Calcium in PDB 6tr4: Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Protein crystallography data
The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4
was solved by
C.D.Owen,
H.Wu,
E.Crost,
A.Colvile,
N.Juge,
M.A.Walsh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
69.64 /
1.45
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.780,
74.060,
76.509,
82.47,
80.43,
70.41
|
R / Rfree (%)
|
14.1 /
16.1
|
Other elements in 6tr4:
The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
(pdb code 6tr4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 6tr4
Go back to
Calcium Binding Sites List in 6tr4
Calcium binding site 1 out
of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca606
b:7.4
occ:1.00
|
O
|
A:ASN397
|
2.2
|
8.7
|
1.0
|
O
|
A:ASN402
|
2.3
|
8.8
|
1.0
|
OE2
|
A:GLU499
|
2.3
|
9.9
|
1.0
|
O
|
A:SER498
|
2.4
|
7.8
|
1.0
|
OD1
|
A:ASP400
|
2.4
|
9.6
|
1.0
|
O
|
A:THR405
|
2.5
|
8.4
|
1.0
|
OG1
|
A:THR405
|
2.5
|
9.5
|
1.0
|
CD
|
A:GLU499
|
3.4
|
9.2
|
1.0
|
C
|
A:THR405
|
3.4
|
9.0
|
1.0
|
C
|
A:ASN402
|
3.4
|
9.1
|
1.0
|
C
|
A:ASN397
|
3.5
|
9.2
|
1.0
|
CG
|
A:ASP400
|
3.5
|
9.6
|
1.0
|
C
|
A:SER498
|
3.6
|
7.8
|
1.0
|
CB
|
A:THR405
|
3.7
|
9.7
|
1.0
|
OD2
|
A:ASP400
|
3.9
|
9.8
|
1.0
|
CA
|
A:THR405
|
3.9
|
9.7
|
1.0
|
N
|
A:ASN402
|
4.0
|
9.4
|
1.0
|
N
|
A:THR405
|
4.0
|
9.9
|
1.0
|
CA
|
A:ASN402
|
4.1
|
9.3
|
1.0
|
CG
|
A:GLU499
|
4.1
|
8.6
|
1.0
|
CA
|
A:SER498
|
4.2
|
7.7
|
1.0
|
OE1
|
A:GLU499
|
4.2
|
10.0
|
1.0
|
CA
|
A:ASN397
|
4.3
|
9.6
|
1.0
|
CB
|
A:ASN402
|
4.3
|
9.7
|
1.0
|
N
|
A:MET398
|
4.4
|
8.8
|
1.0
|
N
|
A:TYR406
|
4.4
|
8.8
|
1.0
|
N
|
A:ASP403
|
4.5
|
9.0
|
1.0
|
CB
|
A:SER498
|
4.5
|
7.7
|
1.0
|
CA
|
A:MET398
|
4.5
|
8.8
|
1.0
|
CB
|
A:ASN397
|
4.6
|
9.9
|
1.0
|
N
|
A:GLU499
|
4.7
|
7.8
|
1.0
|
N
|
A:ASP400
|
4.7
|
9.7
|
1.0
|
CA
|
A:ASP403
|
4.7
|
9.2
|
1.0
|
CB
|
A:ASP400
|
4.8
|
10.0
|
1.0
|
N
|
A:ASP401
|
4.8
|
9.8
|
1.0
|
C
|
A:ASP403
|
4.8
|
9.4
|
1.0
|
C
|
A:MET398
|
4.8
|
8.8
|
1.0
|
CA
|
A:TYR406
|
4.8
|
8.8
|
1.0
|
CG2
|
A:THR405
|
4.9
|
10.0
|
1.0
|
CA
|
A:GLU499
|
4.9
|
8.1
|
1.0
|
|
Calcium binding site 2 out
of 6 in 6tr4
Go back to
Calcium Binding Sites List in 6tr4
Calcium binding site 2 out
of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca607
b:8.3
occ:1.00
|
O
|
A:LYS174
|
2.2
|
9.8
|
1.0
|
O
|
A:GLY158
|
2.3
|
7.6
|
1.0
|
O
|
A:HOH1097
|
2.3
|
