Calcium in PDB 2z8r: Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
Protein crystallography data
The structure of Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution, PDB code: 2z8r
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)
|
28.40 /
1.40
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.897,
106.153,
101.041,
90.00,
95.11,
90.00
|
|
R / Rfree (%)
|
16.4 /
18.2
|
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 at 1.40 A Resolution
(pdb code 2z8r). 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 at 1.40 A Resolution, PDB code: 2z8r:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 1 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca640
b:12.4
occ:1.00
|
OD1
|
A:ASP160
|
2.3
|
13.9
|
1.0
|
|
O
|
A:GLN164
|
2.3
|
12.1
|
1.0
|
|
OD1
|
A:ASP162
|
2.4
|
14.3
|
1.0
|
|
OD1
|
A:ASP158
|
2.4
|
12.0
|
1.0
|
|
OE2
|
A:GLU166
|
2.5
|
12.6
|
1.0
|
|
O
|
A:HOH988
|
2.5
|
20.7
|
1.0
|
|
OE1
|
A:GLU166
|
2.5
|
11.2
|
1.0
|
|
CD
|
A:GLU166
|
2.8
|
11.2
|
1.0
|
|
CG
|
A:ASP162
|
3.4
|
15.7
|
1.0
|
|
CG
|
A:ASP160
|
3.4
|
15.8
|
1.0
|
|
C
|
A:GLN164
|
3.5
|
12.0
|
1.0
|
|
CG
|
A:ASP158
|
3.5
|
11.7
|
1.0
|
|
OD2
|
A:ASP162
|
3.8
|
17.6
|
1.0
|
|
OD2
|
A:ASP160
|
3.9
|
18.3
|
1.0
|
|
NZ
|
A:LYS194
|
4.0
|
25.7
|
1.0
|
|
N
|
A:GLN164
|
4.1
|
12.8
|
1.0
|
|
CA
|
A:GLN164
|
4.2
|
12.3
|
1.0
|
|
CA
|
A:ASP158
|
4.2
|
10.5
|
1.0
|
|
CB
|
A:GLN164
|
4.3
|
12.5
|
1.0
|
|
OD2
|
A:ASP158
|
4.3
|
13.6
|
1.0
|
|
N
|
A:ASP160
|
4.3
|
12.8
|
1.0
|
|
CB
|
A:ASP158
|
4.4
|
10.8
|
1.0
|
|
CG
|
A:GLU166
|
4.4
|
10.7
|
1.0
|
|
N
|
A:ASP162
|
4.4
|
15.5
|
1.0
|
|
N
|
A:VAL159
|
4.4
|
11.4
|
1.0
|
|
O
|
A:HOH767
|
4.5
|
12.5
|
1.0
|
|
N
|
A:TYR165
|
4.6
|
10.7
|
1.0
|
|
N
|
A:GLU166
|
4.6
|
10.2
|
1.0
|
|
C
|
A:ASP158
|
4.6
|
11.0
|
1.0
|
|
N
|
A:GLY161
|
4.6
|
14.5
|
1.0
|
|
CB
|
A:ASP162
|
4.6
|
15.4
|
1.0
|
|
C
|
A:TYR165
|
4.6
|
10.7
|
1.0
|
|
CB
|
A:ASP160
|
4.7
|
14.2
|
1.0
|
|
CA
|
A:TYR165
|
4.8
|
10.7
|
1.0
|
|
N
|
A:GLY163
|
4.8
|
14.6
|
1.0
|
|
CA
|
A:ASP160
|
4.8
|
13.9
|
1.0
|
