO304
|
4.8
|
25.2
|
1.0
|
|
O
|
B:ALA309
|
4.8
|
22.0
|
1.0
|
|
O
|
B:HOH1097
|
4.8
|
30.0
|
1.0
|
|
O
|
B:HOH976
|
4.9
|
27.9
|
1.0
|
|
N
|
B:ALA309
|
4.9
|
23.0
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 6 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca603
b:31.2
occ:1.00
|
O
|
B:HOH823
|
3.0
|
28.4
|
1.0
|
|
N
|
B:GLY351
|
3.2
|
24.5
|
1.0
|
|
N
|
B:GLY312
|
3.2
|
18.2
|
1.0
|
|
CD
|
B:PRO350
|
3.3
|
20.6
|
1.0
|
|
N
|
B:PRO350
|
3.4
|
23.9
|
1.0
|
|
CZ
|
B:PHE307
|
3.6
|
26.7
|
1.0
|
|
C
|
B:ARG349
|
3.6
|
23.8
|
1.0
|
|
CA
|
B:ARG349
|
3.7
|
25.7
|
1.0
|
|
CE1
|
B:PHE307
|
3.7
|
24.9
|
1.0
|
|
CA
|
B:GLY312
|
3.8
|
21.7
|
1.0
|
|
CB
|
B:ARG349
|
3.8
|
31.8
|
1.0
|
|
CA
|
B:GLY351
|
3.9
|
24.4
|
1.0
|
|
CD
|
B:ARG349
|
4.0
|
34.8
|
1.0
|
|
C
|
B:PRO350
|
4.2
|
26.7
|
1.0
|
|
CB
|
B:ASP311
|
4.2
|
25.8
|
1.0
|
|
CA
|
B:PRO350
|
4.2
|
24.4
|
1.0
|
|
C
|
B:ASP311
|
4.3
|
23.5
|
1.0
|
|
CG
|
B:PRO350
|
4.3
|
27.6
|
1.0
|
|
CA
|
B:ASP311
|
4.4
|
23.5
|
1.0
|
|
O
|
B:ARG349
|
4.4
|
26.2
|
1.0
|
|
CB
|
B:PRO350
|
4.5
|
26.5
|
1.0
|
|
CG
|
B:ARG349
|
4.5
|
37.4
|
1.0
|
|
CE2
|
B:PHE307
|
4.7
|
28.3
|
1.0
|
|
C
|
B:GLY312
|
4.8
|
22.3
|
1.0
|
|
CD1
|
B:PHE307
|
4.9
|
23.4
|
1.0
|
|
C
|
B:GLY351
|
5.0
|
26.2
|
1.0
|
|
OD2
|
B:ASP311
|
5.0
|
30.2
|
1.0
|
|
N
|
B:ASP352
|
5.0
|
30.5
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 7 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca604
b:49.7
occ:1.00
|
O
|
B:HOH1066
|
2.4
|
58.3
|
1.0
|
|
O
|
B:GLU375
|
2.5
|
30.7
|
1.0
|
|
OD1
|
B:ASP290
|
2.7
|
37.3
|
1.0
|
|
O
|
B:HOH966
|
2.8
|
37.6
|
1.0
|
|
O
|
B:HOH1085
|
3.0
|
30.0
|
1.0
|
|
O
|
B:HOH1035
|
3.1
|
42.2
|
1.0
|
|
O
|
B:HOH1023
|
3.3
|
30.0
|
1.0
|
|
C
|
B:GLU375
|
3.6
|
31.6
|
1.0
|
|
CG
|
B:ASP290
|
3.7
|
38.2
|
1.0
|
|
OD2
|
B:ASP290
|
4.1
|
36.5
|
1.0
|
|
O
|
B:HOH1119
|
4.2
|
43.0
|
1.0
|
|
CA
|
B:GLU375
|
4.2
|
32.5
|
1.0
|
|
N
|
B:ASN376
|
4.6
|
31.2
|
1.0
|
|
CB
|
B:GLU375
|
4.6
|
37.8
|
1.0
|
|
CA
|
B:ASN376
|
4.8
|
30.5
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7czh
Go back to
Calcium Binding Sites List in 7czh
Calcium binding site 8 out
of 8 in the PL24 Ulvan Lyase-ULY1
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of PL24 Ulvan Lyase-ULY1 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca605
b:26.6
occ:1.00
|
OD2
|
B:ASP91
|
2.3
|
25.6
|
1.0
|
|
O
|
B:HOH777
|
2.4
|
24.3
|
1.0
|
|
OD1
|
A:ASN376
|
2.5
|
24.1
|
1.0
|
|
O
|
B:HOH1048
|
2.6
|
38.2
|
1.0
|
|
O
|
A:HOH1118
|
2.7
|
27.7
|
1.0
|
|
O
|
B:HOH1039
|
2.7
|
29.1
|
1.0
|
|
O
|
A:HOH1138
|
2.9
|
36.8
|
1.0
|
|
CG
|
B:ASP91
|
3.5
|
26.2
|
1.0
|
|
CG
|
A:ASN376
|
3.5
|
28.1
|
1.0
|
|
NE
|
B:ARG86
|
3.9
|
20.6
|
1.0
|
|
O
|
B:GLY87
|
4.1
|
23.8
|
1.0
|
|
O
|
A:HOH808
|
4.1
|
33.8
|
1.0
|
|
CB
|
B:ASP91
|
4.1
|
24.8
|
1.0
|
|
NH2
|
B:ARG86
|
4.3
|
23.5
|
1.0
|
|
CB
|
A:ASN376
|
4.3
|
20.1
|
1.0
|
|
CZ
|
B:ARG86
|
4.3
|
27.6
|
1.0
|
|
OD1
|
B:ASP91
|
4.4
|
23.1
|
1.0
|
|
ND2
|
A:ASN376
|
4.4
|
30.0
|
1.0
|
|
O
|
B:HOH1076
|
4.4
|
37.1
|
1.0
|
|
CD
|
B:ARG86
|
4.5
|
22.3
|
1.0
|
|
CA
|
A:ASN376
|
4.5
|
21.1
|
1.0
|
|
O
|
A:HOH938
|
4.5
|
18.6
|
1.0
|
|
O
|
B:HOH1098
|
4.6
|
40.9
|
1.0
|
|
O
|
A:GLU375
|
4.6
|
26.5
|
1.0
|
|
OE1
|
B:GLN33
|
4.8
|
21.4
|
1.0
|
|
CG
|
B:ARG86
|
4.9
|
19.6
|
1.0
|
|
Reference:
Y.Z.Zhang,
X.L.Chen,
F.Dong,
F.Xu.
PL24 Ulvan Lyase-ULY1 To Be Published.
Page generated: Sat Apr 17 14:08:23 2021
|
