Barium in PDB 6kaj: Crystal Structure of Fkrp in Complex with Ba Ion
Protein crystallography data
The structure of Crystal Structure of Fkrp in Complex with Ba Ion, PDB code: 6kaj
was solved by
N.Kuwabara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.16 /
2.22
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.369,
118.820,
253.080,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.9 /
24.4
|
Other elements in 6kaj:
The structure of Crystal Structure of Fkrp in Complex with Ba Ion also contains other interesting chemical elements:
Barium Binding Sites:
The binding sites of Barium atom in the Crystal Structure of Fkrp in Complex with Ba Ion
(pdb code 6kaj). This binding sites where shown within
5.0 Angstroms radius around Barium atom.
In total 4 binding sites of Barium where determined in the
Crystal Structure of Fkrp in Complex with Ba Ion, PDB code: 6kaj:
Jump to Barium binding site number:
1;
2;
3;
4;
Barium binding site 1 out
of 4 in 6kaj
Go back to
Barium Binding Sites List in 6kaj
Barium binding site 1 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 1 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba506
b:0.4
occ:1.00
|
O2A
|
A:CDP504
|
2.6
|
59.4
|
1.0
|
OD1
|
A:ASP362
|
2.6
|
47.8
|
1.0
|
OD2
|
A:ASP364
|
2.8
|
62.9
|
1.0
|
O3B
|
A:CDP504
|
3.0
|
60.5
|
1.0
|
OD2
|
A:ASP360
|
3.2
|
51.3
|
1.0
|
OD1
|
A:ASP360
|
3.3
|
49.3
|
1.0
|
PA
|
A:CDP504
|
3.6
|
59.8
|
1.0
|
CG
|
A:ASP360
|
3.6
|
49.1
|
1.0
|
O
|
A:ASP362
|
3.7
|
44.8
|
1.0
|
O5'
|
A:CDP504
|
3.8
|
63.9
|
1.0
|
CG
|
A:ASP362
|
3.8
|
50.8
|
1.0
|
O3A
|
A:CDP504
|
4.0
|
64.5
|
1.0
|
CG
|
A:ASP364
|
4.0
|
56.7
|
1.0
|
PB
|
A:CDP504
|
4.1
|
66.8
|
1.0
|
CA
|
A:GLY345
|
4.1
|
47.0
|
1.0
|
N
|
A:GLY345
|
4.2
|
50.5
|
1.0
|
C
|
A:ASP362
|
4.2
|
47.2
|
1.0
|
OD2
|
A:ASP362
|
4.5
|
55.2
|
1.0
|
N
|
A:ASP362
|
4.6
|
46.9
|
1.0
|
C4'
|
A:CDP504
|
4.7
|
57.7
|
1.0
|
C5'
|
A:CDP504
|
4.7
|
58.3
|
1.0
|
C
|
A:GLY345
|
4.7
|
43.3
|
1.0
|
N
|
A:SER346
|
4.7
|
41.1
|
1.0
|
O
|
A:HOH631
|
4.8
|
38.8
|
1.0
|
O1B
|
A:CDP504
|
4.8
|
68.0
|
1.0
|
CA
|
A:ASP362
|
4.8
|
46.3
|
1.0
|
OD1
|
A:ASP364
|
4.8
|
56.6
|
1.0
|
N
|
A:VAL363
|
4.8
|
48.2
|
1.0
|
CB
|
A:ASP364
|
4.9
|
50.4
|
1.0
|
OG
|
A:SER346
|
4.9
|
43.5
|
1.0
|
CB
|
A:ASP362
|
4.9
|
48.3
|
1.0
|
O1A
|
A:CDP504
|
4.9
|
68.4
|
1.0
|
N
|
A:ASP364
|
4.9
|
47.3
|
1.0
|
|
Barium binding site 2 out
