Barium in PDB 6kam: Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor
Protein crystallography data
The structure of Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor, PDB code: 6kam
was solved by
N.Kuwabara,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.69 /
2.46
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
78.571,
119.240,
254.646,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.8 /
24.9
|
Other elements in 6kam:
The structure of Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor 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, Cdp-Ribtol, and Sugar Acceptor
(pdb code 6kam). 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, Cdp-Ribtol, and Sugar Acceptor, PDB code: 6kam:
Jump to Barium binding site number:
1;
2;
3;
4;
Barium binding site 1 out
of 4 in 6kam
Go back to
Barium Binding Sites List in 6kam
Barium binding site 1 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor
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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ba506
b:0.2
occ:1.00
|
O2A
|
A:CDP504
|
2.6
|
91.4
|
1.0
|
OD1
|
A:ASP362
|
2.6
|
69.0
|
1.0
|
O3B
|
A:CDP504
|
2.7
|
95.1
|
1.0
|
OD1
|
A:ASP360
|
2.9
|
69.7
|
1.0
|
PA
|
A:CDP504
|
3.2
|
91.5
|
1.0
|
OD2
|
A:ASP364
|
3.3
|
76.7
|
1.0
|
OD2
|
A:ASP360
|
3.3
|
71.2
|
1.0
|
O5'
|
A:CDP504
|
3.4
|
87.6
|
1.0
|
O3A
|
A:CDP504
|
3.4
|
94.5
|
1.0
|
CG
|
A:ASP360
|
3.5
|
68.0
|
1.0
|
PB
|
A:CDP504
|
3.6
|
95.9
|
1.0
|
CG
|
A:ASP362
|
3.8
|
66.0
|
1.0
|
O
|
A:ASP362
|
4.1
|
60.5
|
1.0
|
C5'
|
A:CDP504
|
4.3
|
84.4
|
1.0
|
OD2
|
A:ASP362
|
4.4
|
67.4
|
1.0
|
C4'
|
A:CDP504
|
4.4
|
82.0
|
1.0
|
CG
|
A:ASP364
|
4.5
|
74.5
|
1.0
|
O1B
|
A:CDP504
|
4.5
|
96.9
|
1.0
|
N
|
A:ASP362
|
4.6
|
63.5
|
1.0
|
C
|
A:ASP362
|
4.6
|
59.4
|
1.0
|
CA
|
A:GLY345
|
4.6
|
60.0
|
1.0
|
N
|
A:GLY345
|
4.6
|
63.5
|
1.0
|
O1A
|
A:CDP504
|
4.7
|
97.2
|
1.0
|
O3'
|
A:CDP504
|
4.7
|
80.3
|
1.0
|
CZ
|
A:TYR361
|
4.8
|
82.2
|
1.0
|
O2B
|
A:CDP504
|
4.8
|
98.8
|
1.0
|
CB
|
A:ASP362
|
4.8
|
63.1
|
1.0
|
CE2
|
A:TYR361
|
4.9
|
79.5
|
1.0
|
C3'
|
A:CDP504
|
4.9
|
81.1
|
1.0
|
CA
|
A:ASP362
|
4.9
|
61.4
|
1.0
|
CB
|
A:ASP360
|
4.9
|
63.5
|
1.0
|
|
Barium binding site 2 out
of 4 in 6kam
Go back to
Barium Binding Sites List in 6kam
Barium binding site 2 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor
