Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Fkrp in Complex with Ba Ion, Cdp-Ribtol, and Sugar Acceptor, PDB code: 6kam:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6kam
Go back to
Zinc Binding Sites List in 6kam
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:57.5
occ:1.00
|
SG
|
A:CYS317
|
2.3
|
50.3
|
1.0
|
SG
|
A:CYS318
|
2.3
|
53.7
|
1.0
|
SG
|
A:CYS296
|
2.4
|
60.2
|
1.0
|
SG
|
A:CYS289
|
2.4
|
56.8
|
1.0
|
N
|
A:CYS318
|
3.2
|
56.5
|
1.0
|
CB
|
A:CYS289
|
3.3
|
56.9
|
1.0
|
CB
|
A:CYS317
|
3.4
|
51.6
|
1.0
|
CB
|
A:CYS296
|
3.4
|
58.9
|
1.0
|
CB
|
A:CYS318
|
3.4
|
54.2
|
1.0
|
CA
|
A:CYS318
|
3.6
|
56.1
|
1.0
|
N
|
A:CYS289
|
3.6
|
56.5
|
1.0
|
C
|
A:CYS317
|
3.7
|
57.7
|
1.0
|
N
|
A:CYS296
|
3.8
|
58.5
|
1.0
|
CB
|
A:PRO315
|
4.0
|
53.3
|
1.0
|
CA
|
A:CYS289
|
4.1
|
57.4
|
1.0
|
CA
|
A:CYS317
|
4.1
|
56.2
|
1.0
|
CA
|
A:CYS296
|
4.2
|
58.3
|
1.0
|
O
|
A:CYS317
|
4.5
|
58.6
|
1.0
|
N
|
A:CYS317
|
4.5
|
54.6
|
1.0
|
CG
|
A:PRO315
|
4.7
|
53.5
|
1.0
|
C
|
A:GLY288
|
4.7
|
57.5
|
1.0
|
C
|
A:CYS289
|
4.9
|
58.9
|
1.0
|
C
|
A:ARG295
|
4.9
|
59.9
|
1.0
|
O
|
A:PRO315
|
4.9
|
55.7
|
1.0
|
CA
|
A:GLY288
|
4.9
|
57.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6kam
Go back to
Zinc Binding Sites List in 6kam
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:59.4
occ:1.00
|
SG
|
B:CYS289
|
2.3
|
71.8
|
1.0
|
SG
|
B:CYS318
|
2.3
|
57.0
|
1.0
|
SG
|
B:CYS317
|
2.3
|
58.1
|
1.0
|
SG
|
B:CYS296
|
2.4
|
64.1
|
1.0
|
N
|
B:CYS318
|
3.1
|
51.4
|
1.0
|
CB
|
B:CYS289
|
3.3
|
69.9
|
1.0
|
CB
|
B:CYS296
|
3.4
|
62.1
|
1.0
|
CB
|
B:CYS318
|
3.5
|
52.4
|
1.0
|
CB
|
B:CYS317
|
3.5
|
59.2
|
1.0
|
N
|
B:CYS289
|
3.5
|
69.8
|
1.0
|
CA
|
B:CYS318
|
3.5
|
52.0
|
1.0
|
C
|
B:CYS317
|
3.6
|
53.9
|
1.0
|
N
|
B:CYS296
|
3.9
|
66.9
|
1.0
|
CA
|
B:CYS289
|
4.0
|
69.9
|
1.0
|
CB
|
B:PRO315
|
4.0
|
53.1
|
1.0
|
CA
|
B:CYS317
|
4.1
|
57.1
|
1.0
|
CA
|
B:CYS296
|
4.2
|
64.4
|
1.0
|
O
|
B:CYS317
|
4.3
|
53.9
|
1.0
|
N
|
B:CYS317
|
4.5
|
57.6
|
1.0
|
C
|
B:GLY288
|
4.6
|
67.2
|
1.0
|
CG
|
B:PRO315
|
4.7
|
51.7
|
1.0
|
O
|
B:PRO315
|
4.8
|
53.0
|
1.0
|
CA
|
B:GLY288
|
4.8
|
64.3
|
1.0
|
CD1
|
B:LEU413
|
4.9
|
53.4
|
1.0
|
C
|
B:ARG295
|
4.9