of 4 in 6kaj
Go back to
Barium Binding Sites List in 6kaj
Barium binding site 2 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 2 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ba506
b:0.3
occ:1.00
|
OD1
|
B:ASP362
|
2.6
|
37.0
|
1.0
|
O2A
|
B:CDP504
|
2.6
|
39.3
|
1.0
|
OD1
|
B:ASP360
|
2.8
|
47.7
|
1.0
|
OD2
|
B:ASP360
|
2.8
|
45.4
|
1.0
|
OD2
|
B:ASP364
|
3.1
|
51.3
|
1.0
|
CG
|
B:ASP360
|
3.1
|
44.8
|
1.0
|
O1B
|
B:CDP504
|
3.3
|
41.2
|
1.0
|
O
|
B:ASP362
|
3.5
|
37.9
|
1.0
|
PA
|
B:CDP504
|
3.7
|
42.9
|
1.0
|
CG
|
B:ASP362
|
3.8
|
37.8
|
1.0
|
O5'
|
B:CDP504
|
4.0
|
45.5
|
1.0
|
C
|
B:ASP362
|
4.1
|
39.4
|
1.0
|
CA
|
B:GLY345
|
4.3
|
31.1
|
1.0
|
N
|
B:ASP362
|
4.3
|
39.9
|
1.0
|
CG
|
B:ASP364
|
4.3
|
49.5
|
1.0
|
O3A
|
B:CDP504
|
4.3
|
47.9
|
1.0
|
PB
|
B:CDP504
|
4.4
|
53.1
|
1.0
|
N
|
B:GLY345
|
4.4
|
36.5
|
1.0
|
OD2
|
B:ASP362
|
4.5
|
43.1
|
1.0
|
CA
|
B:ASP362
|
4.5
|
38.3
|
1.0
|
C4'
|
B:CDP504
|
4.6
|
39.5
|
1.0
|
CB
|
B:ASP360
|
4.6
|
42.0
|
1.0
|
C5'
|
B:CDP504
|
4.7
|
40.9
|
1.0
|
CB
|
B:ASP362
|
4.7
|
34.4
|
1.0
|
C
|
B:GLY345
|
4.8
|
30.2
|
1.0
|
N
|
B:VAL363
|
4.8
|
41.1
|
1.0
|
O
|
B:HOH657
|
4.8
|
36.3
|
1.0
|
N
|
B:SER346
|
4.8
|
33.1
|
1.0
|
O
|
B:HOH624
|
4.9
|
28.9
|
1.0
|
OD1
|
B:ASP364
|
4.9
|
53.1
|
1.0
|
N
|
B:TYR361
|
5.0
|
34.7
|
1.0
|
O3'
|
B:CDP504
|
5.0
|
36.2
|
1.0
|
O1A
|
B:CDP504
|
5.0
|
42.4
|
1.0
|
|
Barium binding site 3 out
of 4 in 6kaj
Go back to
Barium Binding Sites List in 6kaj
Barium binding site 3 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 3 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ba506
b:0.5
occ:1.00
|
OD2
|
C:ASP364
|
2.7
|
55.4
|
1.0
|
O2A
|
C:CDP504
|
2.7
|
65.0
|
1.0
|
OD1
|
C:ASP362
|
2.7
|
54.2
|
1.0
|
OD2
|
C:ASP360
|
2.8
|
56.5
|
1.0
|
O
|
C:HOH602
|
2.8
|
65.7
|
1.0
|
O3B
|
C:CDP504
|
3.2
|
66.1
|
1.0
|
O
|
C:ASP362
|
3.3
|
45.4
|
1.0
|
CG
|
C:ASP360
|
3.4
|
50.9
|
1.0
|
OD1
|
C:ASP360
|
3.5
|
53.3
|
1.0
|
PA
|
C:CDP504
|
3.9
|
61.4
|
1.0
|
CG
|
C:ASP364
|
3.9
|
53.5
|
1.0
|
CA
|
C:GLY345
|
3.9
|
47.6
|
1.0
|
O5'
|
C:CDP504
|
4.0
|
61.7
|
1.0
|
C
|
C:ASP362
|
4.0
|
46.7
|
1.0
|
CG
|
C:ASP362
|
4.0
|
53.8
|
1.0
|
N
|
C:GLY345
|
4.0
|
51.3
|
1.0
|
O
|
C:HOH647
|
4.4
|
36.6
|
1.0
|
N
|
C:SER346
|
4.4
|
46.5
|
1.0
|
C
|
C:GLY345
|
4.4
|
45.5
|
1.0
|
PB
|
C:CDP504
|
4.5
|
66.0
|
1.0
|
OG
|
C:SER346
|
4.5
