Manganese 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:
Manganese Binding Sites:
The binding sites of Manganese atom in the BOGH13ASUS From Bacteroides Ovatus
(pdb code 8dge). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
BOGH13ASUS From Bacteroides Ovatus, PDB code: 8dge:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 8dge
Go back to
Manganese Binding Sites List in 8dge
Manganese binding site 1 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn802
b:35.0
occ:1.00
|
OD1
|
A:ASP446
|
2.1
|
24.5
|
1.0
|
O
|
A:HOH960
|
2.1
|
23.7
|
1.0
|
O
|
A:GLY481
|
2.2
|
27.1
|
1.0
|
O
|
A:HOH926
|
2.2
|
29.3
|
1.0
|
NE2
|
A:HIS437
|
2.3
|
23.0
|
1.0
|
OD1
|
A:ASN404
|
2.3
|
24.0
|
1.0
|
CG
|
A:ASP446
|
3.0
|
24.5
|
1.0
|
C
|
A:GLY481
|
3.2
|
26.9
|
1.0
|
CE1
|
A:HIS437
|
3.2
|
23.8
|
1.0
|
CD2
|
A:HIS437
|
3.3
|
23.9
|
1.0
|
OD2
|
A:ASP446
|
3.3
|
26.3
|
1.0
|
CG
|
A:ASN404
|
3.5
|
21.1
|
1.0
|
CA
|
A:GLY481
|
3.8
|
26.4
|
1.0
|
O
|
A:ASN404
|
3.8
|
23.4
|
1.0
|
O
|
A:PHE447
|
4.0
|
25.1
|
1.0
|
ND2
|
A:ASN404
|
4.2
|
19.9
|
1.0
|
N
|
A:PHE482
|
4.3
|
26.6
|
1.0
|
ND1
|
A:HIS437
|
4.4
|
24.4
|
1.0
|
CB
|
A:ASP446
|
4.4
|
25.8
|
1.0
|
O
|
A:THR483
|
4.4
|
23.3
|
1.0
|
CG
|
A:HIS437
|
4.4
|
24.4
|
1.0
|
CB
|
A:ASN404
|
4.5
|
23.8
|
1.0
|
C
|
A:ASN404
|
4.5
|
23.4
|
1.0
|
CA
|
A:ASN404
|
4.5
|
23.4
|
1.0
|
N
|
A:THR483
|
4.5
|
23.4
|
1.0
|
CA
|
A:PHE482
|
4.6
|
26.4
|
1.0
|
O
|
A:HOH1019
|
4.6
|
25.6
|
1.0
|
N
|
A:PHE447
|
4.8
|
24.6
|
1.0
|
CA
|
A:ASP446
|
4.9
|
25.4
|
1.0
|
|
Manganese binding site 2 out
of 4 in 8dge
Go back to
Manganese Binding Sites List in 8dge
Manganese binding site 2 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn802
b:33.3
occ:1.00
|
O
|
B:GLY481
|
2.0
|
25.2
|
1.0
|
OD1
|
B:ASP446
|
2.1
|
25.4
|
1.0
|
NE2
|
B:HIS437
|
2.2
|
25.3
|
1.0
|
OD1
|
B:ASN404
|
2.2
|
23.6
|
1.0
|
O
|
B:HOH934
|
2.2
|
27.1
|
1.0
|
O
|
B:HOH951
|
2.3
|
29.4
|
1.0
|
C
|
B:GLY481
|
3.0
|
25.2
|
1.0
|
CG
|
B:ASP446
|
3.0
|
24.6
|
1.0
|
CD2
|
B:HIS437
|
3.1
|
27.0
|
1.0
|
CE1
|
B:HIS437
|
3.3
|
26.8
|
1.0
|
OD2
|
B:ASP446
|
3.3
|
27.7
|
1.0
|
CG
|
B:ASN404
|
3.3
|
23.0
|
1.0
|
CA
|
B:GLY481
|
3.5
|
23.9
|
1.0
|
O
|
B:ASN404
|
3.7
|
26.4
|
1.0
|
ND2
|
B:ASN404
|
3.9
|
26.0
|
1.0
|
O
|
B:PHE447
|
4.1
|
24.4
|
1.0
|
N
|
B:PHE482
|
4.2
|
25.5
|
1.0
|
CG
|
B:HIS437
|
4.3
|
27.1
|
1.0
|
ND1
|
B:HIS437
|
4.3
|
26.5
|
1.0
|
O
|
B:THR483
|
4.4
|
24.2
|
1.0
|
CB
|
B:ASP446
|
4.4
|
24.5
|
1.0
|
CB
|
B:ASN404
|
4.4
|
22.5
|
1.0
|
C
|
B:ASN404
|
4.5
|
23.6
|
1.0
|
N
|
B:THR483
|
4.5
|
25.4
|
1.0
|
CA
|
B:ASN404
|
4.5
|
24.5
|
1.0
|
CA
|
B:PHE482
|
4.6
|
25.6
|
1.0
|
O
|
B:HOH1162
|
4.7
|
26.8
|
1.0
|
N
|
B:GLY481
|
5.0
|
25.3
