Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose, PDB code: 6tr4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6tr4
Go back to
Magnesium Binding Sites List in 6tr4
Magnesium binding site 1 out
of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg603
b:8.8
occ:1.00
|
O
|
A:SER107
|
2.0
|
9.4
|
1.0
|
O
|
A:HOH749
|
2.0
|
12.1
|
1.0
|
O
|
A:HOH748
|
2.1
|
11.5
|
1.0
|
O
|
A:THR110
|
2.1
|
8.9
|
1.0
|
O
|
A:HOH781
|
2.1
|
11.8
|
1.0
|
OD2
|
A:ASP113
|
2.1
|
8.9
|
1.0
|
CG
|
A:ASP113
|
3.1
|
8.7
|
1.0
|
C
|
A:SER107
|
3.2
|
9.6
|
1.0
|
C
|
A:THR110
|
3.3
|
9.3
|
1.0
|
OD1
|
A:ASP113
|
3.5
|
9.0
|
1.0
|
N
|
A:SER107
|
3.8
|
9.3
|
1.0
|
CA
|
A:GLU111
|
4.0
|
10.8
|
0.5
|
CA
|
A:SER107
|
4.0
|
9.4
|
1.0
|
N
|
A:GLU111
|
4.1
|
9.9
|
0.5
|
N
|
A:GLU111
|
4.1
|
9.8
|
0.5
|
CA
|
A:GLU111
|
4.1
|
10.6
|
0.5
|
O
|
A:HOH1331
|
4.1
|
26.9
|
1.0
|
OE2
|
A:GLU111
|
4.2
|
15.7
|
0.5
|
N
|
A:GLU108
|
4.2
|
10.0
|
0.5
|
N
|
A:GLU108
|
4.2
|
9.9
|
0.5
|
N
|
A:THR110
|
4.3
|
9.1
|
1.0
|
CB
|
A:ASP113
|
4.4
|
8.0
|
1.0
|
OD1
|
A:ASP106
|
4.4
|
15.9
|
1.0
|
CA
|
A:GLU108
|
4.4
|
10.6
|
0.5
|
CA
|
A:GLU108
|
4.4
|
10.5
|
0.5
|
O
|
A:HOH702
|
4.4
|
25.7
|
1.0
|
O
|
A:HOH1069
|
4.4
|
21.4
|
1.0
|
CA
|
A:THR110
|
4.4
|
9.1
|
1.0
|
CB
|
A:SER107
|
4.4
|
9.1
|
1.0
|
CD
|
A:GLU111
|
4.6
|
14.2
|
0.5
|
C
|
A:GLU108
|
4.7
|
10.4
|
0.5
|
C
|
A:GLU111
|
4.7
|
9.9
|
0.5
|
C
|
A:GLU111
|
4.7
|
10.0
|
0.5
|
OE2
|
A:GLU108
|
4.7
|
15.7
|
0.5
|
C
|
A:GLU108
|
4.8
|
10.5
|
0.5
|
C
|
A:ASP106
|
4.8
|
9.8
|
1.0
|
CG2
|
A:THR110
|
4.8
|
8.8
|
1.0
|
OE1
|
A:GLU111
|
4.9
|
15.9
|
0.5
|
|
Magnesium binding site 2 out
of 5 in 6tr4
Go back to
Magnesium Binding Sites List in 6tr4
Magnesium binding site 2 out
of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg604
b:8.8
occ:1.00
|
O
|
B:HOH1380
|
2.0
|
10.3
|
1.0
|
O
|
A:HOH1319
|
2.0
|
10.0
|
1.0
|
O
|
A:HOH920
|
2.1
|
7.6
|
1.0
|
O
|
B:HOH1315
|
2.1
|
11.2
|
1.0
|
O
|
A:HOH892
|
2.1
|
7.7
|
1.0
|
O
|
A:HOH795
|
2.1
|
8.2
|
1.0
|
O
|
A:HOH962
|
4.1
|
14.6
|
1.0
|
O
|
B:HOH1200
|
4.1
|
15.2
|
1.0
|
O
|
B:HOH1234
|
4.1
|
14.8
|
1.0
|
O
|
A:HOH1084
|
4.2
|
12.7
|
1.0
|
O
|
A:LYS37
|
4.2
|
7.2
|
1.0
|
OD1
|
A:ASP403
|
4.2
|
9.5
|
1.0
|
O
|
A:HOH1364
|
4.2
|
