Calcium in PDB 8dge: BOGH13ASUS From Bacteroides Ovatus
Protein crystallography data
The structure of BOGH13ASUS From Bacteroides Ovatus, PDB code: 8dge
was solved by
H.A.Brown,
A.L.Deveaux,
N.M.Koropatkin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
62.00 /
1.89
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.387,
148.443,
112.77,
90,
91,
90
|
R / Rfree (%)
|
20.9 /
27.1
|
Other elements in 8dge:
The structure of BOGH13ASUS From Bacteroides Ovatus also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the BOGH13ASUS From Bacteroides Ovatus
(pdb code 8dge). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
BOGH13ASUS From Bacteroides Ovatus, PDB code: 8dge:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 8dge
Go back to
Calcium Binding Sites List in 8dge
Calcium binding site 1 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca801
b:25.9
occ:1.00
|
O
|
A:PHE357
|
2.2
|
24.3
|
1.0
|
OD2
|
A:ASP374
|
2.3
|
24.1
|
1.0
|
OE1
|
A:GLU274
|
2.4
|
23.7
|
1.0
|
O
|
A:HOH1048
|
2.4
|
26.0
|
1.0
|
O
|
A:GLY359
|
2.4
|
24.3
|
1.0
|
OE1
|
A:GLU356
|
2.5
|
32.0
|
1.0
|
OE2
|
A:GLU356
|
2.8
|
32.9
|
1.0
|
CD
|
A:GLU356
|
2.9
|
27.8
|
1.0
|
CG
|
A:ASP374
|
3.3
|
24.8
|
1.0
|
C
|
A:PHE357
|
3.5
|
23.8
|
1.0
|
CD
|
A:GLU274
|
3.6
|
26.5
|
1.0
|
C
|
A:GLY359
|
3.6
|
23.7
|
1.0
|
OD1
|
A:ASP374
|
3.7
|
26.4
|
1.0
|
N
|
A:PHE357
|
3.9
|
25.2
|
1.0
|
N
|
A:GLY359
|
3.9
|
25.7
|
1.0
|
OE2
|
A:GLU274
|
4.1
|
27.2
|
1.0
|
CA
|
A:GLY359
|
4.3
|
25.2
|
1.0
|
C
|
A:ALA358
|
4.3
|
26.1
|
1.0
|
CA
|
A:PHE357
|
4.3
|
24.4
|
1.0
|
CD1
|
A:PHE357
|
4.4
|
26.7
|
1.0
|
CG
|
A:GLU356
|
4.4
|
29.4
|
1.0
|
N
|
A:ALA358
|
4.5
|
25.1
|
1.0
|
OH
|
A:TYR289
|
4.6
|
30.5
|
1.0
|
CB
|
A:ASP374
|
4.6
|
24.3
|
1.0
|
CA
|
A:ALA358
|
4.6
|
26.4
|
1.0
|
CE1
|
A:PHE357
|
4.6
|
30.3
|
1.0
|
N
|
A:ASN360
|
4.7
|
23.2
|
1.0
|
C
|
A:GLU356
|
4.7
|
25.1
|
1.0
|
CG
|
A:GLU274
|
4.7
|
27.5
|
1.0
|
O
|
A:HOH971
|
4.7
|
33.5
|
1.0
|
CB
|
A:GLU274
|
4.8
|
28.0
|
1.0
|
CG
|
A:PHE357
|
4.8
|
26.9
|
1.0
|
O
|
A:ALA358
|
4.8
|
23.7
|
1.0
|
CA
|
A:GLU356
|
4.8
|
25.9
|
1.0
|
O
|
A:HOH942
|
4.9
|
38.0
|
1.0
|
CA
|
A:ASN360
|
4.9
|
25.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 8dge
Go back to
Calcium Binding Sites List in 8dge