|
CA
|
A:ASP162
|
4.9
|
15.2
|
1.0
|
|
C
|
A:ASP160
|
5.0
|
14.7
|
1.0
|
|
CG
|
A:GLN164
|
5.0
|
12.9
|
1.0
|
|
Calcium binding site 2 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 2 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca641
b:9.6
occ:1.00
|
O
|
A:LEU545
|
2.3
|
10.7
|
0.5
|
|
O
|
A:LEU545
|
2.3
|
10.3
|
0.5
|
|
O
|
A:ARG549
|
2.3
|
8.7
|
1.0
|
|
O
|
A:ASP547
|
2.4
|
9.8
|
1.0
|
|
OD1
|
A:ASP543
|
2.4
|
9.5
|
1.0
|
|
O
|
A:HOH720
|
2.4
|
10.4
|
1.0
|
|
OE2
|
A:GLU551
|
2.5
|
9.9
|
1.0
|
|
OE1
|
A:GLU551
|
2.6
|
9.7
|
1.0
|
|
CD
|
A:GLU551
|
2.9
|
10.4
|
1.0
|
|
CG
|
A:ASP543
|
3.4
|
9.4
|
1.0
|
|
C
|
A:ARG549
|
3.5
|
9.2
|
1.0
|
|
C
|
A:LEU545
|
3.5
|
10.7
|
0.5
|
|
C
|
A:LEU545
|
3.5
|
10.3
|
0.5
|
|
C
|
A:ASP547
|
3.6
|
10.1
|
1.0
|
|
C
|
A:GLY546
|
3.8
|
10.3
|
1.0
|
|
N
|
A:ASP547
|
3.9
|
10.2
|
1.0
|
|
N
|
A:ARG549
|
4.0
|
9.1
|
1.0
|
|
O
|
A:GLY546
|
4.1
|
10.8
|
1.0
|
|
CA
|
A:ASP543
|
4.1
|
9.0
|
1.0
|
|
CB
|
A:ASP543
|
4.2
|
9.3
|
1.0
|
|
N
|
A:LEU545
|
4.2
|
10.7
|
0.5
|
|
CA
|
A:GLY546
|
4.2
|
10.5
|
1.0
|
|
N
|
A:LEU545
|
4.3
|
10.4
|
0.5
|
|
CA
|
A:ARG549
|
4.3
|
9.2
|
1.0
|
|
OD2
|
A:ASP543
|
4.3
|
9.2
|
1.0
|
|
C
|
A:TRP548
|
4.3
|
9.9
|
1.0
|
|
O
|
A:HOH761
|
4.3
|
14.3
|
1.0
|
|
N
|
A:GLY546
|
4.3
|
10.2
|
1.0
|
|
O
|
A:HOH686
|
4.3
|
10.6
|
1.0
|
|
CA
|
A:ASP547
|
4.4
|
10.1
|
1.0
|
|
CG
|
A:GLU551
|
4.4
|
9.4
|
1.0
|
|
N
|
A:GLU550
|
4.4
|
9.2
|
1.0
|
|
OD1
|
A:ASP547
|
4.4
|
9.8
|
1.0
|
|
CA
|
A:LEU545
|
4.5
|
10.8
|
0.5
|
|
C
|
A:ASP543
|
4.5
|
9.7
|
1.0
|
|
N
|
A:TRP548
|
4.5
|
9.9
|
1.0
|
|
N
|
A:LEU544
|
4.5
|
9.9
|
0.5
|
|
N
|
A:LEU544
|
4.6
|
9.9
|
0.5
|
|
CA
|
A:LEU545
|
4.6
|
10.3
|
0.5
|
|
CA
|
A:GLU550
|
4.6
|
8.9
|
1.0
|
|
N
|
A:GLU551
|
4.6
|
8.9
|
1.0
|
|
OG1
|
A:THR566
|
4.7
|
11.2
|
1.0
|
|
O
|
A:HOH659
|
4.7
|
11.0
|
1.0
|
|
CA
|
A:TRP548
|
4.7
|
9.3
|
1.0
|
|
O
|
A:TRP548
|
4.7
|
9.5
|
1.0
|
|
C
|
A:GLU550
|
4.7
|
8.9
|
1.0
|
|
CB
|
A:ARG549
|
4.9
|
9.2
|
1.0
|
|
O
|
A:HOH694
|
5.0
|
11.1
|
1.0
|
|