|
1.0
|
N
|
B:PHE447
|
5.0
|
25.5
|
1.0
|
|
Manganese binding site 3 out
of 4 in 8dge
Go back to
Manganese Binding Sites List in 8dge
Manganese binding site 3 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn802
b:33.2
occ:1.00
|
OD1
|
C:ASN404
|
2.1
|
25.5
|
1.0
|
O
|
C:GLY481
|
2.1
|
24.7
|
1.0
|
OD1
|
C:ASP446
|
2.2
|
23.4
|
1.0
|
O
|
C:HOH935
|
2.3
|
24.3
|
1.0
|
NE2
|
C:HIS437
|
2.3
|
22.6
|
1.0
|
O
|
C:HOH923
|
2.3
|
26.4
|
1.0
|
CG
|
C:ASP446
|
3.0
|
24.4
|
1.0
|
C
|
C:GLY481
|
3.2
|
25.5
|
1.0
|
CE1
|
C:HIS437
|
3.2
|
23.5
|
1.0
|
CG
|
C:ASN404
|
3.2
|
22.9
|
1.0
|
OD2
|
C:ASP446
|
3.2
|
25.4
|
1.0
|
CD2
|
C:HIS437
|
3.3
|
22.8
|
1.0
|
O
|
C:ASN404
|
3.6
|
22.6
|
1.0
|
CA
|
C:GLY481
|
3.7
|
25.8
|
1.0
|
ND2
|
C:ASN404
|
3.9
|
24.1
|
1.0
|
O
|
C:PHE447
|
4.1
|
21.2
|
1.0
|
N
|
C:PHE482
|
4.2
|
26.1
|
1.0
|
ND1
|
C:HIS437
|
4.3
|
21.8
|
1.0
|
CB
|
C:ASN404
|
4.4
|
22.2
|
1.0
|
O
|
C:THR483
|
4.4
|
27.2
|
1.0
|
C
|
C:ASN404
|
4.4
|
22.1
|
1.0
|
CG
|
C:HIS437
|
4.4
|
22.0
|
1.0
|
CB
|
C:ASP446
|
4.4
|
24.4
|
1.0
|
O
|
C:HOH1178
|
4.5
|
26.4
|
1.0
|
CA
|
C:ASN404
|
4.5
|
22.8
|
1.0
|
N
|
C:THR483
|
4.6
|
25.3
|
1.0
|
CA
|
C:PHE482
|
4.6
|
26.3
|
1.0
|
N
|
C:PHE447
|
5.0
|
23.9
|
1.0
|
|
Manganese binding site 4 out
of 4 in 8dge
Go back to
Manganese Binding Sites List in 8dge
Manganese binding site 4 out
of 4 in the BOGH13ASUS From Bacteroides Ovatus
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of BOGH13ASUS From Bacteroides Ovatus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn802
b:31.0
occ:1.00
|
O
|
D:HOH938
|
2.0
|
24.9
|
1.0
|
O
|
D:GLY481
|
2.1
|
24.2
|
1.0
|
OD1
|
D:ASP446
|
2.1
|
23.0
|
1.0
|
O
|
D:HOH972
|
2.2
|
23.6
|
1.0
|
NE2
|
D:HIS437
|
2.2
|
23.9
|
1.0
|
OD1
|
D:ASN404
|
2.2
|
24.0
|
1.0
|
CG
|
D:ASP446
|
3.0
|
23.8
|
1.0
|
CE1
|
D:HIS437
|
3.1
|
26.1
|
1.0
|
C
|
D:GLY481
|
3.2
|
25.7
|
1.0
|
CD2
|
D:HIS437
|
3.2
|
25.2
|
1.0
|
OD2
|
D:ASP446
|
3.3
|
24.9
|
1.0
|
CG
|
D:ASN404
|
3.3
|
23.4
|
1.0
|
CA
|
D:GLY481
|
3.6
|
26.5
|
1.0
|
O
|
D:ASN404
|
3.8
|
27.9
|
1.0
|
ND2
|
D:ASN404
|
4.0
|
23.6
|
1.0
|
O
|
D:PHE447
|
4.1
|
25.0
|
1.0
|
N
|
D:PHE482
|
4.3
|
26.2
|
1.0
|
ND1
|
D:HIS437
|
4.3
|
23.3
|
1.0
|
CG
|
D:HIS437
|
4.3
|
25.0
|
1.0
|
CB
|
D:ASP446
|
4.4
|
23.8
|
1.0
|
O
|
D:THR483
|
4.4
|
25.9
|
1.0
|
CB
|
D:ASN404
|
4.5
|
22.7
|
1.0
|
C
|
D:ASN404
|
4.5
|
24.8
|
1.0
|
CA
|
D:ASN404
|
4.6
|
25.1
|
1.0
|
N
|
D:THR483
|
4.6
|
27.6
|
1.0
|
CA
|
D:PHE482
|
4.6
|
24.9
|
1.0
|
O
|
D:HOH1127
|
4.6
|
26.3
|
1.0
|
N
|
D:PHE447
|
4.9
|
26.7
|
1.0
|
|
Reference:
H.A.Brown,
A.L.Deveaux,
N.M.Koropatkin.
BOGH13ASUS From Bacteroides Ovatus To Be Published.
Page generated: Sun Oct 6 11:31:57 2024
|