13.9
|
1.0
|
OD2
|
A:ASP403
|
4.2
|
10.1
|
1.0
|
O
|
A:HOH719
|
4.3
|
19.0
|
1.0
|
O
|
A:HOH1000
|
4.3
|
26.0
|
1.0
|
NZ
|
B:LYS391
|
4.3
|
12.7
|
1.0
|
OE1
|
A:GLU434
|
4.4
|
8.2
|
1.0
|
O
|
A:HOH861
|
4.5
|
13.2
|
1.0
|
CE
|
A:LYS37
|
4.6
|
7.7
|
1.0
|
OE2
|
A:GLU39
|
4.6
|
8.8
|
1.0
|
CG
|
A:ASP403
|
4.7
|
9.3
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6tr4
Go back to
Magnesium Binding Sites List in 6tr4
Magnesium binding site 3 out
of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg605
b:16.4
occ:1.00
|
O
|
A:PHE75
|
2.1
|
12.1
|
1.0
|
OD1
|
A:ASP74
|
2.1
|
19.2
|
1.0
|
OE1
|
A:GLU131
|
2.1
|
11.9
|
1.0
|
O
|
A:HOH766
|
2.1
|
15.7
|
1.0
|
O
|
A:HOH1141
|
2.1
|
19.3
|
1.0
|
O
|
A:HOH1113
|
2.2
|
22.8
|
1.0
|
CG
|
A:ASP74
|
3.1
|
18.2
|
1.0
|
CD
|
A:GLU131
|
3.3
|
10.7
|
1.0
|
C
|
A:PHE75
|
3.3
|
11.5
|
1.0
|
OD2
|
A:ASP74
|
3.6
|
21.5
|
1.0
|
N
|
A:PHE75
|
3.9
|
12.2
|
1.0
|
CA
|
A:PHE75
|
4.0
|
11.3
|
1.0
|
CG
|
A:GLU131
|
4.1
|
10.1
|
1.0
|
OE2
|
A:GLU131
|
4.1
|
11.7
|
1.0
|
O
|
A:HOH1112
|
4.2
|
25.0
|
1.0
|
C
|
A:ASP74
|
4.2
|
13.8
|
1.0
|
OE1
|
A:GLU78
|
4.3
|
15.5
|
0.5
|
OE1
|
A:GLU78
|
4.3
|
13.7
|
0.5
|
N
|
A:ASP76
|
4.3
|
11.3
|
1.0
|
CB
|
A:GLU131
|
4.3
|
9.2
|
1.0
|
CB
|
A:PHE75
|
4.3
|
10.5
|
1.0
|
CB
|
A:ASP74
|
4.4
|
16.7
|
1.0
|
N
|
A:ALA77
|
4.5
|
10.8
|
1.0
|
O
|
A:HOH828
|
4.5
|
12.5
|
1.0
|
CA
|
A:ASP76
|
4.6
|
11.9
|
1.0
|
OH
|
A:TYR119
|
4.6
|
10.8
|
1.0
|
O
|
A:ASP74
|
4.7
|
14.4
|
1.0
|
CA
|
A:ASP74
|
4.7
|
15.2
|
1.0
|
CB
|
A:ASN121
|
4.8
|
21.9
|
1.0
|
O
|
A:HOH1351
|
4.8
|
21.8
|
1.0
|
ND2
|
A:ASN121
|
4.9
|
22.4
|
1.0
|
OE2
|
A:GLU78
|
5.0
|
14.9
|
0.5
|
|
Magnesium binding site 4 out
of 5 in 6tr4
Go back to
Magnesium Binding Sites List in 6tr4
Magnesium binding site 4 out
of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg702
b:8.5
occ:1.00
|
O
|
B:SER107
|
2.0
|
8.6
|
1.0
|
O
|
B:HOH832
|
2.1
|
13.1
|
1.0
|
O
|
B:HOH820
|
2.1
|
12.2
|
1.0
|
O
|
B:HOH980
|
2.1
|
10.7
|
1.0
|
OD2
|
B:ASP113
|
2.1
|
8.6
|
1.0
|
O
|
B:THR110
|
2.1
|
8.8
|
1.0
|
CG
|
B:ASP113
|
3.1
|
8.5
|
1.0
|
C
|
B:SER107
|
3.2
|
8.9
|
1.0
|
C
|
B:THR110
|
3.3
|
9.0
|
1.0
|
OD1
|
B:ASP113
|
3.5
|
8.9
|
1.0
|
N
|
B:SER107
|
3.8
|
8.7
|
1.0
|
CA
|
B:SER107
|