Calcium binding site 3 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 3 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca642
b:4.0
occ:1.00
|
OE1
|
A:GLU422
|
2.1
|
9.2
|
1.0
|
|
O
|
A:HOH1087
|
2.1
|
9.7
|
1.0
|
|
NE2
|
A:HIS363
|
2.1
|
8.5
|
1.0
|
|
OD1
|
A:ASP401
|
2.1
|
9.9
|
1.0
|
|
O
|
A:HOH1086
|
2.2
|
11.2
|
1.0
|
|
NE2
|
A:HIS399
|
2.2
|
8.1
|
1.0
|
|
CD2
|
A:HIS363
|
3.0
|
8.4
|
1.0
|
|
CD
|
A:GLU422
|
3.0
|
8.9
|
1.0
|
|
CG
|
A:ASP401
|
3.1
|
11.5
|
1.0
|
|
CD2
|
A:HIS399
|
3.1
|
8.4
|
1.0
|
|
CE1
|
A:HIS363
|
3.2
|
9.2
|
1.0
|
|
CE1
|
A:HIS399
|
3.2
|
8.7
|
1.0
|
|
OE2
|
A:GLU422
|
3.4
|
10.6
|
1.0
|
|
OD2
|
A:ASP401
|
3.4
|
14.7
|
1.0
|
|
O
|
A:HOH725
|
4.0
|
11.8
|
1.0
|
|
OH
|
A:TYR326
|
4.1
|
10.7
|
1.0
|
|
O
|
A:HOH1054
|
4.1
|
26.3
|
1.0
|
|
CG
|
A:HIS363
|
4.2
|
7.1
|
1.0
|
|
ND1
|
A:HIS363
|
4.2
|
8.9
|
1.0
|
|
ND1
|
A:HIS399
|
4.3
|
7.9
|
1.0
|
|
CG
|
A:HIS399
|
4.3
|
8.7
|
1.0
|
|
CG
|
A:GLU422
|
4.4
|
9.2
|
1.0
|
|
O
|
A:HOH855
|
4.4
|
18.0
|
1.0
|
|
CB
|
A:ASP401
|
4.5
|
9.0
|
1.0
|
|
O
|
A:GLY400
|
4.6
|
8.1
|
1.0
|
|
CB
|
A:GLU422
|
4.7
|
9.3
|
1.0
|
|
C
|
A:GLY400
|
4.7
|
7.8
|
1.0
|
|
CA
|
A:ASP401
|
4.8
|
8.3
|
1.0
|
|
N
|
A:ASP401
|
4.9
|
7.6
|
1.0
|
|
CE1
|
A:TYR326
|
4.9
|
10.5
|
1.0
|
|
CZ
|
A:TYR326
|
5.0
|
9.9
|
1.0
|
|
CE2
|
A:TYR595
|
5.0
|
9.5
|
1.0
|
|
Calcium binding site 4 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 4 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca643
b:9.0
occ:1.00
|
OD1
|
A:ASP457
|
2.3
|
8.4
|
1.0
|
|
O
|
A:TYR462
|
2.3
|
9.8
|
1.0
|
|
O
|
A:ASP459
|
2.4
|
10.0
|
1.0
|
|
OE2
|
A:GLU466
|
2.4
|
8.8
|
1.0
|
|
O
|
A:GLY464
|
2.4
|
10.0
|
1.0
|
|
O
|
A:HOH777
|
2.4
|
10.8
|
1.0
|
|
OE1
|
A:GLU466
|
2.6
|
9.2
|
1.0
|
|
CD
|
A:GLU466
|
2.8
|
8.5
|
1.0
|
|
CG
|
A:ASP457
|
3.3
|
8.8
|
1.0
|
|
C
|
A:ASP459
|
3.4
|
10.0
|
1.0
|
|
C
|
A:TYR462
|
3.5
|
10.4
|
1.0
|
|
C
|
A:GLY464
|
3.6
|
10.2
|
1.0
|
|
OD2
|
A:ASP457
|
3.9
|
8.6
|
1.0
|
|
N
|
A:GLY464
|
3.9
|
9.8
|
1.0
|
|
N
|
A:ASP459
|
4.0
|
10.3
|
1.0
|
|
C
|
A:PRO463
|
4.1
|
11.1
|
1.0
|
|
O
|
A:HOH741
|
4.2