10.9
|
1.0
|
O
|
A:SER156
|
2.3
|
7.2
|
1.0
|
OD1
|
A:ASP172
|
2.4
|
9.0
|
1.0
|
O
|
A:HOH821
|
2.5
|
8.2
|
1.0
|
OD2
|
A:ASP172
|
2.5
|
10.4
|
1.0
|
CG
|
A:ASP172
|
2.8
|
9.7
|
1.0
|
C
|
A:SER156
|
3.3
|
7.5
|
1.0
|
C
|
A:LYS174
|
3.5
|
10.7
|
1.0
|
C
|
A:GLY158
|
3.5
|
7.4
|
1.0
|
CA
|
A:SER156
|
3.9
|
7.8
|
1.0
|
O
|
A:HOH947
|
3.9
|
14.5
|
1.0
|
N
|
A:TYR176
|
4.2
|
8.2
|
1.0
|
N
|
A:GLY158
|
4.2
|
7.0
|
1.0
|
C
|
A:TYR157
|
4.3
|
7.1
|
1.0
|
CB
|
A:ASP172
|
4.3
|
10.1
|
1.0
|
N
|
A:ASP175
|
4.3
|
10.3
|
1.0
|
CA
|
A:TYR159
|
4.4
|
8.0
|
1.0
|
CA
|
A:ASP175
|
4.4
|
10.2
|
1.0
|
OE1
|
A:GLN215
|
4.4
|
7.9
|
1.0
|
N
|
A:TYR157
|
4.4
|
7.1
|
1.0
|
N
|
A:TYR159
|
4.4
|
7.5
|
1.0
|
CB
|
A:SER156
|
4.4
|
8.1
|
1.0
|
N
|
A:LYS174
|
4.4
|
10.7
|
1.0
|
N
|
A:LYS160
|
4.4
|
9.4
|
1.0
|
CA
|
A:LYS174
|
4.5
|
11.4
|
1.0
|
CA
|
A:GLY158
|
4.5
|
7.1
|
1.0
|
O
|
A:TYR157
|
4.6
|
7.6
|
1.0
|
CA
|
A:TYR157
|
4.7
|
7.0
|
1.0
|
C
|
A:ASP175
|
4.7
|
9.1
|
1.0
|
O
|
A:HOH823
|
4.8
|
17.1
|
1.0
|
O
|
A:PRO155
|
4.8
|
8.7
|
1.0
|
CB
|
A:LYS174
|
4.9
|
13.0
|
1.0
|
O
|
A:HOH1111
|
4.9
|
14.6
|
1.0
|
C
|
A:TYR159
|
4.9
|
8.7
|
1.0
|
CB
|
A:TYR176
|
5.0
|
7.2
|
1.0
|
|
Calcium binding site 3 out
of 6 in 6tr4
Go back to
Calcium Binding Sites List in 6tr4
Calcium binding site 3 out
of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca608
b:12.8
occ:1.00
|
O
|
A:GLY197
|
2.2
|
8.3
|
1.0
|
O
|
A:LEU188
|
2.2
|
7.6
|
1.0
|
OE2
|
A:GLU230
|
2.3
|
8.1
|
1.0
|
O
|
A:HOH1222
|
2.3
|
13.8
|
1.0
|
O
|
A:HOH1062
|
2.4
|
20.0
|
1.0
|
O
|
A:HOH1025
|
2.4
|
9.3
|
1.0
|
O
|
A:HOH928
|
2.7
|
16.2
|
1.0
|
CD
|
A:GLU230
|
3.3
|
7.8
|
1.0
|
C
|
A:LEU188
|
3.4
|
7.2
|
1.0
|
C
|
A:GLY197
|
3.5
|
7.8
|
1.0
|
OE1
|
A:GLU230
|
3.6
|
8.0
|
1.0
|
CA
|
A:LEU188
|
4.0
|
6.8
|
1.0
|
CA
|
A:GLY197
|
4.2
|
8.4
|
1.0
|
O
|
A:ASN229
|
4.2
|
8.4
|
1.0
|
N
|
A:HIS198
|
4.5
|
7.5
|
1.0
|
N
|
A:GLY189
|
4.5
|
7.9
|
1.0
|
O
|
A:HOH1050
|
4.5
|
23.6
|
1.0
|
O
|
A:ASN190
|
4.6
|
8.9
|
1.0
|
CA
|
A:HIS198
|
4.6
|
7.6
|
1.0
|
CG
|
A:GLU230
|
4.6
|
7.3
|
1.0
|
O
|
A:TYR193
|
4.6
|
7.4
|
1.0
|
CB
|
A:LEU188
|
4.7
|
6.7
|
1.0
|
CB
|
A:ASN229
|
4.8
|
8.2
|
1.0
|
CA
|
A:GLY189
|
4.8
|
8.4
|
1.0
|
O
|
A:ILE187
|
4.9
|
7.4
|
1.0
|
N
|
A:ASN190
|
4.9
|
9.0
|
1.0
|
O
|
A:HOH1173
|
4.9
|
35.4
|
1.0
|
C
|
A:GLY189
|
4.9
|
8.9
|
1.0
|
C
|
A:ASN229
|
5.0
|
7.9
|
1.0
|
C
|
A:ASN190
|
5.0
|
9.2