Calcium binding site 2 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca801
b:25.8
occ:1.00
|
O
|
B:PHE357
|
2.2
|
26.3
|
1.0
|
OE1
|
B:GLU274
|
2.4
|
23.3
|
1.0
|
OD2
|
B:ASP374
|
2.4
|
22.2
|
1.0
|
O
|
B:GLY359
|
2.4
|
23.9
|
1.0
|
OE1
|
B:GLU356
|
2.5
|
28.5
|
1.0
|
O
|
B:HOH972
|
2.6
|
23.5
|
1.0
|
OE2
|
B:GLU356
|
2.6
|
32.1
|
1.0
|
CD
|
B:GLU356
|
2.9
|
25.7
|
1.0
|
CG
|
B:ASP374
|
3.3
|
24.0
|
1.0
|
C
|
B:PHE357
|
3.4
|
25.0
|
1.0
|
CD
|
B:GLU274
|
3.5
|
26.1
|
1.0
|
OD1
|
B:ASP374
|
3.6
|
26.5
|
1.0
|
C
|
B:GLY359
|
3.6
|
25.2
|
1.0
|
N
|
B:PHE357
|
3.8
|
24.9
|
1.0
|
N
|
B:GLY359
|
3.9
|
26.1
|
1.0
|
OE2
|
B:GLU274
|
4.1
|
26.5
|
1.0
|
C
|
B:ALA358
|
4.2
|
25.0
|
1.0
|
CA
|
B:PHE357
|
4.3
|
24.8
|
1.0
|
CA
|
B:GLY359
|
4.3
|
25.4
|
1.0
|
CG
|
B:GLU356
|
4.3
|
27.6
|
1.0
|
CD1
|
B:PHE357
|
4.4
|
26.9
|
1.0
|
N
|
B:ALA358
|
4.4
|
26.0
|
1.0
|
CA
|
B:ALA358
|
4.5
|
25.1
|
1.0
|
C
|
B:GLU356
|
4.6
|
24.4
|
1.0
|
O
|
B:HOH1231
|
4.6
|
34.5
|
1.0
|
O
|
B:HOH932
|
4.6
|
41.1
|
1.0
|
N
|
B:ASN360
|
4.7
|
26.8
|
1.0
|
CB
|
B:ASP374
|
4.7
|
23.6
|
1.0
|
CG
|
B:GLU274
|
4.7
|
28.4
|
1.0
|
OH
|
B:TYR289
|
4.7
|
28.4
|
1.0
|
CE1
|
B:PHE357
|
4.7
|
26.8
|
1.0
|
CB
|
B:GLU274
|
4.7
|
28.4
|
1.0
|
CG2
|
B:VAL277
|
4.8
|
30.6
|
1.0
|
O
|
B:ALA358
|
4.8
|
22.8
|
1.0
|
CA
|
B:GLU356
|
4.8
|
26.3
|
1.0
|
CG
|
B:PHE357
|
4.8
|
25.3
|
1.0
|
CA
|
B:ASN360
|
4.9
|
29.2
|
1.0
|
|
Calcium binding site 3 out
of 4 in 8dge
Go back to
Calcium Binding Sites List in 8dge
Calcium binding site 3 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca801
b:28.8
occ:1.00
|
O
|
C:PHE357
|
2.3
|
23.8
|
1.0
|
O
|
C:HOH1097
|
2.4
|
25.4
|
1.0
|
O
|
C:GLY359
|
2.4
|
23.3
|
1.0
|
OE1
|
C:GLU274
|
2.4
|
23.8
|
1.0
|
OD2
|
C:ASP374
|
2.5
|
24.0
|
1.0
|
OE1
|
C:GLU356
|
2.6
|
30.0
|
1.0
|
OE2
|
C:GLU356
|
2.7
|
29.6
|
1.0
|
CD
|
C:GLU356
|
3.0
|
27.3
|
1.0
|
CG
|
C:ASP374
|
3.4
|
24.1
|
1.0
|
C
|
C:PHE357
|
3.5
|
23.9
|
1.0
|
C
|
C:GLY359
|
3.6
|
24.2
|
1.0
|
CD
|
C:GLU274
|
3.6
|
25.9
|
1.0
|
OD1
|
C:ASP374
|
3.7
|
26.9
|
1.0
|
N
|
C:GLY359
|
3.9
|
25.2
|
1.0
|
N
|
C:PHE357
|
4.0
|
22.5
|
1.0
|
OE2
|
C:GLU274
|
4.1
|
24.6
|
1.0
|
CA
|
C:GLY359
|
4.2
|
26.1
|
1.0
|
C
|
C:ALA358
|
4.3
|
26.6
|
1.0
|
CD1
|
C:PHE357
|
4.4
