Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Fkrp in Complex with Ba Ion, PDB code: 6kaj:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6kaj
Go back to
Zinc Binding Sites List in 6kaj
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:45.3
occ:1.00
|
SG
|
A:CYS317
|
2.3
|
41.6
|
1.0
|
SG
|
A:CYS318
|
2.3
|
36.6
|
1.0
|
SG
|
A:CYS296
|
2.3
|
44.2
|
1.0
|
SG
|
A:CYS289
|
2.4
|
39.2
|
1.0
|
N
|
A:CYS318
|
3.0
|
41.0
|
1.0
|
CB
|
A:CYS289
|
3.3
|
41.8
|
1.0
|
CB
|
A:CYS296
|
3.4
|
36.4
|
1.0
|
CB
|
A:CYS317
|
3.4
|
44.9
|
1.0
|
CB
|
A:CYS318
|
3.4
|
37.7
|
1.0
|
CA
|
A:CYS318
|
3.5
|
39.8
|
1.0
|
C
|
A:CYS317
|
3.6
|
45.2
|
1.0
|
N
|
A:CYS289
|
3.7
|
48.7
|
1.0
|
N
|
A:CYS296
|
3.8
|
43.0
|
1.0
|
CB
|
A:PRO315
|
3.9
|
37.1
|
1.0
|
CA
|
A:CYS317
|
4.0
|
47.9
|
1.0
|
CA
|
A:CYS289
|
4.1
|
48.2
|
1.0
|
CA
|
A:CYS296
|
4.2
|
40.4
|
1.0
|
O
|
A:CYS317
|
4.3
|
47.2
|
1.0
|
N
|
A:CYS317
|
4.5
|
43.7
|
1.0
|
CG
|
A:PRO315
|
4.6
|
37.1
|
1.0
|
C
|
A:GLY288
|
4.8
|
48.8
|
1.0
|
C
|
A:ARG295
|
4.9
|
45.9
|
1.0
|
C
|
A:CYS289
|
4.9
|
45.5
|
1.0
|
O
|
A:PRO315
|
4.9
|
44.3
|
1.0
|
CA
|
A:GLY288
|
5.0
|
41.8
|
1.0
|
O
|
A:CYS289
|
5.0
|
46.4
|
1.0
|
CD1
|
A:LEU413
|
5.0
|
42.1
|
1.0
|
C
|
A:CYS318
|
5.0
|
39.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6kaj
Go back to
Zinc Binding Sites List in 6kaj
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:43.0
occ:1.00
|
SG
|
B:CYS289
|
2.3
|
53.4
|
1.0
|
SG
|
B:CYS317
|
2.3
|
42.1
|
1.0
|
SG
|
B:CYS318
|
2.3
|
38.9
|
1.0
|
SG
|
B:CYS296
|
2.4
|
44.8
|
1.0
|
N
|
B:CYS318
|
3.1
|
36.9
|
1.0
|
CB
|
B:CYS289
|
3.2
|
48.2
|
1.0
|
CB
|
B:CYS296
|
3.4
|
43.4
|
1.0
|
CB
|
B:CYS318
|
3.5
|
36.5
|
1.0
|
N
|
B:CYS289
|
3.5
|
49.8
|
1.0
|
CB
|
B:CYS317
|
3.5
|
42.8
|
1.0
|
CA
|
B:CYS318
|
3.5
|
36.1
|
1.0
|
C
|
B:CYS317
|
3.7
|
37.3
|
1.0
|
CA
|
B:CYS289
|
3.8
|
47.7
|
1.0
|
N
|
B:CYS296
|
3.9
|
47.1
|
1.0
|
CB
|
B:PRO315
|
4.0
|
37.1
|
1.0
|
CA
|
B:CYS317
|
4.1
|
38.9
|
1.0
|
CA
|
B:CYS296
|
4.2
|
46.1
|
1.0
|
O
|
B:CYS317
|
4.4
|
42.3
|
1.0
|
N
|
B:CYS317
|
4.5
|
40.7
|
1.0
|
C
|
B:GLY288
|
4.6
|
50.8
|
1.0
|
CG
|
B:PRO315
|
4.7
|
36.8
|
1.0
|
O
|
B:PRO315
|
4.7
|
45.5
|
1.0
|
CA
|
B:GLY288
|
4.8
|
46.3
|
1.0
|
C
|
B:ARG295
|
4.8
|
46.9
|
1.0
|
NE
|
B:ARG275
|
4.9
|
47.6
|
1.0
|
CA
|
B:ARG295
|
5.0
|
43.1
|
1.0
|
CD1
|
B:LEU413
|
5.0
|
41.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6kaj
