Calcium in PDB 2z8s: Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
Protein crystallography data
The structure of Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid, PDB code: 2z8s
was solved by
A.Ochiai,
T.Itoh,
Y.Maruyama,
A.Kawamata,
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)
|
26.15 /
2.50
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.617,
105.152,
100.668,
90.00,
95.22,
90.00
|
|
R / Rfree (%)
|
16.2 /
24.2
|
Calcium Binding Sites:
Pages:
>>> 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 Digalacturonic Acid
(pdb code 2z8s). 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 Digalacturonic Acid, PDB code: 2z8s:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 1 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca640
b:4.5
occ:1.00
|
OE1
|
A:GLU422
|
2.0
|
20.1
|
1.0
|
|
OD1
|
A:ASP401
|
2.0
|
15.5
|
1.0
|
|
O
|
A:HOH816
|
2.0
|
20.9
|
1.0
|
|
NE2
|
A:HIS399
|
2.1
|
18.6
|
1.0
|
|
NE2
|
A:HIS363
|
2.1
|
13.4
|
1.0
|
|
O
|
A:HOH772
|
2.3
|
2.0
|
1.0
|
|
CD2
|
A:HIS363
|
2.8
|
14.0
|
1.0
|
|
CD
|
A:GLU422
|
2.9
|
20.4
|
1.0
|
|
CD2
|
A:HIS399
|
3.1
|
18.2
|
1.0
|
|
CG
|
A:ASP401
|
3.1
|
17.1
|
1.0
|
|
CE1
|
A:HIS399
|
3.1
|
18.5
|
1.0
|
|
CE1
|
A:HIS363
|
3.3
|
14.3
|
1.0
|
|
OE2
|
A:GLU422
|
3.3
|
20.6
|
1.0
|
|
OD2
|
A:ASP401
|
3.5
|
18.0
|
1.0
|
|
OH
|
A:TYR326
|
3.9
|
17.5
|
1.0
|
|
O
|
A:HOH702
|
3.9
|
18.2
|
1.0
|
|
CG
|
A:HIS363
|
4.0
|
14.0
|
1.0
|
|
CG
|
A:GLU422
|
4.2
|
19.6
|
1.0
|
|
ND1
|
A:HIS363
|
4.2
|
13.9
|
1.0
|
|
CG
|
A:HIS399
|
4.2
|
17.7
|
1.0
|
|
ND1
|
A:HIS399
|
4.2
|
17.2
|
1.0
|
|
O6B
|
A:ADA630
|
4.2
|
23.7
|
1.0
|
|
CB
|
A:ASP401
|
4.4
|
16.6
|
1.0
|
|
O
|
A:GLY400
|
4.4
|
16.2
|
1.0
|
|
C
|
A:GLY400
|
4.5
|
16.3
|
1.0
|
|
CB
|
A:GLU422
|
4.5
|
20.2
|
1.0
|
|
CA
|
A:ASP401
|
4.6
|
16.4
|
1.0
|
|
N
|
A:ASP401
|
4.6
|
16.2
|
1.0
|
|
CE1
|
A:TYR326
|
4.7
|
17.8
|
1.0
|
|
CZ
|
A:TYR326
|
4.7
|
17.7
|
1.0
|
|
CE2
|
A:TYR595
|
5.0
|
13.9
|
1.0
|
|
Calcium binding site 2 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 2 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca641
b:7.2
occ:1.00
|
OD2
|
A:ASP153
|
2.2
|
10.8
|
