Zinc in PDB 5d7n: Crystal Structure of Human SIRT3 at An Improved Resolution
Protein crystallography data
The structure of Crystal Structure of Human SIRT3 at An Improved Resolution, PDB code: 5d7n
was solved by
T.Rumpf,
S.Gerhardt,
O.Einsle,
M.Jung,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.66 /
1.83
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.990,
143.850,
89.460,
90.00,
116.33,
90.00
|
R / Rfree (%)
|
17.5 /
20.3
|
Other elements in 5d7n:
The structure of Crystal Structure of Human SIRT3 at An Improved Resolution also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Human SIRT3 at An Improved Resolution
(pdb code 5d7n). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of Human SIRT3 at An Improved Resolution, PDB code: 5d7n:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5d7n
Go back to
Zinc Binding Sites List in 5d7n
Zinc binding site 1 out
of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution
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 Human SIRT3 at An Improved Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:21.9
occ:1.00
|
SG
|
A:CYS280
|
2.3
|
22.8
|
1.0
|
SG
|
A:CYS259
|
2.3
|
24.9
|
1.0
|
SG
|
A:CYS256
|
2.3
|
20.1
|
1.0
|
SG
|
A:CYS283
|
2.3
|
22.6
|
1.0
|
CB
|
A:CYS280
|
3.0
|
22.0
|
1.0
|
CB
|
A:CYS256
|
3.2
|
19.6
|
1.0
|
CB
|
A:CYS259
|
3.3
|
25.6
|
1.0
|
CB
|
A:CYS283
|
3.4
|
23.7
|
1.0
|
N
|
A:CYS259
|
3.7
|
24.3
|
1.0
|
N
|
A:CYS283
|
3.8
|
25.0
|
1.0
|
CA
|
A:CYS259
|
4.0
|
25.6
|
1.0
|
CA
|
A:CYS283
|
4.2
|
23.7
|
1.0
|
CA
|
A:CYS280
|
4.5
|
22.1
|
1.0
|
N
|
A:GLY285
|
4.6
|
20.5
|
1.0
|
CA
|
A:CYS256
|
4.6
|
18.8
|
1.0
|
C
|
A:CYS283
|
4.7
|
22.4
|
1.0
|
CB
|
A:VAL282
|
4.7
|
27.4
|
1.0
|
CB
|
A:VAL258
|
4.7
|
21.1
|
1.0
|
C
|
A:CYS259
|
4.7
|
26.0
|
1.0
|
N
|
A:THR284
|
4.8
|
22.9
|
1.0
|
C
|
A:VAL258
|
4.8
|
23.4
|
1.0
|
C
|
A:VAL282
|
4.9
|
26.6
|
1.0
|
N
|
A:GLN260
|
4.9
|
26.2
|
1.0
|
NH1
|
A:ARG261
|
5.0
|
32.9
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5d7n
Go back to
Zinc Binding Sites List in 5d7n
Zinc binding site 2 out
of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution
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 Human SIRT3 at An Improved Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:13.5
occ:1.00
|
SG
|
B:CYS283
|
2.3
|
14.3
|
1.0
|
SG
|
B:CYS259
|
2.3
|
14.0
|
1.0
|
SG
|
B:CYS280
|
2.3
|
13.3
|
1.0
|
SG
|
B:CYS256
|
2.4
|
12.7
|
1.0
|
CB
|
B:CYS280
|
3.1
|
13.7
|
1.0
|
CB
|
B:CYS256
|
3.2
|
12.7
|
1.0
|
CB
|
B:CYS259
|
3.3
|
14.5
|
1.0
|
CB
|
B:CYS283
|
3.5
|
14.3
|
1.0
|
N
|
B:CYS259
|
3.7
|
14.4
|
1.0
|
N
|
B:CYS283
|
3.9
|
14.6
|
1.0
|
CA
|
B:CYS259
|
4.1
|
14.7
|
1.0
|
CA
|
B:CYS283
|
4.2
|
14.5
|
1.0
|
CA
|