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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ba505
b:0.8
occ:1.00
|
O2A
|
B:CDP503
|
2.5
|
56.6
|
1.0
|
OD1
|
B:ASP362
|
2.5
|
53.1
|
1.0
|
OD2
|
B:ASP364
|
2.6
|
65.6
|
1.0
|
O1B
|
B:CDP503
|
2.8
|
64.6
|
1.0
|
OD2
|
B:ASP360
|
3.3
|
65.8
|
1.0
|
OD1
|
B:ASP360
|
3.4
|
64.9
|
1.0
|
O
|
B:ASP362
|
3.4
|
51.5
|
1.0
|
CG
|
B:ASP360
|
3.7
|
63.5
|
1.0
|
CG
|
B:ASP362
|
3.7
|
54.6
|
1.0
|
PA
|
B:CDP503
|
3.8
|
59.3
|
1.0
|
CG
|
B:ASP364
|
3.8
|
63.8
|
1.0
|
C
|
B:ASP362
|
4.0
|
52.5
|
1.0
|
PB
|
B:CDP503
|
4.0
|
68.1
|
1.0
|
O3A
|
B:CDP503
|
4.2
|
64.0
|
1.0
|
N
|
B:GLY345
|
4.2
|
46.0
|
1.0
|
O5'
|
B:CDP503
|
4.3
|
59.4
|
1.0
|
CA
|
B:GLY345
|
4.4
|
42.0
|
1.0
|
OD1
|
B:ASP364
|
4.4
|
66.5
|
1.0
|
OD2
|
B:ASP362
|
4.4
|
57.5
|
1.0
|
N
|
B:ASP362
|
4.5
|
57.2
|
1.0
|
CA
|
B:ASP362
|
4.6
|
55.9
|
1.0
|
N
|
B:VAL363
|
4.7
|
52.2
|
1.0
|
CB
|
B:ASP362
|
4.8
|
55.5
|
1.0
|
N
|
B:SER346
|
4.8
|
44.1
|
1.0
|
CB
|
B:ASP364
|
4.8
|
60.3
|
1.0
|
N
|
B:ASP364
|
4.8
|
54.2
|
1.0
|
C
|
B:GLY345
|
4.9
|
42.2
|
1.0
|
CA
|
B:VAL363
|
4.9
|
52.4
|
1.0
|
OG
|
B:SER346
|
4.9
|
53.1
|
1.0
|
C4'
|
B:CDP503
|
4.9
|
55.7
|
1.0
|
O3B
|
B:CDP503
|
4.9
|
66.7
|
1.0
|
O2B
|
B:CDP503
|
5.0
|
77.2
|
1.0
|
O1A
|
B:CDP503
|
5.0
|
59.7
|
1.0
|
C
|
B:VAL363
|
5.0
|
54.1
|
1.0
|
|
Barium binding site 3 out
of 4 in 6kam
Go back to
Barium Binding Sites List in 6kam
Barium binding site 3 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor
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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ba506
b:0.7
occ:1.00
|
OD1
|
C:ASP362
|
2.6
|
73.8
|
1.0
|
OD2
|
C:ASP364
|
2.6
|
72.0
|
1.0
|
O3B
|
C:CDP504
|
2.7
|
97.4
|
1.0
|
O2A
|
C:CDP504
|
2.7
|
98.7
|
1.0
|
OD2
|
C:ASP360
|
3.2
|
61.5
|
1.0
|
PA
|
C:CDP504
|
3.4
|
94.2
|
1.0
|
O5'
|
C:CDP504
|
3.4
|
88.3
|
1.0
|
OD1
|
C:ASP360
|
3.5
|
58.7
|
1.0
|
O3A
|
C:CDP504
|
3.7
|
98.3
|
1.0
|
PB
|
C:CDP504
|
3.7
|
99.3
|
1.0
|
CG
|
C:ASP360
|
3.8
|
58.7
|
1.0
|
O
|
C:ASP362
|
3.8
|
62.0
|
1.0
|
CG
|
C:ASP362
|
3.8
|
71.9
|
1.0
|
CG
|
C:ASP364
|
3.9
|
71.1
|
1.0
|
N
|
C:GLY345
|
4.3
|
65.2
|
1.0
|
C
|
C:ASP362
|
4.3
|
61.9
|
1.0
|
OD2
|
C:ASP362
|
4.4
|
75.9
|
1.0
|
C5'
|
C:CDP504
|
4.6
|
81.9
|
1.0
|
CA
|
C:GLY345
|
4.6
|
63.5
|
1.0
|