1.0
|
|
O
|
A:ALA594
|
2.2
|
10.9
|
1.0
|
|
OD1
|
A:ASN596
|
2.3
|
3.2
|
1.0
|
|
O
|
A:ASN592
|
2.4
|
11.7
|
1.0
|
|
O
|
A:HOH678
|
2.4
|
2.0
|
1.0
|
|
O
|
A:HOH767
|
2.5
|
11.2
|
1.0
|
|
CG
|
A:ASP153
|
3.3
|
12.7
|
1.0
|
|
C
|
A:ALA594
|
3.3
|
10.9
|
1.0
|
|
CG
|
A:ASN596
|
3.3
|
6.2
|
1.0
|
|
C
|
A:ASN592
|
3.5
|
11.4
|
1.0
|
|
OD1
|
A:ASP153
|
3.7
|
12.6
|
1.0
|
|
ND2
|
A:ASN596
|
3.7
|
4.6
|
1.0
|
|
N
|
A:ALA594
|
3.7
|
11.1
|
1.0
|
|
C
|
A:ILE593
|
3.7
|
11.5
|
1.0
|
|
O
|
A:ILE593
|
3.8
|
11.9
|
1.0
|
|
CA
|
A:ALA594
|
3.9
|
10.9
|
1.0
|
|
ND2
|
A:ASN532
|
4.0
|
14.1
|
1.0
|
|
O
|
A:HOH765
|
4.0
|
2.0
|
1.0
|
|
O
|
A:HOH766
|
4.1
|
3.7
|
1.0
|
|
O
|
A:HOH774
|
4.3
|
9.8
|
1.0
|
|
N
|
A:ASN596
|
4.3
|
10.1
|
1.0
|
|
CA
|
A:ASN592
|
4.3
|
11.3
|
1.0
|
|
N
|
A:ILE593
|
4.4
|
11.7
|
1.0
|
|
O
|
A:ALA213
|
4.4
|
10.6
|
1.0
|
|
N
|
A:TYR595
|
4.4
|
10.9
|
1.0
|
|
NZ
|
A:LYS170
|
4.4
|
11.2
|
1.0
|
|
CA
|
A:ILE593
|
4.5
|
11.6
|
1.0
|
|
O
|
A:HOH742
|
4.5
|
15.7
|
1.0
|
|
CB
|
A:ASP153
|
4.5
|
13.0
|
1.0
|
|
CB
|
A:ASN596
|
4.6
|
8.4
|
1.0
|
|
CA
|
A:TYR595
|
4.7
|
10.9
|
1.0
|
|
CG
|
A:ASN532
|
4.8
|
14.1
|
1.0
|
|
CB
|
A:ALA213
|
4.8
|
10.8
|
1.0
|
|
CA
|
A:ALA213
|
4.9
|
11.1
|
1.0
|
|
CA
|
A:ASN596
|
4.9
|
9.4
|
1.0
|
|
O
|
A:GLN591
|
4.9
|
11.0
|
1.0
|
|
C
|
A:TYR595
|
4.9
|
10.6
|
1.0
|
|
NE2
|
A:GLN217
|
5.0
|
9.7
|
1.0
|
|
Calcium binding site 3 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 3 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca642
b:25.2
occ:1.00
|
O
|
A:LEU500
|
2.1
|
12.3
|
1.0
|
|
O
|
A:HOH723
|
2.2
|
2.0
|
1.0
|
|
OD1
|
A:ASP496
|
2.3
|
20.5
|
1.0
|
|
OD1
|
A:ASP498
|
2.4
|
14.8
|
1.0
|
|
OE2
|
A:GLU502
|
2.4
|
15.6
|
1.0
|
|
OE1
|
A:GLU502
|
2.8
|
15.1
|
1.0
|
|
CD
|
A:GLU502
|
2.9
|
14.9
|
1.0
|
|
O
|
A:ASP498
|
3.0
|
15.1
|
1.0
|
|
C
|
A:LEU500
|
3.3
|
12.3
|
1.0
|
|
CG
|
A:ASP496
|
3.5
|
18.5
|
1.0
|
|
CG
|
A:ASP498
|
3.6
|
15.5
|
1.0
|
|
C
|
A:ASP498
|
3.7
|
14.9
|
1.0
|
|
N
|
A:LEU500
|
3.9
|
13.1
|
1.0
|
|
N
|
A:ASP498
|
4.0
|
15.6
|
1.0
|
|
O
|
A:ASP496
|
4.0
|
16.2
|
1.0
|
|
OD2
|
A:ASP496
|
4.1
|
21.6
|
1.0
|
|
CA
|
A:LEU500
|
4.1
|
12.5
|
1.0
|
|