4.0
|
8.6
|
1.0
|
CA
|
B:GLU111
|
4.0
|
11.1
|
1.0
|
N
|
B:GLU111
|
4.1
|
9.8
|
1.0
|
O
|
B:HOH813
|
4.1
|
31.7
|
1.0
|
OE2
|
B:GLU111
|
4.1
|
27.0
|
1.0
|
O
|
B:HOH1462
|
4.2
|
36.5
|
1.0
|
N
|
B:GLU108
|
4.2
|
9.2
|
0.5
|
N
|
B:GLU108
|
4.2
|
9.4
|
0.5
|
OD1
|
B:ASP106
|
4.3
|
15.9
|
1.0
|
N
|
B:THR110
|
4.3
|
8.9
|
1.0
|
CB
|
B:ASP113
|
4.3
|
8.0
|
1.0
|
CB
|
B:SER107
|
4.4
|
8.5
|
1.0
|
O
|
B:HOH804
|
4.4
|
22.5
|
1.0
|
CA
|
B:GLU108
|
4.4
|
9.9
|
0.5
|
CA
|
B:THR110
|
4.5
|
8.7
|
1.0
|
O
|
B:HOH1180
|
4.5
|
22.0
|
1.0
|
CA
|
B:GLU108
|
4.5
|
10.2
|
0.5
|
CD
|
B:GLU111
|
4.6
|
21.3
|
1.0
|
C
|
B:GLU111
|
4.7
|
10.1
|
1.0
|
C
|
B:GLU108
|
4.7
|
9.6
|
0.5
|
C
|
B:ASP106
|
4.8
|
9.1
|
1.0
|
CG2
|
B:THR110
|
4.9
|
8.3
|
1.0
|
OE1
|
B:GLU111
|
4.9
|
28.0
|
1.0
|
C
|
B:GLU108
|
4.9
|
9.9
|
0.5
|
|
Magnesium binding site 5 out
of 5 in 6tr4
Go back to
Magnesium Binding Sites List in 6tr4
Magnesium binding site 5 out
of 5 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 D221A Mutant in Complex with Fucose
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg 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:Mg703
b:12.3
occ:1.00
|
OD1
|
B:ASP74
|
2.0
|
14.8
|
1.0
|
O
|
B:PHE75
|
2.0
|
11.1
|
1.0
|
OE1
|
B:GLU131
|
2.1
|
11.1
|
1.0
|
O
|
B:HOH1168
|
2.1
|
16.9
|
1.0
|
O
|
B:HOH1184
|
2.1
|
16.4
|
1.0
|
O
|
B:HOH1099
|
2.2
|
13.7
|
1.0
|
CG
|
B:ASP74
|
3.0
|
15.3
|
1.0
|
CD
|
B:GLU131
|
3.2
|
9.9
|
1.0
|
C
|
B:PHE75
|
3.3
|
10.5
|
1.0
|
OD2
|
B:ASP74
|
3.5
|
16.8
|
1.0
|
N
|
B:PHE75
|
3.8
|
11.0
|
1.0
|
CA
|
B:PHE75
|
4.0
|
10.4
|
1.0
|
OE2
|
B:GLU131
|
4.1
|
10.7
|
1.0
|
CG
|
B:GLU131
|
4.1
|
9.2
|
1.0
|
C
|
B:ASP74
|
4.1
|
12.2
|
1.0
|
O
|
B:HOH1228
|
4.1
|
22.6
|
1.0
|
CB
|
B:ASP74
|
4.2
|
14.2
|
1.0
|
O
|
B:HOH1410
|
4.3
|
33.5
|
1.0
|
N
|
B:ASP76
|
4.3
|
10.7
|
1.0
|
OE1
|
B:GLU78
|
4.3
|
17.9
|
1.0
|
CB
|
B:PHE75
|
4.3
|
9.9
|
1.0
|
CB
|
B:GLU131
|
4.4
|
8.5
|
1.0
|
O
|
B:HOH824
|
4.5
|
12.0
|
1.0
|
N
|
B:ALA77
|
4.5
|
10.6
|
1.0
|
OH
|
B:TYR119
|
4.5
|
10.0
|
1.0
|
CA
|
B:ASP76
|
4.5
|
11.4
|
1.0
|
O
|
B:ASP74
|
4.6
|
12.4
|
1.0
|
CA
|
B:ASP74
|
4.6
|
13.3
|
1.0
|
CB
|
B:ASN121
|
4.7
|
17.7
|
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 Oct 1 19:05:46 2024
|