B:CYS280
|
4.5
|
13.9
|
1.0
|
CA
|
B:CYS256
|
4.6
|
12.4
|
1.0
|
N
|
B:GLY285
|
4.6
|
13.1
|
1.0
|
CB
|
B:VAL258
|
4.7
|
14.0
|
1.0
|
N
|
B:THR284
|
4.7
|
13.9
|
1.0
|
C
|
B:CYS283
|
4.7
|
14.2
|
1.0
|
NH1
|
B:ARG261
|
4.8
|
16.6
|
1.0
|
CB
|
B:VAL282
|
4.8
|
15.2
|
1.0
|
C
|
B:CYS259
|
4.8
|
15.2
|
1.0
|
C
|
B:VAL258
|
4.8
|
14.5
|
1.0
|
N
|
B:GLN260
|
5.0
|
15.6
|
1.0
|
C
|
B:VAL282
|
5.0
|
15.3
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5d7n
Go back to
Zinc Binding Sites List in 5d7n
Zinc binding site 3 out
of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution
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 Human SIRT3 at An Improved Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn401
b:22.7
occ:1.00
|
SG
|
C:CYS280
|
2.3
|
25.8
|
1.0
|
SG
|
C:CYS256
|
2.3
|
20.2
|
1.0
|
SG
|
C:CYS283
|
2.3
|
25.3
|
1.0
|
SG
|
C:CYS259
|
2.3
|
24.1
|
1.0
|
CB
|
C:CYS280
|
3.0
|
24.4
|
1.0
|
CB
|
C:CYS256
|
3.1
|
19.1
|
1.0
|
CB
|
C:CYS259
|
3.3
|
23.7
|
1.0
|
CB
|
C:CYS283
|
3.5
|
26.3
|
1.0
|
N
|
C:CYS259
|
3.7
|
21.9
|
1.0
|
N
|
C:CYS283
|
3.9
|
27.9
|
1.0
|
CA
|
C:CYS259
|
4.1
|
23.2
|
1.0
|
CA
|
C:CYS283
|
4.2
|
27.0
|
1.0
|
CA
|
C:CYS280
|
4.5
|
24.8
|
1.0
|
CA
|
C:CYS256
|
4.6
|
18.1
|
1.0
|
N
|
C:GLY285
|
4.7
|
21.7
|
1.0
|
CB
|
C:VAL258
|
4.7
|
20.1
|
1.0
|
NH1
|
C:ARG261
|
4.7
|
32.9
|
1.0
|
C
|
C:CYS283
|
4.8
|
25.9
|
1.0
|
N
|
C:THR284
|
4.8
|
25.8
|
1.0
|
C
|
C:CYS259
|
4.8
|
23.5
|
1.0
|
CB
|
C:VAL282
|
4.8
|
31.6
|
1.0
|
C
|
C:VAL258
|
4.9
|
21.2
|
1.0
|
N
|
C:GLN260
|
5.0
|
23.9
|
1.0
|
C
|
C:VAL282
|
5.0
|
29.5
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5d7n
Go back to
Zinc Binding Sites List in 5d7n
Zinc binding site 4 out
of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution
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 Human SIRT3 at An Improved Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn401
b:23.3
occ:1.00
|
SG
|
D:CYS280
|
2.3
|
25.0
|
1.0
|
SG
|
D:CYS259
|
2.3
|
24.7
|
1.0
|
SG
|
D:CYS256
|
2.3
|
20.1
|
1.0
|
SG
|
D:CYS283
|
2.3
|
23.2
|
1.0
|
CB
|
D:CYS280
|
3.0
|
24.5
|
1.0
|
CB
|
D:CYS256
|
3.2
|
19.7
|
1.0
|
CB
|
D:CYS259
|
3.3
|
24.8
|
1.0
|
CB
|
D:CYS283
|
3.5
|
24.8
|
1.0
|
N
|
D:CYS259
|
3.7
|
24.2
|
1.0
|
N
|
D:CYS283
|
3.9
|
26.4
|
1.0
|
CA
|
D:CYS259
|
4.1
|
24.7
|
1.0
|
CA
|
D:CYS283
|
4.2
|
25.1
|
1.0
|
CA
|
D:CYS280
|
4.5
|
24.6
|
1.0
|
CA
|
D:CYS256
|
4.6
|
18.7
|
1.0
|
N
|
D:GLY285
|
4.7
|
20.4
|
1.0
|
NH1
|
D:ARG261
|
4.7
|
34.1
|
1.0
|
C
|
D:CYS283
|
4.8
|
24.0
|
1.0
|
CB
|
D:VAL258
|
4.8
|
22.9
|
1.0
|
C
|
D:CYS259
|
4.8
|
25.0
|
1.0
|
N
|
D:THR284
|
4.8
|
23.2
|
1.0
|
CB
|
D:VAL282
|
4.8
|
30.6
|
1.0
|
C
|
D:VAL258
|
4.9
|
23.6
|
1.0
|
N
|
D:GLN260
|