N
|
A:ASP496
|
4.1
|
16.1
|
1.0
|
|
CA
|
A:ASP498
|
4.2
|
15.4
|
1.0
|
|
C
|
A:ASP496
|
4.2
|
16.6
|
1.0
|
|
N
|
A:ARG501
|
4.3
|
12.6
|
1.0
|
|
CA
|
A:ARG501
|
4.3
|
12.9
|
1.0
|
|
NZ
|
A:LYS511
|
4.3
|
20.5
|
1.0
|
|
C
|
A:LEU499
|
4.4
|
13.7
|
1.0
|
|
N
|
A:TRP495
|
4.4
|
14.5
|
1.0
|
|
CD1
|
A:TRP494
|
4.4
|
13.4
|
1.0
|
|
OD2
|
A:ASP498
|
4.4
|
16.4
|
1.0
|
|
CG
|
A:GLU502
|
4.4
|
14.8
|
1.0
|
|
N
|
A:LEU499
|
4.5
|
14.3
|
1.0
|
|
CB
|
A:LEU500
|
4.5
|
12.4
|
1.0
|
|
N
|
A:GLU502
|
4.5
|
13.8
|
1.0
|
|
CB
|
A:ASP498
|
4.5
|
15.6
|
1.0
|
|
CA
|
A:ASP496
|
4.5
|
16.7
|
1.0
|
|
C
|
A:ARG501
|
4.6
|
13.3
|
1.0
|
|
CB
|
A:ASP496
|
4.6
|
17.0
|
1.0
|
|
CA
|
A:TRP494
|
4.7
|
13.9
|
1.0
|
|
CA
|
A:LEU499
|
4.8
|
13.9
|
1.0
|
|
N
|
A:GLY497
|
4.8
|
16.7
|
1.0
|
|
C
|
A:TRP494
|
4.9
|
14.1
|
1.0
|
|
C
|
A:GLY497
|
4.9
|
16.1
|
1.0
|
|
O
|
A:LEU499
|
4.9
|
13.8
|
1.0
|
|
Calcium binding site 4 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 4 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca643
b:14.9
occ:1.00
|
O
|
A:LEU545
|
2.2
|
16.1
|
1.0
|
|
OE2
|
A:GLU551
|
2.3
|
10.9
|
1.0
|
|
O
|
A:ARG549
|
2.4
|
13.8
|
1.0
|
|
O
|
A:ASP547
|
2.4
|
14.9
|
1.0
|
|
OD1
|
A:ASP543
|
2.5
|
11.9
|
1.0
|
|
OE1
|
A:GLU551
|
2.7
|
12.2
|
1.0
|
|
O
|
A:HOH676
|
2.8
|
7.2
|
1.0
|
|
CD
|
A:GLU551
|
2.9
|
11.4
|
1.0
|
|
C
|
A:LEU545
|
3.5
|
15.6
|
1.0
|
|
C
|
A:ARG549
|
3.5
|
13.6
|
1.0
|
|
CG
|
A:ASP543
|
3.6
|
13.3
|
1.0
|
|
C
|
A:ASP547
|
3.6
|
14.9
|
1.0
|
|
C
|
A:GLY546
|
3.8
|
14.7
|
1.0
|
|
O
|
A:GLY546
|
3.9
|
14.2
|
1.0
|
|
N
|
A:ASP547
|
3.9
|
14.6
|
1.0
|
|
CA
|
A:ASP543
|
4.1
|
13.4
|
1.0
|
|
N
|
A:LEU545
|
4.1
|
15.3
|
1.0
|
|
O
|
A:HOH651
|
4.2
|
2.7
|
1.0
|
|
CA
|
A:GLY546
|
4.2
|
15.0
|
1.0
|
|
N
|
A:ARG549
|
4.2
|
14.2
|
1.0
|
|
CB
|
A:ASP543
|
4.3
|
13.2
|
1.0
|
|
OG1
|
A:THR566
|
4.3
|
11.8
|
1.0
|
|
OD1
|
A:ASP547
|
4.3
|
14.2
|
1.0
|
|
N
|
A:GLY546
|
4.3
|
15.4
|
1.0
|
|
CG
|
A:GLU551
|
4.4
|
10.2
|
1.0
|
|
CA
|
A:ARG549
|
4.4
|
13.7
|
1.0
|
|
CA
|
A:ASP547
|
4.4
|
14.6
|
1.0
|
|
N
|
A:LEU544
|
4.4
|
14.6
|
1.0
|
|
N
|
A:GLU550
|
4.5
|
12.8
|
1.0
|
|
CA
|
A:LEU545
|
4.5
|
15.5
|
1.0
|
|
C
|