|
11.3
|
1.0
|
|
CA
|
A:ASP459
|
4.2
|
10.0
|
1.0
|
|
CB
|
A:ASP457
|
4.3
|
8.2
|
1.0
|
|
CA
|
A:ASP457
|
4.3
|
8.6
|
1.0
|
|
N
|
A:PRO460
|
4.3
|
9.6
|
1.0
|
|
CA
|
A:GLY464
|
4.3
|
10.0
|
1.0
|
|
CA
|
A:PRO460
|
4.3
|
9.8
|
1.0
|
|
CA
|
A:TYR462
|
4.4
|
10.6
|
1.0
|
|
CG
|
A:GLU466
|
4.4
|
8.5
|
1.0
|
|
N
|
A:TYR462
|
4.4
|
11.0
|
1.0
|
|
O
|
A:PRO463
|
4.5
|
12.3
|
1.0
|
|
CB
|
A:TYR462
|
4.5
|
10.7
|
1.0
|
|
N
|
A:PRO463
|
4.5
|
10.4
|
1.0
|
|
CA
|
A:PRO463
|
4.5
|
11.1
|
1.0
|
|
N
|
A:ILE458
|
4.6
|
9.2
|
1.0
|
|
N
|
A:GLN465
|
4.6
|
9.5
|
1.0
|
|
N
|
A:GLU466
|
4.6
|
8.8
|
1.0
|
|
CB
|
A:ASP459
|
4.6
|
10.6
|
1.0
|
|
C
|
A:ASP457
|
4.7
|
9.0
|
1.0
|
|
CA
|
A:GLN465
|
4.8
|
9.6
|
1.0
|
|
C
|
A:PRO460
|
4.8
|
10.1
|
1.0
|
|
C
|
A:GLN465
|
4.9
|
9.2
|
1.0
|
|
O
|
A:HOH789
|
4.9
|
13.6
|
1.0
|
|
Calcium binding site 5 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 5 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca644
b:9.6
occ:1.00
|
OD1
|
A:ASP496
|
2.3
|
10.2
|
1.0
|
|
O
|
A:LEU500
|
2.3
|
8.9
|
1.0
|
|
OD1
|
A:ASP498
|
2.4
|
10.5
|
1.0
|
|
OE2
|
A:GLU502
|
2.4
|
10.8
|
1.0
|
|
O
|
A:HOH774
|
2.5
|
8.9
|
1.0
|
|
O
|
A:ASP498
|
2.5
|
9.5
|
1.0
|
|
OE1
|
A:GLU502
|
2.5
|
9.1
|
1.0
|
|
CD
|
A:GLU502
|
2.8
|
9.5
|
1.0
|
|
C
|
A:ASP498
|
3.3
|
10.2
|
1.0
|
|
CG
|
A:ASP496
|
3.3
|
10.9
|
1.0
|
|
C
|
A:LEU500
|
3.4
|
9.1
|
1.0
|
|
CG
|
A:ASP498
|
3.5
|
10.7
|
1.0
|
|
N
|
A:ASP498
|
3.8
|
10.7
|
1.0
|
|
OD2
|
A:ASP496
|
3.9
|
13.0
|
1.0
|
|
N
|
A:LEU500
|
3.9
|
9.7
|
1.0
|
|
CA
|
A:ASP498
|
3.9
|
10.2
|
1.0
|
|
O
|
A:ASP496
|
4.1
|
10.1
|
1.0
|
|
CA
|
A:LEU500
|
4.1
|
9.4
|
1.0
|
|
NZ
|
A:LYS511
|
4.1
|
10.4
|
0.5
|
|
NZ
|
A:LYS511
|
4.2
|
12.3
|
0.5
|
|
N
|
A:ASP496
|
4.2
|
10.1
|
1.0
|
|
C
|
A:ASP496
|
4.2
|
10.4
|
1.0
|
|
N
|
A:LEU499
|
4.3
|
10.3
|
1.0
|
|
CB
|
A:ASP498
|
4.3
|
10.7
|
1.0
|
|
N
|
A:ARG501
|
4.3
|
9.4
|
1.0
|
|
CG
|
A:GLU502
|
4.3
|
9.4
|
1.0
|
|
C
|
A:LEU499
|
4.3
|
9.9
|
1.0
|
|
OD2
|
A:ASP498
|
4.3
|
12.4
|
1.0
|
|
CA
|
A:ASP496
|
4.5
|
10.2
|
1.0
|
|
CB
|
A:ASP496