|
48.4
|
1.0
|
N
|
C:VAL363
|
4.6
|
48.5
|
1.0
|
O3A
|
C:CDP504
|
4.6
|
64.1
|
1.0
|
N
|
C:ASP362
|
4.6
|
40.5
|
1.0
|
N
|
C:ASP364
|
4.6
|
47.0
|
1.0
|
CA
|
C:VAL363
|
4.7
|
47.1
|
1.0
|
O
|
C:HOH657
|
4.7
|
36.2
|
1.0
|
OD2
|
C:ASP362
|
4.7
|
58.5
|
1.0
|
CA
|
C:ASP362
|
4.7
|
43.8
|
1.0
|
OD1
|
C:ASP364
|
4.7
|
54.7
|
1.0
|
CB
|
C:ASP364
|
4.8
|
51.9
|
1.0
|
CB
|
C:ASP360
|
4.8
|
42.3
|
1.0
|
C5'
|
C:CDP504
|
4.9
|
54.0
|
1.0
|
C4'
|
C:CDP504
|
4.9
|
53.7
|
1.0
|
C
|
C:VAL363
|
4.9
|
47.0
|
1.0
|
CB
|
C:ASP362
|
5.0
|
47.8
|
1.0
|
|
Barium binding site 4 out
of 4 in 6kaj
Go back to
Barium Binding Sites List in 6kaj
Barium binding site 4 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion
Mono view
Stereo pair view
|
A full contact list of Barium with other atoms in the Ba binding
site number 4 of Crystal Structure of Fkrp in Complex with Ba Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ba506
b:0.8
occ:1.00
|
O2A
|
D:CDP504
|
2.6
|
43.7
|
1.0
|
OD1
|
D:ASP362
|
2.6
|
0.0
|
1.0
|
OD1
|
D:ASP360
|
2.7
|
57.9
|
1.0
|
O1B
|
D:CDP504
|
2.8
|
47.1
|
1.0
|
OD2
|
D:ASP360
|
2.9
|
47.5
|
1.0
|
CG
|
D:ASP360
|
3.1
|
51.1
|
1.0
|
OD2
|
D:ASP364
|
3.4
|
51.5
|
1.0
|
CG
|
D:ASP362
|
3.4
|
0.7
|
1.0
|
PA
|
D:CDP504
|
3.5
|
45.5
|
1.0
|
O5'
|
D:CDP504
|
3.6
|
47.7
|
1.0
|
OD2
|
D:ASP362
|
3.7
|
0.2
|
1.0
|
PB
|
D:CDP504
|
3.8
|
50.0
|
1.0
|
O3A
|
D:CDP504
|
3.9
|
51.0
|
1.0
|
O
|
D:ASP362
|
4.3
|
52.5
|
1.0
|
O3B
|
D:CDP504
|
4.4
|
57.1
|
1.0
|
C4'
|
D:CDP504
|
4.4
|
42.9
|
1.0
|
N
|
D:ASP362
|
4.5
|
58.7
|
1.0
|
C5'
|
D:CDP504
|
4.5
|
43.7
|
1.0
|
CB
|
D:ASP362
|
4.5
|
0.8
|
1.0
|
CG
|
D:ASP364
|
4.6
|
51.1
|
1.0
|
CA
|
D:GLY345
|
4.6
|
39.4
|
1.0
|
CB
|
D:ASP360
|
4.6
|
43.7
|
1.0
|
C
|
D:ASP362
|
4.6
|
63.2
|
1.0
|
N
|
D:GLY345
|
4.7
|
41.7
|
1.0
|
CA
|
D:ASP362
|
4.8
|
75.0
|
1.0
|
O3'
|
D:CDP504
|
4.8
|
41.5
|
1.0
|
O1A
|
D:CDP504
|
4.8
|
49.3
|
1.0
|
C3'
|
D:CDP504
|
4.9
|
43.9
|
1.0
|
N
|
D:TYR361
|
4.9
|
38.8
|
1.0
|
|
Reference:
N.Kuwabara,
R.Imae,
H.Manya,
T.Tanaka,
M.Mizuno,
H.Tsumoto,
M.Kanagawa,
K.Kobayashi,
T.Toda,
T.Senda,
T.Endo,
R.Kato.
Crystal Structures of Fukutin-Related Protein (Fkrp), A Ribitol-Phosphate Transferase Related to Muscular Dystrophy. Nat Commun V. 11 303 2020.
ISSN: ESSN 2041-1723
PubMed: 31949166
DOI: 10.1038/S41467-019-14220-Z
Page generated: Wed Jul 10 15:55:21 2024
|