A:TRP548
|
4.5
|
14.9
|
1.0
|
|
OD2
|
A:ASP543
|
4.5
|
14.8
|
1.0
|
|
C
|
A:ASP543
|
4.5
|
13.9
|
1.0
|
|
CA
|
A:GLU550
|
4.5
|
11.9
|
1.0
|
|
N
|
A:GLU551
|
4.6
|
11.2
|
1.0
|
|
N
|
A:TRP548
|
4.6
|
15.1
|
1.0
|
|
C
|
A:GLU550
|
4.7
|
11.7
|
1.0
|
|
O
|
A:HOH759
|
4.7
|
14.8
|
1.0
|
|
CB
|
A:ARG549
|
4.8
|
13.3
|
1.0
|
|
O
|
A:TRP548
|
4.9
|
15.2
|
1.0
|
|
CA
|
A:TRP548
|
4.9
|
15.2
|
1.0
|
|
Calcium binding site 5 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 5 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca644
b:40.8
occ:1.00
|
OD1
|
A:ASP158
|
2.2
|
13.9
|
1.0
|
|
OE1
|
A:GLU166
|
2.4
|
13.6
|
1.0
|
|
O
|
A:GLN164
|
2.4
|
15.8
|
1.0
|
|
OD1
|
A:ASP160
|
2.4
|
21.5
|
1.0
|
|
OE2
|
A:GLU166
|
2.6
|
16.6
|
1.0
|
|
OD1
|
A:ASP162
|
2.6
|
18.8
|
1.0
|
|
CD
|
A:GLU166
|
2.8
|
15.1
|
1.0
|
|
CG
|
A:ASP158
|
3.3
|
15.6
|
1.0
|
|
N
|
A:VAL159
|
3.5
|
16.4
|
1.0
|
|
CA
|
A:ASP158
|
3.5
|
16.0
|
1.0
|
|
CG
|
A:ASP162
|
3.5
|
18.9
|
1.0
|
|
C
|
A:GLN164
|
3.6
|
15.9
|
1.0
|
|
CG
|
A:ASP160
|
3.6
|
20.0
|
1.0
|
|
N
|
A:ASP160
|
3.7
|
18.2
|
1.0
|
|
C
|
A:ASP158
|
3.7
|
16.3
|
1.0
|
|
N
|
A:GLY161
|
3.9
|
18.8
|
1.0
|
|
N
|
A:ASP162
|
3.9
|
18.1
|
1.0
|
|
CB
|
A:ASP158
|
4.0
|
15.9
|
1.0
|
|
N
|
A:GLN164
|
4.1
|
16.7
|
1.0
|
|
NZ
|
A:LYS194
|
4.1
|
19.6
|
1.0
|
|
OD2
|
A:ASP162
|
4.1
|
20.1
|
1.0
|
|
OD2
|
A:ASP158
|
4.2
|
17.5
|
1.0
|
|
OD2
|
A:ASP160
|
4.3
|
20.8
|
1.0
|
|
CG
|
A:GLU166
|
4.3
|
13.3
|
1.0
|
|
CA
|
A:GLN164
|
4.3
|
16.3
|
1.0
|
|
C
|
A:ASP160
|
4.4
|
18.7
|
1.0
|
|
CA
|
A:ASP160
|
4.4
|
18.7
|
1.0
|
|
CB
|
A:ASP162
|
4.5
|
18.1
|
1.0
|
|
CA
|
A:VAL159
|
4.5
|
16.8
|
1.0
|
|
N
|
A:GLU166
|
4.6
|
14.2
|
1.0
|
|
CA
|
A:ASP162
|
4.6
|
18.0
|
1.0
|
|
N
|
A:GLY163
|
4.6
|
17.2
|
1.0
|
|
C
|
A:VAL159
|
4.6
|
17.4
|
1.0
|
|
O
|
A:GLY157
|
4.6
|
15.8
|
1.0
|
|
CB
|
A:ASP160
|
4.6
|
19.0
|
1.0
|
|
CA
|
A:GLY161
|
4.6
|
18.4
|
1.0
|
|
N
|
A:TYR165
|
4.6
|
15.7
|
1.0
|
|
O
|
A:ASP158
|
4.7
|
16.8
|
1.0
|
|
C
|
A:GLY161
|
4.7
|
18.5
|
1.0
|
|
O
|
A:HOH659
|
4.7
|
11.0
|
1.0
|
|
CB
|
A:GLN164
|
4.8
|
16.4
|
1.0
|
|
N
|
A:ASP158
|
4.8
|
15.9
|
1.0
|
|
C
|
A:TYR165
|
4.8
|
14.8
|
1.0
|
|
CA