|
1.0
|
OD1
|
A:ASN229
|
5.0
|
9.4
|
1.0
|
|
Calcium binding site 4 out
of 6 in 6tr4
Go back to
Calcium Binding Sites List in 6tr4
Calcium binding site 4 out
of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca704
b:8.5
occ:1.00
|
O
|
B:LYS174
|
2.2
|
9.8
|
1.0
|
O
|
B:GLY158
|
2.3
|
7.5
|
1.0
|
O
|
B:SER156
|
2.3
|
7.4
|
1.0
|
O
|
B:HOH1201
|
2.4
|
10.2
|
1.0
|
OD1
|
B:ASP172
|
2.4
|
9.3
|
1.0
|
O
|
B:HOH911
|
2.5
|
9.5
|
1.0
|
OD2
|
B:ASP172
|
2.5
|
10.5
|
1.0
|
CG
|
B:ASP172
|
2.8
|
9.6
|
1.0
|
C
|
B:SER156
|
3.3
|
7.3
|
1.0
|
C
|
B:LYS174
|
3.5
|
10.7
|
1.0
|
C
|
B:GLY158
|
3.5
|
7.4
|
1.0
|
CA
|
B:SER156
|
3.9
|
7.8
|
1.0
|
O
|
B:HOH986
|
4.0
|
14.1
|
1.0
|
N
|
B:TYR176
|
4.2
|
8.4
|
1.0
|
N
|
B:GLY158
|
4.2
|
6.9
|
1.0
|
C
|
B:TYR157
|
4.3
|
7.0
|
1.0
|
CB
|
B:ASP172
|
4.3
|
9.9
|
1.0
|
N
|
B:ASP175
|
4.3
|
10.6
|
1.0
|
CA
|
B:TYR159
|
4.4
|
8.1
|
1.0
|
CA
|
B:ASP175
|
4.4
|
10.5
|
1.0
|
OE1
|
B:GLN215
|
4.4
|
8.0
|
1.0
|
N
|
B:TYR159
|
4.4
|
7.6
|
1.0
|
N
|
B:TYR157
|
4.4
|
7.2
|
1.0
|
N
|
B:LYS174
|
4.4
|
10.8
|
1.0
|
CB
|
B:SER156
|
4.4
|
7.9
|
1.0
|
CA
|
B:LYS174
|
4.4
|
11.5
|
1.0
|
N
|
B:LYS160
|
4.4
|
9.2
|
1.0
|
CA
|
B:GLY158
|
4.5
|
7.1
|
1.0
|
O
|
B:TYR157
|
4.6
|
7.1
|
1.0
|
C
|
B:ASP175
|
4.7
|
9.5
|
1.0
|
CA
|
B:TYR157
|
4.7
|
6.9
|
1.0
|
O
|
B:HOH879
|
4.8
|
16.0
|
1.0
|
O
|
B:PRO155
|
4.8
|
9.0
|
1.0
|
CB
|
B:LYS174
|
4.8
|
12.9
|
1.0
|
O
|
B:HOH1224
|
4.9
|
13.7
|
1.0
|
C
|
B:TYR159
|
4.9
|
8.6
|
1.0
|
CB
|
B:TYR176
|
5.0
|
7.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 6tr4
Go back to
Calcium Binding Sites List in 6tr4
Calcium binding site 5 out
of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca705
b:7.2
occ:1.00
|
O
|
B:ASN397
|
2.3
|
8.4
|
1.0
|
OE2
|
B:GLU499
|
2.3
|
11.1
|
1.0
|
O
|
B:ASN402
|
2.3
|
8.7
|
1.0
|
O
|
B:SER498
|
2.4
|
7.6
|
1.0
|
OD1
|
B:ASP400
|
2.4
|
9.5
|
1.0
|
OG1
|
B:THR405
|
2.5
|
8.7
|
1.0
|
O
|
B:THR405
|
2.5
|
7.8
|
1.0
|
CD
|
B:GLU499
|
3.3
|
10.7
|
1.0
|
C
|
B:THR405
|
3.4
|
8.5
|
1.0
|
C
|
B:ASN402
|
3.5
|
9.3
|
1.0
|
CG
|
B:ASP400
|
3.5
|
10.2
|
1.0
|
C
|
B:ASN397
|
3.5
|
8.5
|
1.0
|
C
|
B:SER498
|
3.6
|
7.7
|
1.0
|
CB
|
B:THR405
|
3.7
|
8.9
|
1.0
|
OD2
|
B:ASP400
|
3.8
|
11.1
|
1.0
|
CA
|
B:THR405
|
3.9
|
9.1
|
1.0
|
N
|
B:ASN402
|
3.9
|
10.3
|
1.0
|
N
|
B:THR405
|
4.0
|
9.3
|
1.0
|
CA
|
B:ASN402
|
4.1
|
9.7
|
1.0
|
CG
|
B:GLU499
|
4.1
|
9.7
|