|
4.5
|
10.0
|
1.0
|
|
CA
|
A:ARG501
|
4.5
|
9.4
|
1.0
|
|
CB
|
A:LEU500
|
4.5
|
9.4
|
1.0
|
|
N
|
A:TRP495
|
4.6
|
9.3
|
1.0
|
|
CA
|
A:LEU499
|
4.7
|
10.3
|
1.0
|
|
CD1
|
A:TRP494
|
4.7
|
9.2
|
1.0
|
|
N
|
A:GLU502
|
4.7
|
9.5
|
1.0
|
|
N
|
A:GLY497
|
4.8
|
10.6
|
1.0
|
|
C
|
A:GLY497
|
4.8
|
10.9
|
1.0
|
|
C
|
A:ARG501
|
4.8
|
9.4
|
1.0
|
|
O
|
A:LEU499
|
5.0
|
10.2
|
1.0
|
|
Calcium binding site 6 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 6 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca645
b:9.6
occ:1.00
|
O
|
A:GLY414
|
2.3
|
11.2
|
1.0
|
|
O
|
A:ARG412
|
2.3
|
11.6
|
1.0
|
|
OD1
|
A:ASP407
|
2.3
|
10.6
|
1.0
|
|
O
|
A:ASP409
|
2.4
|
10.2
|
1.0
|
|
O
|
A:HOH772
|
2.4
|
10.9
|
1.0
|
|
OE2
|
A:GLU416
|
2.5
|
9.7
|
1.0
|
|
OE1
|
A:GLU416
|
2.7
|
9.5
|
1.0
|
|
CD
|
A:GLU416
|
2.9
|
9.0
|
1.0
|
|
C
|
A:ASP409
|
3.4
|
10.6
|
1.0
|
|
CG
|
A:ASP407
|
3.4
|
10.6
|
1.0
|
|
C
|
A:GLY414
|
3.5
|
10.6
|
1.0
|
|
C
|
A:ARG412
|
3.5
|
12.6
|
1.0
|
|
OD2
|
A:ASP407
|
3.9
|
11.7
|
1.0
|
|
N
|
A:GLY414
|
4.0
|
12.2
|
1.0
|
|
N
|
A:PRO410
|
4.2
|
10.8
|
1.0
|
|
N
|
A:ASP409
|
4.2
|
10.0
|
1.0
|
|
CA
|
A:PRO410
|
4.2
|
11.4
|
1.0
|
|
C
|
A:PRO413
|
4.2
|
12.7
|
1.0
|
|
CA
|
A:ASP409
|
4.2
|
10.5
|
1.0
|
|
CA
|
A:ARG412
|
4.3
|
12.6
|
1.0
|
|
N
|
A:ARG412
|
4.3
|
12.2
|
1.0
|
|
CA
|
A:GLY414
|
4.3
|
11.5
|
1.0
|
|
CB
|
A:ARG412
|
4.4
|
12.8
|
1.0
|
|
N
|
A:LEU415
|
4.4
|
10.1
|
1.0
|
|
CG
|
A:GLU416
|
4.5
|
8.3
|
1.0
|
|
CA
|
A:LEU415
|
4.5
|
9.5
|
1.0
|
|
CB
|
A:ASP409
|
4.5
|
10.9
|
1.0
|
|
N
|
A:PRO413
|
4.5
|
13.0
|
1.0
|
|
CB
|
A:ASP407
|
4.5
|
9.8
|
1.0
|
|
CA
|
A:ASP407
|
4.5
|
9.1
|
1.0
|
|
CA
|
A:PRO413
|
4.6
|
13.2
|
1.0
|
|
O
|
A:HOH1060
|
4.7
|
30.4
|
1.0
|
|
C
|
A:PRO410
|
4.7
|
12.4
|
1.0
|
|
O
|
A:PRO413
|
4.7
|
13.1
|
1.0
|
|
NE
|
A:ARG412
|
4.7
|
13.1
|
1.0
|
|
C
|
A:LEU415
|
4.8
|
8.9
|
1.0
|
|
N
|
A:LEU408
|
4.8
|
9.0
|
1.0
|
|
C
|
A:ASP407
|
4.8
|
9.7
|
1.0
|
|
Calcium binding site 7 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 7 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca646