|
A:TYR165
|
4.8
|
15.2
|
1.0
|
|
C
|
A:ASP162
|
4.9
|
17.8
|
1.0
|
|
CB
|
A:GLU166
|
5.0
|
13.4
|
1.0
|
|
Calcium binding site 6 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 6 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca645
b:34.5
occ:1.00
|
O
|
A:LYS375
|
2.2
|
20.1
|
1.0
|
|
OE2
|
A:GLU377
|
2.2
|
24.2
|
1.0
|
|
OD1
|
A:ASP371
|
2.2
|
25.6
|
1.0
|
|
OD1
|
A:ASP369
|
2.3
|
20.4
|
1.0
|
|
OE1
|
A:GLU377
|
2.4
|
24.4
|
1.0
|
|
OD1
|
A:ASP373
|
2.5
|
26.3
|
1.0
|
|
CD
|
A:GLU377
|
2.6
|
23.4
|
1.0
|
|
CG
|
A:ASP371
|
3.3
|
24.4
|
1.0
|
|
C
|
A:LYS375
|
3.3
|
20.1
|
1.0
|
|
CG
|
A:ASP373
|
3.3
|
25.1
|
1.0
|
|
CG
|
A:ASP369
|
3.3
|
20.8
|
1.0
|
|
CA
|
A:ASP369
|
3.5
|
20.4
|
1.0
|
|
CA
|
A:CA649
|
3.7
|
29.7
|
1.0
|
|
OD2
|
A:ASP371
|
3.7
|
24.1
|
1.0
|
|
CB
|
A:ASP369
|
3.7
|
20.6
|
1.0
|
|
N
|
A:VAL370
|
3.7
|
21.1
|
1.0
|
|
OD2
|
A:ASP373
|
3.8
|
26.9
|
1.0
|
|
N
|
A:LYS375
|
3.9
|
21.2
|
1.0
|
|
N
|
A:ASP371
|
3.9
|
22.1
|
1.0
|
|
C
|
A:ASP369
|
4.0
|
20.6
|
1.0
|
|
CA
|
A:LYS375
|
4.0
|
20.7
|
1.0
|
|
N
|
A:ASP373
|
4.1
|
23.1
|
1.0
|
|
CG
|
A:GLU377
|
4.1
|
21.2
|
1.0
|
|
N
|
A:GLY374
|
4.3
|
22.9
|
1.0
|
|
N
|
A:ASP376
|
4.3
|
19.5
|
1.0
|
|
CB
|
A:LYS375
|
4.3
|
20.7
|
1.0
|
|
N
|
A:GLU377
|
4.3
|
19.2
|
1.0
|
|
CB
|
A:ASP373
|
4.4
|
23.7
|
1.0
|
|
OD2
|
A:ASP369
|
4.4
|
21.8
|
1.0
|
|
CA
|
A:ASP376
|
4.4
|
18.8
|
1.0
|
|
C
|
A:ASP376
|
4.5
|
19.2
|
1.0
|
|
N
|
A:GLY372
|
4.5
|
22.9
|
1.0
|
|
CB
|
A:ASP371
|
4.5
|
22.6
|
1.0
|
|
CA
|
A:ASP373
|
4.5
|
23.4
|
1.0
|
|
C
|
A:ASP373
|
4.5
|
23.3
|
1.0
|
|
CA
|
A:ASP371
|
4.6
|
22.7
|
1.0
|
|
O
|
A:ALA368
|
4.6
|
20.0
|
1.0
|
|
C
|
A:ASP371
|
4.7
|
22.9
|
1.0
|
|
C
|
A:GLY374
|
4.7
|
21.7
|
1.0
|
|
N
|
A:ASP369
|
4.7
|
20.0
|
1.0
|
|
CG
|
A:LYS375
|
4.9
|
21.5
|
1.0
|
|
CA
|
A:VAL370
|
4.9
|
21.2
|
1.0
|
|
C
|
A:VAL370
|
4.9
|
21.6
|
1.0
|
|
O
|
A:ASP369
|
5.0
|
20.8
|
1.0
|
|
CB
|
A:GLU377
|
5.0
|
19.4
|
1.0
|
|
CA
|
A:GLY374
|
5.0
|
22.2
|
1.0
|
|
Calcium binding site 7 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 7 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca646
b:30.8
occ:1.00
|
O
|
A:ARG412
|
2.2
|
26.3