1.0
|
OE1
|
B:GLU499
|
4.2
|
11.8
|
1.0
|
CA
|
B:SER498
|
4.2
|
7.5
|
1.0
|
CA
|
B:ASN397
|
4.3
|
9.0
|
1.0
|
CB
|
B:ASN402
|
4.3
|
10.0
|
1.0
|
N
|
B:MET398
|
4.4
|
8.6
|
1.0
|
CB
|
B:SER498
|
4.5
|
7.7
|
1.0
|
N
|
B:TYR406
|
4.5
|
8.2
|
1.0
|
N
|
B:ASP403
|
4.5
|
9.1
|
1.0
|
CA
|
B:MET398
|
4.5
|
8.4
|
1.0
|
CB
|
B:ASN397
|
4.6
|
9.3
|
1.0
|
N
|
B:ASP400
|
4.6
|
10.5
|
1.0
|
N
|
B:GLU499
|
4.7
|
7.9
|
1.0
|
CA
|
B:ASP403
|
4.7
|
9.3
|
1.0
|
CB
|
B:ASP400
|
4.8
|
10.5
|
1.0
|
N
|
B:ASP401
|
4.8
|
11.7
|
1.0
|
CG2
|
B:THR405
|
4.8
|
9.1
|
1.0
|
C
|
B:MET398
|
4.8
|
8.8
|
1.0
|
CA
|
B:TYR406
|
4.9
|
8.2
|
1.0
|
C
|
B:ASP403
|
4.9
|
9.4
|
1.0
|
CA
|
B:GLU499
|
4.9
|
8.5
|
1.0
|
|
Calcium binding site 6 out
of 6 in 6tr4
Go back to
Calcium Binding Sites List in 6tr4
Calcium binding site 6 out
of 6 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca706
b:14.7
occ:1.00
|
O
|
B:HOH1292
|
2.2
|
18.6
|
1.0
|
O
|
B:LEU188
|
2.2
|
7.2
|
1.0
|
O
|
B:GLY197
|
2.2
|
8.5
|
1.0
|
O
|
B:HOH1171
|
2.2
|
28.3
|
1.0
|
OE2
|
B:GLU230
|
2.3
|
8.2
|
1.0
|
O
|
B:HOH1137
|
2.4
|
9.9
|
1.0
|
O
|
B:HOH1000
|
2.8
|
21.9
|
1.0
|
CD
|
B:GLU230
|
3.3
|
8.0
|
1.0
|
C
|
B:LEU188
|
3.4
|
7.2
|
1.0
|
C
|
B:GLY197
|
3.4
|
8.2
|
1.0
|
OE1
|
B:GLU230
|
3.6
|
8.1
|
1.0
|
CA
|
B:LEU188
|
4.0
|
6.8
|
1.0
|
CA
|
B:GLY197
|
4.2
|
8.5
|
1.0
|
O
|
B:ASN229
|
4.2
|
8.4
|
1.0
|
O
|
B:HOH1199
|
4.3
|
25.0
|
1.0
|
N
|
B:HIS198
|
4.4
|
7.8
|
1.0
|
N
|
B:GLY189
|
4.5
|
7.6
|
1.0
|
O
|
B:ASN190
|
4.5
|
9.4
|
1.0
|
O
|
B:TYR193
|
4.6
|
7.3
|
1.0
|
CG
|
B:GLU230
|
4.6
|
7.7
|
1.0
|
CA
|
B:HIS198
|
4.6
|
7.7
|
1.0
|
CB
|
B:LEU188
|
4.6
|
6.9
|
1.0
|
O
|
B:HOH1443
|
4.7
|
23.1
|
1.0
|
CA
|
B:GLY189
|
4.8
|
8.4
|
1.0
|
CB
|
B:ASN229
|
4.8
|
8.1
|
1.0
|
O
|
B:ILE187
|
4.8
|
7.2
|
1.0
|
N
|
B:ASN190
|
4.8
|
9.1
|
1.0
|
C
|
B:GLY189
|
4.8
|
9.0
|
1.0
|
C
|
B:ASN190
|
4.9
|
9.4
|
1.0
|
C
|
B:ASN229
|
5.0
|
8.0
|
1.0
|
OD1
|
B:ASN229
|
5.0
|
9.3
|
1.0
|
|
Reference:
H.Wu,
O.Rebello,
E.H.Crost,
C.D.Owen,
S.Walpole,
C.Bennati-Granier,
D.Ndeh,
S.Monaco,
T.Hicks,
A.Colvile,
P.A.Urbanowicz,
M.A.Walsh,
J.Angulo,
D.I.R.Spencer,
N.Juge.
Fucosidases From the Human Gut Symbiont Ruminococcus Gnavus. Cell.Mol.Life Sci. 2020.
ISSN: ESSN 1420-9071
PubMed: 32333083
DOI: 10.1007/S00018-020-03514-X
Page generated: Tue Jul 16 15:26:08 2024
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