b:11.2
occ:1.00
|
O
|
A:LYS228
|
2.3
|
11.8
|
0.5
|
|
O
|
A:LYS228
|
2.3
|
12.0
|
0.5
|
|
OD1
|
A:ASP226
|
2.3
|
12.7
|
1.0
|
|
OD1
|
A:ASP224
|
2.3
|
13.8
|
1.0
|
|
OE2
|
A:GLU230
|
2.5
|
12.1
|
1.0
|
|
OD1
|
A:ASP222
|
2.5
|
10.0
|
1.0
|
|
OE1
|
A:GLU230
|
2.5
|
10.0
|
1.0
|
|
CD
|
A:GLU230
|
2.8
|
11.0
|
1.0
|
|
CG
|
A:ASP226
|
3.3
|
14.6
|
1.0
|
|
CG
|
A:ASP224
|
3.4
|
15.1
|
1.0
|
|
C
|
A:LYS228
|
3.5
|
11.8
|
0.5
|
|
C
|
A:LYS228
|
3.5
|
12.0
|
0.5
|
|
CG
|
A:ASP222
|
3.5
|
10.2
|
1.0
|
|
OD2
|
A:ASP224
|
3.8
|
16.6
|
1.0
|
|
OD2
|
A:ASP226
|
3.8
|
15.7
|
1.0
|
|
N
|
A:LYS228
|
4.1
|
12.2
|
0.5
|
|
N
|
A:LYS228
|
4.1
|
12.4
|
0.5
|
|
CA
|
A:ASP222
|
4.1
|
10.2
|
1.0
|
|
CA
|
A:LYS228
|
4.2
|
12.1
|
0.5
|
|
CA
|
A:LYS228
|
4.2
|
12.4
|
0.5
|
|
N
|
A:ASP226
|
4.2
|
13.8
|
1.0
|
|
N
|
A:ASP224
|
4.2
|
12.7
|
1.0
|
|
CB
|
A:ASP222
|
4.3
|
9.9
|
1.0
|
|
CG
|
A:GLU230
|
4.4
|
12.2
|
1.0
|
|
CB
|
A:LYS228
|
4.4
|
12.1
|
0.5
|
|
OD2
|
A:ASP222
|
4.4
|
10.9
|
1.0
|
|
CB
|
A:ASP226
|
4.4
|
14.1
|
1.0
|
|
CB
|
A:LYS228
|
4.4
|
12.4
|
0.5
|
|
N
|
A:GLY225
|
4.4
|
13.7
|
1.0
|
|
O
|
A:HOH724
|
4.5
|
13.6
|
1.0
|
|
N
|
A:LEU223
|
4.5
|
10.6
|
1.0
|
|
C
|
A:ASP222
|
4.5
|
10.5
|
1.0
|
|
N
|
A:ALA229
|
4.5
|
11.4
|
1.0
|
|
CB
|
A:ASP224
|
4.6
|
13.8
|
1.0
|
|
C
|
A:ALA229
|
4.7
|
11.0
|
1.0
|
|
N
|
A:GLU230
|
4.7
|
10.2
|
1.0
|
|
CA
|
A:ASP224
|
4.7
|
13.2
|
1.0
|
|
CA
|
A:ALA229
|
4.7
|
11.0
|
1.0
|
|
CA
|
A:ASP226
|
4.7
|
13.8
|
1.0
|
|
N
|
A:GLY227
|
4.8
|
13.4
|
1.0
|
|
C
|
A:ASP224
|
4.9
|
13.9
|
1.0
|
|
Calcium binding site 8 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 8 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca647
b:7.7
occ:1.00
|
O
|
A:HOH742
|
2.3
|
9.6
|
1.0
|
|
O
|
A:ASN592
|
2.3
|
8.2
|
1.0
|
|
O
|
A:ALA594
|
2.4
|
8.2
|
1.0
|
|
O
|
A:HOH650
|
2.4
|
8.1
|
1.0
|
|
OD2
|
A:ASP153
|
2.4
|
9.2
|
1.0
|
|
OD1
|
A:ASN596
|
2.4
|
8.2
|
1.0
|
|
CG
|
A:ASP153
|
3.3
|
9.1
|
1.0
|
|
C
|
A:ALA594
|
3.4
|
8.3
|
1.0
|
|
CG
|
A:ASN596
|
3.5
|
7.4
|
1.0
|
|
C
|
A:ASN592