|
1.0
|
|
O
|
A:ASP409
|
2.2
|
21.1
|
1.0
|
|
OD1
|
A:ASP407
|
2.3
|
20.7
|
1.0
|
|
O
|
A:GLY414
|
2.5
|
23.4
|
1.0
|
|
OE1
|
A:GLU416
|
2.6
|
21.8
|
1.0
|
|
OE2
|
A:GLU416
|
2.7
|
22.9
|
1.0
|
|
CD
|
A:GLU416
|
3.0
|
21.7
|
1.0
|
|
C
|
A:ASP409
|
3.1
|
21.3
|
1.0
|
|
C
|
A:ARG412
|
3.3
|
26.0
|
1.0
|
|
CG
|
A:ASP407
|
3.5
|
20.0
|
1.0
|
|
C
|
A:GLY414
|
3.7
|
23.6
|
1.0
|
|
N
|
A:ASP409
|
3.9
|
20.0
|
1.0
|
|
CA
|
A:ASP409
|
3.9
|
20.6
|
1.0
|
|
N
|
A:PRO410
|
4.0
|
22.1
|
1.0
|
|
CB
|
A:ARG412
|
4.0
|
25.9
|
1.0
|
|
CA
|
A:ARG412
|
4.0
|
26.0
|
1.0
|
|
N
|
A:ARG412
|
4.1
|
25.6
|
1.0
|
|
CA
|
A:PRO410
|
4.1
|
22.9
|
1.0
|
|
OD2
|
A:ASP407
|
4.2
|
22.4
|
1.0
|
|
C
|
A:PRO413
|
4.2
|
25.6
|
1.0
|
|
CB
|
A:ASP409
|
4.2
|
20.6
|
1.0
|
|
N
|
A:GLY414
|
4.2
|
25.1
|
1.0
|
|
C
|
A:PRO410
|
4.4
|
23.7
|
1.0
|
|
N
|
A:PRO413
|
4.4
|
26.0
|
1.0
|
|
CG
|
A:GLU416
|
4.4
|
20.7
|
1.0
|
|
CA
|
A:ASP407
|
4.5
|
18.6
|
1.0
|
|
O
|
A:PRO413
|
4.5
|
25.9
|
1.0
|
|
O
|
A:PRO410
|
4.5
|
24.1
|
1.0
|
|
CA
|
A:PRO413
|
4.6
|
25.8
|
1.0
|
|
CB
|
A:ASP407
|
4.6
|
18.8
|
1.0
|
|
CA
|
A:GLY414
|
4.6
|
24.1
|
1.0
|
|
N
|
A:LEU415
|
4.6
|
22.7
|
1.0
|
|
CA
|
A:LEU415
|
4.7
|
21.9
|
1.0
|
|
C
|
A:ASP407
|
4.7
|
18.7
|
1.0
|
|
N
|
A:LEU408
|
4.7
|
19.0
|
1.0
|
|
C
|
A:LEU415
|
4.9
|
21.6
|
1.0
|
|
N
|
A:GLU416
|
4.9
|
20.8
|
1.0
|
|
CG
|
A:ASP409
|
4.9
|
21.3
|
1.0
|
|
N
|
A:GLY411
|
5.0
|
24.3
|
1.0
|
|
Calcium binding site 8 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 8 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca647
b:45.6
occ:1.00
|
O
|
A:LYS228
|
2.1
|
20.8
|
1.0
|
|
OE1
|
A:GLU230
|
2.2
|
20.9
|
1.0
|
|
OD1
|
A:ASP226
|
2.3
|
21.8
|
1.0
|
|
OE2
|
A:GLU230
|
2.4
|
19.4
|
1.0
|
|
CD
|
A:GLU230
|
2.5
|
20.3
|
1.0
|
|
OD1
|
A:ASP222
|
2.7
|
18.8
|
1.0
|
|
OD1
|
A:ASP224
|
2.7
|
21.8
|
1.0
|
|
O
|
A:HOH800
|
3.1
|
10.2
|
1.0
|
|
C
|
A:LYS228
|
3.3
|
20.6
|
1.0
|
|
CG
|
A:ASP226
|
3.3
|
20.9
|
1.0
|
|
CG
|
A:ASP224
|
3.6
|
19.9
|
1.0
|
|
CG
|
A:ASP222
|
3.7
|
17.9
|
1.0
|
|
OD2
|
A:ASP226
|
3.9
|
20.7
|
1.0
|
|
CA
|
A:ASP222
|
4.0
|
17.1
|
1.0
|
|
CG
|
A:GLU230
|
4.0
|
19.4
|
1.0
|
|
OD2
|
A:ASP224
|
4.0
