Magnesium in PDB 5fq8: Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Protein crystallography data
The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq8
was solved by
A.J.Glenwright,
K.R.Pothula,
D.S.Chorev,
A.Basle,
C.V.Robinson,
U.Kleinekathoefer,
D.N.Bolam,
B.Van Den Berg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
52.93 /
2.75
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.110,
122.743,
122.830,
111.41,
98.33,
98.51
|
R / Rfree (%)
|
20.5 /
25.9
|
Other elements in 5fq8:
The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
(pdb code 5fq8). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq8:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5fq8
Go back to
Magnesium Binding Sites List in 5fq8
Magnesium binding site 1 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1481
b:23.9
occ:1.00
|
OD1
|
A:ASP478
|
2.0
|
62.5
|
1.0
|
OXT
|
A:LYS480
|
2.0
|
50.7
|
1.0
|
OD1
|
A:ASP411
|
2.2
|
30.6
|
1.0
|
O
|
A:ARG408
|
2.3
|
26.5
|
1.0
|
OD2
|
A:ASP411
|
2.4
|
31.9
|
1.0
|
OD2
|
A:ASP478
|
2.5
|
26.3
|
1.0
|
CG
|
A:ASP478
|
2.5
|
26.6
|
1.0
|
CG
|
A:ASP411
|
2.6
|
34.4
|
1.0
|
C
|
A:LYS480
|
3.2
|
39.7
|
1.0
|
C
|
A:ARG408
|
3.4
|
26.1
|
1.0
|
O
|
A:LYS480
|
3.8
|
36.5
|
1.0
|
CA
|
A:ARG408
|
3.9
|
29.9
|
1.0
|
CB
|
A:ASP478
|
3.9
|
26.5
|
1.0
|
CB
|
A:ASP411
|
4.1
|
42.6
|
1.0
|
N
|
A:LYS480
|
4.2
|
28.7
|
1.0
|
CA
|
A:LYS480
|
4.4
|
34.2
|
1.0
|
O
|
A:HOH2072
|
4.4
|
21.5
|
1.0
|
O
|
A:ARG409
|
4.5
|
27.6
|
1.0
|
O
|
A:ILE407
|
4.5
|
26.1
|
1.0
|
N
|
A:ARG409
|
4.5
|
26.1
|
1.0
|
CA
|
A:ASP478
|
4.6
|
27.0
|
1.0
|
CB
|
A:ARG408
|
4.6
|
34.6
|
1.0
|
CA
|
A:ASP411
|
4.6
|
34.1
|
1.0
|
N
|
A:ASP411
|
4.6
|
35.4
|
1.0
|
C
|
A:ARG409
|
4.7
|
27.1
|
1.0
|
O
|
A:HOH2091
|
4.7
|
6.9
|
1.0
|
N
|
A:ILE479
|
4.8
|
28.1
|
1.0
|
CA
|
A:ARG409
|
4.8
|
26.6
|
1.0
|
C
|
A:ASP478
|
4.9
|
27.6
|
1.0
|
CG
|
A:LYS480
|
5.0
|
40.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5fq8
Go back to
Magnesium Binding Sites List in 5fq8
Magnesium binding site 2 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1986
b:13.5
occ:1.00
|
O
|
A:HOH2050
|
2.0
|
13.4
|
1.0
|
O
|
A:HOH2051
|
2.0
|
43.1
|
1.0
|
O
|
A:ALA82
|
2.1
|
36.8
|
1.0
|
OD1
|
B:ASN633
|
2.2
|
32.3
|
1.0
|
O
|
B:ALA631
|
2.2
|
37.6
|
1.0
|
C
|
A:ALA82
|
3.3
|
26.4
|
1.0
|
CG
|
B:ASN633
|
3.3
|
25.5
|
1.0
|
C
|
B:ALA631
|
3.4
|
39.3
|
1.0
|
O
|
B:HOH2192
|
3.9
|
10.3
|
1.0
|
CA
|
A:GLY83
|
3.9
|
24.4
|
1.0
|
C
|
B:GLY632
|
4.0
|
26.1
|
1.0
|
N
|
B:ASN633
|
4.0
|
25.8
|
1.0
|
N
|
A:GLY83
|
4.0
|
26.0
|
1.0
|
CA
|
B:ASN633
|
4.1
|
25.9
|
1.0
|
OG
|
B:SER630
|
4.1
|
31.4
|
1.0
|
ND2
|
B:ASN633
|
4.2
|
25.3
|
1.0
|
O
|
B:GLY632
|
4.2
|
29.0
|
1.0
|
CA
|
B:ALA631
|
4.2
|
26.9
|
1.0
|
CB
|
B:ASN633
|
4.3
|
25.5
|
1.0
|
N
|
B:GLY632
|
4.3
|
33.9
|
1.0
|
CB
|
B:ALA631
|
4.4
|
27.4
|
1.0
|
N
|
B:ALA631
|
4.4
|
29.4
|
1.0
|
O
|
B:GLY686
|
4.4
|
30.8
|
1.0
|
CA
|
A:ALA82
|
4.4
|
25.7
|
1.0
|
O
|
A:GLY83
|
4.4
|
37.7