|
3.5
|
7.8
|
1.0
|
|
OD1
|
A:ASP153
|
3.7
|
9.0
|
1.0
|
|
N
|
A:ALA594
|
3.7
|
7.9
|
1.0
|
|
C
|
A:ILE593
|
3.8
|
8.6
|
1.0
|
|
CA
|
A:ALA594
|
3.9
|
8.2
|
1.0
|
|
O
|
A:ILE593
|
4.0
|
7.8
|
1.0
|
|
ND2
|
A:ASN596
|
4.0
|
8.0
|
1.0
|
|
O
|
A:HOH707
|
4.1
|
10.3
|
1.0
|
|
NZ
|
A:LYS170
|
4.3
|
8.9
|
1.0
|
|
O
|
A:HOH663
|
4.3
|
8.9
|
1.0
|
|
N
|
A:ASN596
|
4.3
|
8.0
|
1.0
|
|
CA
|
A:ASN592
|
4.4
|
7.5
|
1.0
|
|
N
|
A:ILE593
|
4.4
|
8.0
|
1.0
|
|
ND2
|
A:ASN532
|
4.4
|
9.0
|
1.0
|
|
CA
|
A:ILE593
|
4.4
|
8.7
|
1.0
|
|
O
|
A:HOH730
|
4.4
|
11.5
|
1.0
|
|
O
|
A:HOH1016
|
4.5
|
11.5
|
1.0
|
|
CB
|
A:ASP153
|
4.5
|
8.2
|
1.0
|
|
N
|
A:TYR595
|
4.6
|
8.0
|
1.0
|
|
O
|
A:ALA213
|
4.6
|
8.2
|
1.0
|
|
CB
|
A:ASN596
|
4.8
|
7.2
|
1.0
|
|
CA
|
A:TYR595
|
4.9
|
8.6
|
1.0
|
|
CA
|
A:ASN596
|
4.9
|
7.3
|
1.0
|
|
CB
|
A:ALA213
|
4.9
|
8.9
|
1.0
|
|
CB
|
A:ASN592
|
5.0
|
7.4
|
1.0
|
|
Calcium binding site 9 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 9 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca648
b:3.2
occ:1.00
|
OE2
|
A:GLU377
|
2.3
|
10.9
|
1.0
|
|
OD2
|
A:ASP373
|
2.3
|
13.7
|
1.0
|
|
OD1
|
A:ASP386
|
2.4
|
12.4
|
1.0
|
|
OD2
|
A:ASP371
|
2.4
|
15.5
|
1.0
|
|
O
|
A:HOH846
|
2.4
|
15.3
|
1.0
|
|
ND1
|
A:HIS387
|
2.5
|
13.4
|
1.0
|
|
CE1
|
A:HIS387
|
3.2
|
13.9
|
1.0
|
|
CG
|
A:ASP371
|
3.3
|
15.2
|
1.0
|
|
CG
|
A:ASP373
|
3.3
|
15.0
|
1.0
|
|
CD
|
A:GLU377
|
3.3
|
10.9
|
1.0
|
|
OD1
|
A:ASP371
|
3.4
|
14.9
|
1.0
|
|
CG
|
A:ASP386
|
3.4
|
12.0
|
1.0
|
|
OD1
|
A:ASP373
|
3.6
|
14.4
|
1.0
|
|
CA
|
A:CA649
|
3.6
|
16.2
|
1.0
|
|
CG
|
A:HIS387
|
3.7
|
11.9
|
1.0
|
|
OD2
|
A:ASP386
|
3.8
|
12.7
|
1.0
|
|
CG
|
A:GLU377
|
3.9
|
11.0
|
1.0
|
|
OE1
|
A:GLU377
|
4.2
|
9.9
|
1.0
|
|
CB
|
A:HIS387
|
4.3
|
10.8
|
1.0
|
|
N
|
A:HIS387
|
4.3
|
10.5
|
1.0
|
|
O
|
A:HOH909
|
4.4
|
21.7
|
1.0
|
|
NE2
|
A:HIS387
|
4.4
|
14.4
|
1.0
|
|
CB
|
A:ASP373
|
4.6
|
15.1
|
1.0
|
|
O
|
A:HOH1282
|
4.7
|
50.6
|
1.0
|
|
CB
|
A:ASP371
|
4.7
|
14.6
|
1.0
|
|
CD2
|
A:HIS387
|
4.7
|
13.3
|
1.0
|
|
CB
|
A:ASP386
|
4.8
|
10.0
|