|
18.9
|
1.0
|
|
N
|
A:GLU230
|
4.0
|
18.6
|
1.0
|
|
N
|
A:LYS228
|
4.2
|
20.9
|
1.0
|
|
CA
|
A:LYS228
|
4.2
|
20.9
|
1.0
|
|
C
|
A:ALA229
|
4.2
|
19.0
|
1.0
|
|
N
|
A:LEU223
|
4.2
|
17.9
|
1.0
|
|
N
|
A:ALA229
|
4.2
|
19.9
|
1.0
|
|
N
|
A:ASP226
|
4.2
|
20.5
|
1.0
|
|
CB
|
A:ASP222
|
4.2
|
16.8
|
1.0
|
|
CA
|
A:ALA229
|
4.3
|
19.3
|
1.0
|
|
O
|
A:HOH670
|
4.3
|
4.8
|
1.0
|
|
N
|
A:ASP224
|
4.4
|
19.0
|
1.0
|
|
C
|
A:ASP222
|
4.4
|
17.5
|
1.0
|
|
CB
|
A:ASP226
|
4.5
|
20.7
|
1.0
|
|
CB
|
A:LYS228
|
4.5
|
21.1
|
1.0
|
|
OD2
|
A:ASP222
|
4.7
|
19.9
|
1.0
|
|
CA
|
A:ASP226
|
4.7
|
20.6
|
1.0
|
|
N
|
A:GLY225
|
4.7
|
20.0
|
1.0
|
|
CB
|
A:GLU230
|
4.7
|
18.2
|
1.0
|
|
O
|
A:ALA229
|
4.8
|
19.0
|
1.0
|
|
CB
|
A:ASP224
|
4.8
|
19.8
|
1.0
|
|
C
|
A:ASP226
|
4.9
|
20.8
|
1.0
|
|
N
|
A:GLY227
|
4.9
|
20.8
|
1.0
|
|
CA
|
A:GLU230
|
4.9
|
18.1
|
1.0
|
|
O
|
A:TYR221
|
4.9
|
15.5
|
1.0
|
|
CA
|
A:ASP224
|
5.0
|
19.5
|
1.0
|
|
Calcium binding site 9 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 9 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca648
b:28.9
occ:1.00
|
OD1
|
A:ASP457
|
2.2
|
16.1
|
1.0
|
|
O
|
A:ASP459
|
2.3
|
15.1
|
1.0
|
|
O
|
A:GLY464
|
2.3
|
17.2
|
1.0
|
|
O
|
A:TYR462
|
2.4
|
18.3
|
1.0
|
|
OE2
|
A:GLU466
|
2.6
|
18.3
|
1.0
|
|
OE1
|
A:GLU466
|
2.9
|
19.0
|
1.0
|
|
CD
|
A:GLU466
|
3.1
|
18.2
|
1.0
|
|
CG
|
A:ASP457
|
3.2
|
16.1
|
1.0
|
|
C
|
A:ASP459
|
3.3
|
15.3
|
1.0
|
|
C
|
A:GLY464
|
3.5
|
17.3
|
1.0
|
|
C
|
A:TYR462
|
3.6
|
17.9
|
1.0
|
|
N
|
A:GLY464
|
3.8
|
17.9
|
1.0
|
|
OD2
|
A:ASP457
|
3.8
|
18.0
|
1.0
|
|
N
|
A:PRO460
|
4.0
|
15.4
|
1.0
|
|
CA
|
A:PRO460
|
4.1
|
15.7
|
1.0
|
|
N
|
A:ASP459
|
4.2
|
14.8
|
1.0
|
|
CA
|
A:ASP457
|
4.2
|
14.5
|
1.0
|
|
O
|
A:HOH681
|
4.2
|
25.2
|
1.0
|
|
CA
|
A:GLY464
|
4.2
|
17.6
|
1.0
|
|
C
|
A:PRO463
|
4.2
|
18.0
|
1.0
|
|
CA
|
A:ASP459
|
4.2
|
15.3
|
1.0
|
|
CB
|
A:ASP457
|
4.2
|
14.7
|
1.0
|
|
CA
|
A:TYR462
|
4.5
|
17.5
|
1.0
|
|
N
|
A:TYR462
|
4.5
|
17.2
|
1.0
|
|
N
|
A:GLN465
|
4.5
|
17.1
|
1.0
|
|
CB
|
A:TYR462
|
4.6
|
17.4
|
1.0
|
|
N
|
A:PRO463
|
4.6
|
17.9
|
1.0
|
|
CG
|
A:GLU466
|
4.6
|
16.8
|
1.0
|
|
CA
|
A:PRO463
|
4.6
|