|
1.0
|
CA
|
B:GLY632
|
4.5
|
26.1
|
1.0
|
CB
|
A:ALA82
|
4.7
|
29.8
|
1.0
|
C
|
A:GLY83
|
4.7
|
29.7
|
1.0
|
O
|
B:HOH2197
|
4.7
|
17.3
|
1.0
|
CB
|
A:GLU86
|
4.8
|
24.4
|
1.0
|
CG
|
A:GLU86
|
4.9
|
24.7
|
1.0
|
OD1
|
A:ASP87
|
4.9
|
24.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5fq8
Go back to
Magnesium Binding Sites List in 5fq8
Magnesium binding site 3 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1480
b:27.6
occ:1.00
|
OD1
|
C:ASP478
|
2.0
|
61.1
|
1.0
|
O
|
C:HOH2099
|
2.0
|
29.3
|
1.0
|
O
|
C:HOH2098
|
2.0
|
26.9
|
1.0
|
OD1
|
C:ASP411
|
2.0
|
44.6
|
1.0
|
OD2
|
C:ASP411
|
2.2
|
44.5
|
1.0
|
CG
|
C:ASP411
|
2.4
|
43.3
|
1.0
|
O
|
C:ARG408
|
2.6
|
47.4
|
1.0
|
O
|
C:ILE479
|
3.1
|
44.9
|
1.0
|
CG
|
C:ASP478
|
3.1
|
54.2
|
1.0
|
OD2
|
C:ASP478
|
3.6
|
55.8
|
1.0
|
C
|
C:ARG408
|
3.8
|
39.7
|
1.0
|
CB
|
C:ASP411
|
3.8
|
43.5
|
1.0
|
N
|
C:ILE479
|
3.9
|
56.4
|
1.0
|
C
|
C:ILE479
|
4.0
|
45.8
|
1.0
|
O
|
C:ARG409
|
4.3
|
46.0
|
1.0
|
CB
|
C:ASP478
|
4.3
|
58.7
|
1.0
|
CA
|
C:ASP411
|
4.4
|
42.2
|
1.0
|
CA
|
C:ARG408
|
4.4
|
38.4
|
1.0
|
N
|
C:ASP411
|
4.5
|
42.6
|
1.0
|
CA
|
C:ASP478
|
4.5
|
41.8
|
1.0
|
C
|
C:ASP478
|
4.5
|
43.1
|
1.0
|
CA
|
C:ILE479
|
4.5
|
45.4
|
1.0
|
C
|
C:ARG409
|
4.7
|
42.2
|
1.0
|
N
|
C:ARG409
|
4.8
|
39.8
|
1.0
|
O
|
C:HOH2117
|
4.9
|
12.7
|
1.0
|
CA
|
C:ARG409
|
4.9
|
41.1
|
1.0
|
O
|
C:ILE407
|
5.0
|
54.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5fq8
Go back to
Magnesium Binding Sites List in 5fq8
Magnesium binding site 4 out
of 4 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1986
b:10.2
occ:1.00
|
OD1
|
D:ASN633
|
2.1
|
29.7
|
1.0
|
O
|
C:ALA82
|
2.2
|
27.5
|
1.0
|
O
|
D:ALA631
|
2.2
|
30.1
|
1.0
|
CG
|
D:ASN633
|
3.2
|
29.2
|
1.0
|
C
|
D:ALA631
|
3.4
|
30.3
|
1.0
|
C
|
C:ALA82
|
3.4
|
29.8
|
1.0
|
OG
|
D:SER630
|
3.6
|
34.4
|
1.0
|
ND2
|
D:ASN633
|
3.8
|
31.2
|
1.0
|
N
|
D:ALA631
|
3.9
|
30.8
|
1.0
|
CA
|
C:GLY83
|
3.9
|
26.0
|
1.0
|
CA
|
D:ALA631
|
4.0
|
30.9
|
1.0
|
OD1
|
C:ASP87
|
4.0
|
26.7
|
1.0
|
CB
|
D:ALA631
|
4.0
|
31.4
|
1.0
|
N
|
C:GLY83
|
4.1
|
31.2
|
1.0
|
O
|
C:GLY83
|
4.3
|
43.8
|
1.0
|
CG
|
C:GLU86
|
4.4
|
32.1
|
1.0
|
CB
|
C:GLU86
|
4.4
|
43.4
|
1.0
|
N
|
D:ASN633
|
4.4
|
29.3
|
1.0
|
CB
|
D:ASN633
|
4.4
|
30.4
|
1.0
|
N
|
D:GLY632
|
4.5
|
30.1
|
1.0
|
C
|
D:GLY632
|
4.5
|
30.1
|
1.0
|
CA
|
D:ASN633
|
4.5
|
31.3
|
1.0
|
CA
|
C:ALA82
|
4.5
|
27.1
|
1.0
|
C
|
C:GLY83
|
4.6
|
43.7
|
1.0
|
CB
|
D:SER630
|
4.6
|
30.1
|
1.0
|
O
|
D:GLY686
|
4.7
|
31.3
|
1.0
|
C
|
D:SER630
|
4.8
|
30.6
|
1.0
|
CB
|
C:ALA82
|
4.8
|
30.0
|
1.0
|
O
|
D:GLY632
|
4.8
|
37.2
|
1.0
|
CA
|
D:GLY632
|
4.8
|
29.6
|
1.0
|
CG
|
C:ASP87
|
4.9
|
26.6
|
1.0
|
|
Reference:
A.J.Glenwright,
K.R.Pothula,
S.P.Bhamidimarri,
D.S.Chorev,
A.Basle,
S.J.Firbank,
H.Zheng,
C.V.Robinson,
M.Winterhalter,
U.Kleinekathofer,
D.N.Bolam,
B.Van Den Berg.
Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828
Page generated: Sun Sep 29 04:22:45 2024
|