O2B
|
C:CDP504
|
4.7
|
100.0
|
1.0
|
OD1
|
C:ASP364
|
4.7
|
73.5
|
1.0
|
CB
|
C:ASP364
|
4.7
|
69.6
|
1.0
|
N
|
C:ASP362
|
4.8
|
61.3
|
1.0
|
C5
|
C:RB0505
|
4.8
|
99.4
|
1.0
|
O1A
|
C:CDP504
|
4.8
|
95.6
|
1.0
|
O1B
|
C:CDP504
|
4.8
|
99.8
|
1.0
|
C4'
|
C:CDP504
|
4.9
|
78.0
|
1.0
|
CA
|
C:ASP362
|
4.9
|
62.8
|
1.0
|
CB
|
C:ASP362
|
5.0
|
67.2
|
1.0
|
N
|
C:ASP364
|
5.0
|
66.2
|
1.0
|
N
|
C:VAL363
|
5.0
|
61.4
|
1.0
|
|
Barium binding site 4 out
of 4 in 6kam
Go back to
Barium Binding Sites List in 6kam
Barium binding site 4 out
of 4 in the Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor
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, Cdp-Ribtol, and Sugar Acceptor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ba506
b:0.5
occ:1.00
|
OD1
|
D:ASP362
|
2.6
|
82.2
|
1.0
|
OD2
|
D:ASP364
|
2.6
|
69.5
|
1.0
|
O1B
|
D:CDP504
|
2.7
|
77.5
|
1.0
|
O2A
|
D:CDP504
|
2.7
|
64.4
|
1.0
|
OD2
|
D:ASP360
|
3.0
|
67.0
|
1.0
|
OD1
|
D:ASP360
|
3.5
|
68.6
|
1.0
|
CG
|
D:ASP360
|
3.6
|
66.4
|
1.0
|
O
|
D:ASP362
|
3.6
|
66.7
|
1.0
|
CG
|
D:ASP362
|
3.8
|
79.5
|
1.0
|
PA
|
D:CDP504
|
3.8
|
68.2
|
1.0
|
CG
|
D:ASP364
|
3.9
|
69.7
|
1.0
|
O5'
|
D:CDP504
|
3.9
|
67.1
|
1.0
|
PB
|
D:CDP504
|
4.0
|
77.4
|
1.0
|
N
|
D:GLY345
|
4.1
|
57.1
|
1.0
|
CA
|
D:GLY345
|
4.1
|
53.3
|
1.0
|
C
|
D:ASP362
|
4.2
|
67.4
|
1.0
|
O3A
|
D:CDP504
|
4.2
|
76.3
|
1.0
|
OD2
|
D:ASP362
|
4.4
|
83.2
|
1.0
|
N
|
D:SER346
|
4.5
|
52.1
|
1.0
|
C
|
D:GLY345
|
4.6
|
52.2
|
1.0
|
OD1
|
D:ASP364
|
4.7
|
72.8
|
1.0
|
O2B
|
D:CDP504
|
4.7
|
82.3
|
1.0
|
N
|
D:ASP362
|
4.7
|
68.7
|
1.0
|
O
|
D:HOH644
|
4.7
|
53.3
|
1.0
|
CB
|
D:ASP364
|
4.8
|
65.9
|
1.0
|
C5'
|
D:CDP504
|
4.8
|
63.4
|
1.0
|
CA
|
D:ASP362
|
4.8
|
70.2
|
1.0
|
N
|
D:VAL363
|
4.8
|
64.7
|
1.0
|
C4'
|
D:CDP504
|
4.8
|
60.4
|
1.0
|
CB
|
D:ASP362
|
4.9
|
74.5
|
1.0
|
OG
|
D:SER346
|
4.9
|
51.0
|
1.0
|
N
|
D:ASP364
|
4.9
|
62.3
|
1.0
|
O
|
D:HOH627
|
5.0
|
65.4
|
1.0
|
CA
|
D:VAL363
|
5.0
|
60.9
|
1.0
|
|
Reference:
K.Kobayashi,
M.Kanagawa,
H.Tsumoto,
R.Kato,
H.Manya,
T.Endo,
T.Senda,
T.Toda,
N.Kuwabara,
R.Imae,
T.Tanaka,
M.Mizuno.
Crystal Structures of Fukutin-Related Protein (Fkrp), A Ribitol-Phosphate Transferase Related to Muscular Dystrophy Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-019-14220-Z
Page generated: Wed Jul 10 15:55:24 2024
|