18.0
|
1.0
|
|
C
|
A:PRO460
|
4.7
|
16.0
|
1.0
|
|
N
|
A:ILE458
|
4.7
|
14.6
|
1.0
|
|
N
|
A:GLU466
|
4.7
|
16.5
|
1.0
|
|
O
|
A:HOH795
|
4.7
|
11.1
|
1.0
|
|
CA
|
A:GLN465
|
4.7
|
16.5
|
1.0
|
|
CB
|
A:ASP459
|
4.8
|
15.3
|
1.0
|
|
C
|
A:ASP457
|
4.8
|
14.5
|
1.0
|
|
O
|
A:PRO463
|
4.8
|
18.0
|
1.0
|
|
O
|
A:HOH793
|
4.9
|
28.6
|
1.0
|
|
C
|
A:GLN465
|
5.0
|
16.5
|
1.0
|
|
Calcium binding site 10 out
of 20 in 2z8s
Go back to
Calcium Binding Sites List in 2z8s
Calcium binding site 10 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw Complexed with Digalacturonic Acid
 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 Digalacturonic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca649
b:29.7
occ:1.00
|
OD2
|
A:ASP371
|
2.3
|
24.1
|
1.0
|
|
OD2
|
A:ASP373
|
2.4
|
26.9
|
1.0
|
|
OD1
|
A:ASP386
|
2.5
|
26.9
|
1.0
|
|
OE2
|
A:GLU377
|
2.6
|
24.2
|
1.0
|
|
ND1
|
A:HIS387
|
2.7
|
25.9
|
1.0
|
|
CG
|
A:ASP371
|
3.2
|
24.4
|
1.0
|
|
CG
|
A:ASP373
|
3.3
|
25.1
|
1.0
|
|
CG
|
A:ASP386
|
3.3
|
26.4
|
1.0
|
|
OD1
|
A:ASP371
|
3.4
|
25.6
|
1.0
|
|
CE1
|
A:HIS387
|
3.4
|
26.3
|
1.0
|
|
CD
|
A:GLU377
|
3.5
|
23.4
|
1.0
|
|
OD2
|
A:ASP386
|
3.6
|
27.8
|
1.0
|
|
OD1
|
A:ASP373
|
3.7
|
26.3
|
1.0
|
|
CA
|
A:CA645
|
3.7
|
34.5
|
1.0
|
|
CG
|
A:HIS387
|
3.8
|
26.2
|
1.0
|
|
CG
|
A:GLU377
|
4.0
|
21.2
|
1.0
|
|
CB
|
A:HIS387
|
4.1
|
26.1
|
1.0
|
|
N
|
A:HIS387
|
4.2
|
25.7
|
1.0
|
|
OE1
|
A:GLU377
|
4.4
|
24.4
|
1.0
|
|
CB
|
A:ASP373
|
4.6
|
23.7
|
1.0
|
|
CB
|
A:ASP371
|
4.6
|
22.6
|
1.0
|
|
NE2
|
A:HIS387
|
4.7
|
26.4
|
1.0
|
|
CB
|
A:ASP386
|
4.7
|
25.4
|
1.0
|
|
CA
|
A:HIS387
|
4.8
|
26.1
|
1.0
|
|
CD2
|
A:HIS387
|
4.8
|
26.0
|
1.0
|
|
CB
|
A:LYS375
|
4.9
|
20.7
|
1.0
|
|
CG
|
A:LYS375
|
4.9
|
21.5
|
1.0
|
|
CA
|
A:ASP386
|
4.9
|
25.2
|
1.0
|
|
Reference:
A.Ochiai,
T.Itoh,
Y.Maruyama,
A.Kawamata,
B.Mikami,
W.Hashimoto,
K.Murata.
A Novel Structural Fold in Polysaccharide Lyases: Bacillus Subtilis Family 11 Rhamnogalacturonan Lyase Yesw with An Eight-Bladed -Propeller J.Biol.Chem. V. 282 37134 2007.
ISSN: ISSN 0021-9258
PubMed: 17947240
DOI: 10.1074/JBC.M704663200
Page generated: Fri Jul 12 19:51:25 2024
|