|
26.6
|
1.0
|
CA
|
C:PHE357
|
4.4
|
23.9
|
1.0
|
CG
|
C:GLU356
|
4.5
|
29.5
|
1.0
|
N
|
C:ALA358
|
4.5
|
25.3
|
1.0
|
O
|
C:HOH993
|
4.6
|
33.0
|
1.0
|
O
|
C:HOH1171
|
4.6
|
35.8
|
1.0
|
N
|
C:ASN360
|
4.6
|
23.6
|
1.0
|
OH
|
C:TYR289
|
4.7
|
30.3
|
1.0
|
CE1
|
C:PHE357
|
4.7
|
26.8
|
1.0
|
CA
|
C:ALA358
|
4.7
|
26.1
|
1.0
|
C
|
C:GLU356
|
4.7
|
24.5
|
1.0
|
CB
|
C:ASP374
|
4.7
|
25.4
|
1.0
|
CG
|
C:GLU274
|
4.8
|
26.0
|
1.0
|
CB
|
C:GLU274
|
4.8
|
27.4
|
1.0
|
CG
|
C:PHE357
|
4.9
|
26.2
|
1.0
|
CG2
|
C:VAL277
|
4.9
|
27.6
|
1.0
|
CA
|
C:ASN360
|
4.9
|
25.8
|
1.0
|
CA
|
C:GLU356
|
4.9
|
26.1
|
1.0
|
O
|
C:ALA358
|
4.9
|
25.6
|
1.0
|
|
Calcium binding site 4 out
of 4 in 8dge
Go back to
Calcium Binding Sites List in 8dge
Calcium binding site 4 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca801
b:27.4
occ:1.00
|
O
|
D:PHE357
|
2.3
|
23.6
|
1.0
|
OD2
|
D:ASP374
|
2.3
|
21.5
|
1.0
|
OE1
|
D:GLU274
|
2.4
|
21.6
|
1.0
|
O
|
D:GLY359
|
2.4
|
23.2
|
1.0
|
O
|
D:HOH1020
|
2.4
|
25.1
|
1.0
|
OE1
|
D:GLU356
|
2.7
|
29.7
|
1.0
|
OE2
|
D:GLU356
|
2.8
|
29.1
|
1.0
|
CD
|
D:GLU356
|
3.1
|
25.4
|
1.0
|
CG
|
D:ASP374
|
3.3
|
22.4
|
1.0
|
C
|
D:PHE357
|
3.5
|
24.7
|
1.0
|
CD
|
D:GLU274
|
3.5
|
24.9
|
1.0
|
C
|
D:GLY359
|
3.6
|
24.4
|
1.0
|
OD1
|
D:ASP374
|
3.7
|
24.3
|
1.0
|
N
|
D:GLY359
|
3.9
|
25.5
|
1.0
|
N
|
D:PHE357
|
3.9
|
23.1
|
1.0
|
OE2
|
D:GLU274
|
4.1
|
26.8
|
1.0
|
CA
|
D:GLY359
|
4.2
|
24.7
|
1.0
|
CD1
|
D:PHE357
|
4.3
|
24.9
|
1.0
|
C
|
D:ALA358
|
4.3
|
26.5
|
1.0
|
CA
|
D:PHE357
|
4.3
|
25.0
|
1.0
|
N
|
D:ALA358
|
4.5
|
25.1
|
1.0
|
OH
|
D:TYR289
|
4.5
|
28.5
|
1.0
|
O
|
D:HOH909
|
4.5
|
31.1
|
1.0
|
CG
|
D:GLU356
|
4.5
|
25.6
|
1.0
|
N
|
D:ASN360
|
4.6
|
25.6
|
1.0
|
CE1
|
D:PHE357
|
4.6
|
24.6
|
1.0
|
CA
|
D:ALA358
|
4.6
|
24.2
|
1.0
|
CB
|
D:ASP374
|
4.7
|
21.6
|
1.0
|
CG
|
D:GLU274
|
4.7
|
24.9
|
1.0
|
CB
|
D:GLU274
|
4.7
|
25.6
|
1.0
|
C
|
D:GLU356
|
4.7
|
24.1
|
1.0
|
CG2
|
D:VAL277
|
4.8
|
27.0
|
1.0
|
CG
|
D:PHE357
|
4.8
|
24.5
|
1.0
|
CA
|
D:ASN360
|
4.9
|
27.3
|
1.0
|
CA
|
D:GLU356
|
4.9
|
24.7
|
1.0
|
O
|
D:ALA358
|
5.0
|
27.1
|
1.0
|
|
Reference:
H.A.Brown,
A.L.Deveaux,
N.M.Koropatkin.
BOGH13ASUS From Bacteroides Ovatus To Be Published.
Page generated: Fri Jul 19 07:56:38 2024
|