Go back to
Zinc Binding Sites List in 6kaj
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:43.2
occ:1.00
|
SG
|
C:CYS317
|
2.3
|
38.3
|
1.0
|
SG
|
C:CYS318
|
2.3
|
38.9
|
1.0
|
SG
|
C:CYS296
|
2.3
|
45.0
|
1.0
|
SG
|
C:CYS289
|
2.3
|
41.7
|
1.0
|
N
|
C:CYS318
|
3.0
|
32.4
|
1.0
|
CB
|
C:CYS289
|
3.4
|
42.6
|
1.0
|
CB
|
C:CYS296
|
3.4
|
38.4
|
1.0
|
CB
|
C:CYS317
|
3.4
|
39.0
|
1.0
|
CB
|
C:CYS318
|
3.4
|
35.2
|
1.0
|
CA
|
C:CYS318
|
3.5
|
36.5
|
1.0
|
C
|
C:CYS317
|
3.6
|
35.7
|
1.0
|
N
|
C:CYS289
|
3.7
|
44.4
|
1.0
|
N
|
C:CYS296
|
3.8
|
42.6
|
1.0
|
CB
|
C:PRO315
|
4.0
|
38.5
|
1.0
|
CA
|
C:CYS317
|
4.0
|
38.6
|
1.0
|
CA
|
C:CYS289
|
4.1
|
44.4
|
1.0
|
CA
|
C:CYS296
|
4.2
|
40.7
|
1.0
|
O
|
C:CYS317
|
4.3
|
36.8
|
1.0
|
N
|
C:CYS317
|
4.5
|
38.1
|
1.0
|
C
|
C:GLY288
|
4.8
|
44.8
|
1.0
|
CG
|
C:PRO315
|
4.8
|
35.8
|
1.0
|
O
|
C:PRO315
|
4.9
|
41.0
|
1.0
|
C
|
C:ARG295
|
4.9
|
44.4
|
1.0
|
C
|
C:CYS289
|
4.9
|
44.1
|
1.0
|
NE
|
C:ARG275
|
4.9
|
40.6
|
1.0
|
CA
|
C:GLY288
|
5.0
|
41.1
|
1.0
|
CD1
|
C:LEU413
|
5.0
|
37.0
|
1.0
|
C
|
C:CYS318
|
5.0
|
43.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6kaj
Go back to
Zinc Binding Sites List in 6kaj
Zinc 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 Zinc with other atoms in the Zn 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:Zn501
b:37.3
occ:1.00
|
SG
|
D:CYS317
|
2.3
|
37.9
|
1.0
|
SG
|
D:CYS318
|
2.3
|
40.2
|
1.0
|
SG
|
D:CYS289
|
2.3
|
39.8
|
1.0
|
SG
|
D:CYS296
|
2.4
|
40.0
|
1.0
|
N
|
D:CYS318
|
3.0
|
29.2
|
1.0
|
CB
|
D:CYS289
|
3.3
|
38.7
|
1.0
|
CB
|
D:CYS296
|
3.4
|
37.9
|
1.0
|
CB
|
D:CYS318
|
3.4
|
35.7
|
1.0
|
CB
|
D:CYS317
|
3.4
|
36.6
|
1.0
|
CA
|
D:CYS318
|
3.5
|
34.3
|
1.0
|
C
|
D:CYS317
|
3.6
|
35.5
|
1.0
|
N
|
D:CYS289
|
3.7
|
35.2
|
1.0
|
N
|
D:CYS296
|
3.8
|
50.3
|
1.0
|
CA
|
D:CYS317
|
4.0
|
34.7
|
1.0
|
CB
|
D:PRO315
|
4.1
|
38.3
|
1.0
|
CA
|
D:CYS289
|
4.1
|
38.2
|
1.0
|
CA
|
D:CYS296
|
4.2
|
47.3
|
1.0
|
O
|
D:CYS317
|
4.3
|
35.5
|
1.0
|
N
|
D:CYS317
|
4.5
|
36.8
|
1.0
|
C
|
D:ARG295
|
4.8
|
49.1
|
1.0
|
CG
|
D:PRO315
|
4.8
|
39.2
|
1.0
|
O
|
D:PRO315
|
4.8
|
40.5
|
1.0
|
C
|
D:GLY288
|
4.8
|
33.7
|
1.0
|
C
|
D:CYS289
|
4.9
|
41.1
|
1.0
|
O
|
D:CYS289
|
4.9
|
37.1
|
1.0
|
CA
|
D:ARG295
|
4.9
|
45.0
|
1.0
|
C
|
D:CYS318
|
5.0
|
37.6
|
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: Tue Oct 29 01:33:03 2024
|