|
70.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6kam
Go back to
Zinc Binding Sites List in 6kam
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:60.8
occ:1.00
|
SG
|
C:CYS317
|
2.3
|
55.6
|
1.0
|
SG
|
C:CYS318
|
2.3
|
53.2
|
1.0
|
SG
|
C:CYS296
|
2.4
|
71.1
|
1.0
|
SG
|
C:CYS289
|
2.4
|
59.1
|
1.0
|
N
|
C:CYS318
|
3.1
|
59.3
|
1.0
|
CB
|
C:CYS296
|
3.4
|
65.7
|
1.0
|
CB
|
C:CYS289
|
3.4
|
58.0
|
1.0
|
CB
|
C:CYS318
|
3.5
|
53.5
|
1.0
|
CB
|
C:CYS317
|
3.5
|
57.6
|
1.0
|
CA
|
C:CYS318
|
3.5
|
58.0
|
1.0
|
C
|
C:CYS317
|
3.6
|
59.6
|
1.0
|
N
|
C:CYS289
|
3.7
|
59.8
|
1.0
|
N
|
C:CYS296
|
3.9
|
64.8
|
1.0
|
CB
|
C:PRO315
|
4.1
|
55.5
|
1.0
|
CA
|
C:CYS317
|
4.1
|
58.6
|
1.0
|
CA
|
C:CYS289
|
4.1
|
60.0
|
1.0
|
CA
|
C:CYS296
|
4.2
|
65.5
|
1.0
|
O
|
C:CYS317
|
4.3
|
61.1
|
1.0
|
N
|
C:CYS317
|
4.6
|
55.8
|
1.0
|
CG
|
C:PRO315
|
4.8
|
55.5
|
1.0
|
C
|
C:GLY288
|
4.8
|
59.5
|
1.0
|
C
|
C:CYS289
|
4.9
|
62.9
|
1.0
|
CD1
|
C:LEU413
|
4.9
|
53.6
|
1.0
|
C
|
C:ARG295
|
4.9
|
65.4
|
1.0
|
NE
|
C:ARG275
|
4.9
|
57.1
|
1.0
|
CA
|
C:GLY288
|
5.0
|
58.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6kam
Go back to
Zinc Binding Sites List in 6kam
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:56.8
occ:1.00
|
SG
|
D:CYS289
|
2.3
|
56.6
|
1.0
|
SG
|
D:CYS317
|
2.3
|
50.5
|
1.0
|
SG
|
D:CYS318
|
2.3
|
52.0
|
1.0
|
SG
|
D:CYS296
|
2.4
|
56.1
|
1.0
|
N
|
D:CYS318
|
3.0
|
48.7
|
1.0
|
CB
|
D:CYS289
|
3.4
|
56.9
|
1.0
|
CB
|
D:CYS296
|
3.4
|
57.4
|
1.0
|
CB
|
D:CYS318
|
3.4
|
49.1
|
1.0
|
CB
|
D:CYS317
|
3.5
|
50.8
|
1.0
|
CA
|
D:CYS318
|
3.5
|
49.1
|
1.0
|
C
|
D:CYS317
|
3.6
|
51.1
|
1.0
|
N
|
D:CYS289
|
3.7
|
54.1
|
1.0
|
N
|
D:CYS296
|
3.9
|
64.3
|
1.0
|
CA
|
D:CYS317
|
4.0
|
50.8
|
1.0
|
CB
|
D:PRO315
|
4.1
|
47.9
|
1.0
|
CA
|
D:CYS289
|
4.1
|
58.1
|
1.0
|
CA
|
D:CYS296
|
4.2
|
62.2
|
1.0
|
O
|
D:CYS317
|
4.3
|
54.3
|
1.0
|
N
|
D:CYS317
|
4.4
|
51.5
|
1.0
|
CG
|
D:PRO315
|
4.7
|
47.2
|
1.0
|
C
|
D:GLY288
|
4.9
|
51.6
|
1.0
|
O
|
D:PRO315
|
4.9
|
50.2
|
1.0
|
C
|
D:ARG295
|
4.9
|
66.8
|
1.0
|
C
|
D:CYS289
|
4.9
|
60.3
|
1.0
|
CA
|
D:GLY288
|
5.0
|
49.3
|
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: Tue Oct 29 01:35:17 2024
|