1.0
|
|
CB
|
A:LYS375
|
4.9
|
11.4
|
1.0
|
|
CA
|
A:HIS387
|
4.9
|
10.7
|
1.0
|
|
O
|
A:LYS375
|
5.0
|
10.9
|
1.0
|
|
Calcium binding site 10 out
of 20 in 2z8r
Go back to
Calcium Binding Sites List in 2z8r
Calcium binding site 10 out
of 20 in the Crystal Structure of Rhamnogalacturonan Lyase Yesw at 1.40 A Resolution
 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 at 1.40 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca649
b:16.2
occ:1.00
|
OD1
|
A:ASP371
|
2.2
|
14.9
|
1.0
|
|
OD1
|
A:ASP373
|
2.2
|
14.4
|
1.0
|
|
O
|
A:LYS375
|
2.2
|
10.9
|
1.0
|
|
OD1
|
A:ASP369
|
2.3
|
12.1
|
1.0
|
|
OE2
|
A:GLU377
|
2.4
|
10.9
|
1.0
|
|
OE1
|
A:GLU377
|
2.4
|
9.9
|
1.0
|
|
CD
|
A:GLU377
|
2.7
|
10.9
|
1.0
|
|
CG
|
A:ASP373
|
3.1
|
15.0
|
1.0
|
|
CG
|
A:ASP371
|
3.2
|
15.2
|
1.0
|
|
CG
|
A:ASP369
|
3.2
|
12.7
|
1.0
|
|
C
|
A:LYS375
|
3.3
|
10.9
|
1.0
|
|
OD2
|
A:ASP373
|
3.6
|
13.7
|
1.0
|
|
CA
|
A:CA648
|
3.6
|
3.2
|
1.0
|
|
OD2
|
A:ASP371
|
3.7
|
15.5
|
1.0
|
|
N
|
A:LYS375
|
3.7
|
11.8
|
1.0
|
|
N
|
A:ASP373
|
3.8
|
15.1
|
1.0
|
|
CA
|
A:ASP369
|
3.8
|
10.8
|
1.0
|
|
N
|
A:ASP371
|
3.9
|
13.5
|
1.0
|
|
CB
|
A:ASP369
|
3.9
|
10.9
|
1.0
|
|
CA
|
A:LYS375
|
3.9
|
11.1
|
1.0
|
|
OD2
|
A:ASP369
|
4.1
|
13.3
|
1.0
|
|
N
|
A:VAL370
|
4.1
|
11.1
|
1.0
|
|
N
|
A:GLY372
|
4.1
|
15.3
|
1.0
|
|
C
|
A:ASP369
|
4.2
|
10.8
|
1.0
|
|
CG
|
A:GLU377
|
4.2
|
11.0
|
1.0
|
|
CB
|
A:LYS375
|
4.2
|
11.4
|
1.0
|
|
CB
|
A:ASP373
|
4.3
|
15.1
|
1.0
|
|
N
|
A:GLY374
|
4.3
|
13.8
|
1.0
|
|
CA
|
A:ASP373
|
4.4
|
14.7
|
1.0
|
|
CB
|
A:ASP371
|
4.4
|
14.6
|
1.0
|
|
N
|
A:ASP376
|
4.4
|
10.2
|
1.0
|
|
CA
|
A:ASP371
|
4.4
|
14.4
|
1.0
|
|
C
|
A:ASP373
|
4.5
|
14.3
|
1.0
|
|
C
|
A:ASP371
|
4.5
|
15.0
|
1.0
|
|
C
|
A:GLY374
|
4.6
|
12.4
|
1.0
|
|
CA
|
A:ASP376
|
4.7
|
9.9
|
1.0
|
|
N
|
A:GLU377
|
4.7
|
9.6
|
1.0
|
|
C
|
A:ASP376
|
4.8
|
9.7
|
1.0
|
|
C
|
A:GLY372
|
4.8
|
15.7
|
1.0
|
|
CA
|
A:GLY372
|
4.9
|
15.8
|
1.0
|
|
C
|
A:VAL370
|
5.0
|
12.5
|
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: Sat Dec 12 04:01:15 2020
|