5.0
|
24.5
|
1.0
|
CB
|
D:ARG261
|
5.0
|
27.9
|
1.0
|
C
|
D:VAL282
|
5.0
|
28.6
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5d7n
Go back to
Zinc Binding Sites List in 5d7n
Zinc binding site 5 out
of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Human SIRT3 at An Improved Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn401
b:18.1
occ:1.00
|
SG
|
E:CYS283
|
2.3
|
18.6
|
1.0
|
SG
|
E:CYS259
|
2.3
|
19.3
|
1.0
|
SG
|
E:CYS280
|
2.3
|
18.7
|
1.0
|
SG
|
E:CYS256
|
2.3
|
16.6
|
1.0
|
CB
|
E:CYS280
|
3.1
|
18.2
|
1.0
|
CB
|
E:CYS256
|
3.2
|
16.5
|
1.0
|
CB
|
E:CYS259
|
3.3
|
19.4
|
1.0
|
CB
|
E:CYS283
|
3.5
|
19.1
|
1.0
|
N
|
E:CYS259
|
3.7
|
18.6
|
1.0
|
N
|
E:CYS283
|
3.8
|
20.3
|
1.0
|
CA
|
E:CYS259
|
4.1
|
19.5
|
1.0
|
CA
|
E:CYS283
|
4.2
|
19.7
|
1.0
|
CA
|
E:CYS280
|
4.5
|
18.5
|
1.0
|
N
|
E:GLY285
|
4.6
|
17.4
|
1.0
|
CA
|
E:CYS256
|
4.7
|
16.1
|
1.0
|
CB
|
E:VAL282
|
4.7
|
23.7
|
1.0
|
N
|
E:THR284
|
4.8
|
18.7
|
1.0
|
C
|
E:CYS283
|
4.8
|
18.9
|
1.0
|
C
|
E:CYS259
|
4.8
|
20.2
|
1.0
|
CB
|
E:VAL258
|
4.8
|
17.8
|
1.0
|
C
|
E:VAL258
|
4.8
|
18.5
|
1.0
|
C
|
E:VAL282
|
4.9
|
21.9
|
1.0
|
NH1
|
E:ARG261
|
4.9
|
28.4
|
1.0
|
N
|
E:GLN260
|
5.0
|
20.3
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5d7n
Go back to
Zinc Binding Sites List in 5d7n
Zinc binding site 6 out
of 6 in the Crystal Structure of Human SIRT3 at An Improved Resolution
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Human SIRT3 at An Improved Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn401
b:20.8
occ:1.00
|
SG
|
F:CYS283
|
2.3
|
22.5
|
1.0
|
SG
|
F:CYS259
|
2.3
|
20.4
|
1.0
|
SG
|
F:CYS280
|
2.3
|
22.5
|
1.0
|
SG
|
F:CYS256
|
2.4
|
19.2
|
1.0
|
CB
|
F:CYS280
|
3.1
|
22.0
|
1.0
|
CB
|
F:CYS256
|
3.2
|
18.7
|
1.0
|
CB
|
F:CYS259
|
3.3
|
21.3
|
1.0
|
CB
|
F:CYS283
|
3.4
|
22.6
|
1.0
|
N
|
F:CYS259
|
3.7
|
21.3
|
1.0
|
N
|
F:CYS283
|
3.8
|
24.3
|
1.0
|
CA
|
F:CYS259
|
4.1
|
21.1
|
1.0
|
CA
|
F:CYS283
|
4.2
|
23.1
|
1.0
|
CB
|
F:VAL282
|
4.5
|
27.5
|
1.0
|
CA
|
F:CYS280
|
4.5
|
22.1
|
1.0
|
CA
|
F:CYS256
|
4.6
|
17.7
|
1.0
|
N
|
F:GLY285
|
4.7
|
20.3
|
1.0
|
C
|
F:CYS259
|
4.7
|
21.0
|
1.0
|
CB
|
F:VAL258
|
4.8
|
20.7
|
1.0
|
C
|
F:CYS283
|
4.8
|
22.6
|
1.0
|
N
|
F:THR284
|
4.8
|
22.0
|
1.0
|
C
|
F:VAL282
|
4.9
|
25.8
|
1.0
|
C
|
F:VAL258
|
4.9
|
21.3
|
1.0
|
CB
|
F:ARG261
|
4.9
|
22.9
|
1.0
|
N
|
F:GLN260
|
4.9
|
20.4
|
1.0
|
|
Reference:
T.Rumpf,
S.Gerhardt,
O.Einsle,
M.Jung.
Seeding For Sirtuins: Microseed Matrix Seeding to Obtain Crystals of Human SIRT3 and SIRT2 Suitable For Soaking. Acta Crystallogr.,Sect.F V. 71 1498 2015.
ISSN: ESSN 2053-230X
PubMed: 26625292
DOI: 10.1107/S2053230X15019986
Page generated: Sun Oct 27 14:39:28 2024
|