Nickel in PDB 5wtq: Crystal Structure of Human Proteasome-Assembling Chaperone PAC4
Protein crystallography data
The structure of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4, PDB code: 5wtq
was solved by
E.Kurimoto,
T.Satoh,
Y.Ito,
E.Ishihara,
K.Tanaka,
K.Kato,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
1.90
|
Space group
|
F 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.548,
152.779,
212.911,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.4 /
25.4
|
Other elements in 5wtq:
The structure of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4
(pdb code 5wtq). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the
Crystal Structure of Human Proteasome-Assembling Chaperone PAC4, PDB code: 5wtq:
Jump to Nickel binding site number:
1;
2;
3;
4;
Nickel binding site 1 out
of 4 in 5wtq
Go back to
Nickel Binding Sites List in 5wtq
Nickel binding site 1 out
of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni201
b:28.4
occ:1.00
|
O
|
A:HOH339
|
1.9
|
28.4
|
1.0
|
NE2
|
A:HIS29
|
2.0
|
25.5
|
1.0
|
NE2
|
A:HIS27
|
2.1
|
34.5
|
1.0
|
NE2
|
A:HIS46
|
2.1
|
29.1
|
1.0
|
O
|
A:HOH353
|
2.2
|
32.2
|
1.0
|
O
|
A:HOH340
|
2.2
|
29.3
|
1.0
|
CD2
|
A:HIS29
|
3.0
|
26.1
|
1.0
|
CE1
|
A:HIS46
|
3.0
|
28.0
|
1.0
|
CD2
|
A:HIS27
|
3.1
|
32.0
|
1.0
|
CE1
|
A:HIS29
|
3.1
|
29.4
|
1.0
|
CE1
|
A:HIS27
|
3.2
|
34.1
|
1.0
|
CD2
|
A:HIS46
|
3.2
|
26.5
|
1.0
|
O
|
A:LEU68
|
4.1
|
36.7
|
1.0
|
CG
|
A:HIS29
|
4.2
|
24.0
|
1.0
|
ND1
|
A:HIS29
|
4.2
|
25.1
|
1.0
|
O
|
A:HOH367
|
4.2
|
34.0
|
1.0
|
ND1
|
A:HIS46
|
4.2
|
27.0
|
1.0
|
CG
|
A:HIS27
|
4.2
|
34.8
|
1.0
|
ND1
|
A:HIS27
|
4.2
|
33.5
|
1.0
|
CG
|
A:HIS46
|
4.3
|
28.0
|
1.0
|
O
|
A:HOH370
|
4.3
|
44.6
|
1.0
|
OG1
|
A:THR44
|
4.7
|
33.1
|
1.0
|
|
Nickel binding site 2 out
of 4 in 5wtq
Go back to
Nickel Binding Sites List in 5wtq
Nickel binding site 2 out
of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni201
b:28.7
occ:1.00
|
NE2
|
B:HIS29
|
2.0
|
27.7
|
1.0
|
NE2
|
B:HIS27
|
2.1
|
31.4
|
1.0
|
O
|
B:HOH321
|
2.1
|
26.0
|
1.0
|
NE2
|
B:HIS46
|
2.1
|
28.3
|
1.0
|
O
|
B:HOH347
|
2.2
|
32.6
|
1.0
|
CD2
|
B:HIS29
|
3.0
|
28.6
|
1.0
|
CD2
|
B:HIS27
|
3.0
|
31.5
|
1.0
|
CE1
|
B:HIS46
|
3.1
|
29.9
|
1.0
|
CE1
|
B:HIS29
|
3.1
|
30.7
|
1.0
|
CE1
|
B:HIS27
|
3.2
|
31.6
|
1.0
|
CD2
|
B:HIS46
|
3.2
|
29.1
|
1.0
|
O
|
B:HOH363
|
4.1
|
45.0
|
1.0
|
CG
|
B:HIS29
|
4.1
|
27.0
|
1.0
|
O
|
B:LEU68
|
4.2
|
30.4
|
1.0
|
ND1
|
B:HIS29
|
4.2
|
31.4
|
1.0
|
CG
|
B:HIS27
|
4.2
|
31.8
|
1.0
|
ND1
|
B:HIS46
|
4.2
|
29.4
|
1.0
|
ND1
|
B:HIS27
|
4.2
|
31.4
|
1.0
|
CG
|
B:HIS46
|
4.3
|
28.1
|
1.0
|
O
|
B:HOH373
|
4.4
|
53.5
|
1.0
|
O
|
B:HOH374
|
4.6
|
39.5
|
1.0
|
OG1
|
B:THR44
|
4.7
|
33.7
|
1.0
|
|
Nickel binding site 3 out
of 4 in 5wtq
Go back to
Nickel Binding Sites List in 5wtq
Nickel binding site 3 out
of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni201
b:26.3
occ:1.00
|
NE2
|
C:HIS29
|
2.1
|
30.3
|
1.0
|
NE2
|
C:HIS46
|
2.1
|
24.0
|
1.0
|
NE2
|
C:HIS27
|
2.2
|
31.1
|
1.0
|
O
|
C:HOH316
|
2.3
|
29.6
|
1.0
|
CD2
|
C:HIS29
|
3.0
|
30.4
|
1.0
|
CE1
|
C:HIS46
|
3.0
|
27.0
|
1.0
|
CE1
|
C:HIS29
|
3.1
|
29.6
|
1.0
|
CD2
|
C:HIS27
|
3.1
|
27.1
|
1.0
|
CE1
|
C:HIS27
|
3.2
|
26.5
|
1.0
|
CD2
|
C:HIS46
|
3.2
|
24.1
|
1.0
|
O
|
C:LEU68
|
4.1
|
32.1
|
1.0
|
ND1
|
C:HIS29
|
4.2
|
29.8
|
1.0
|
CG
|
C:HIS29
|
4.2
|
28.2
|
1.0
|
ND1
|
C:HIS46
|
4.2
|
27.9
|
1.0
|
ND1
|
C:HIS27
|
4.3
|
25.8
|
1.0
|
CG
|
C:HIS27
|
4.3
|
25.2
|
1.0
|
CG
|
C:HIS46
|
4.3
|
25.2
|
1.0
|
NH2
|
C:ARG48
|
4.7
|
48.1
|
1.0
|
CB
|
C:ASN16
|
5.0
|
28.0
|
1.0
|
|
Nickel binding site 4 out
of 4 in 5wtq
Go back to
Nickel Binding Sites List in 5wtq
Nickel binding site 4 out
of 4 in the Crystal Structure of Human Proteasome-Assembling Chaperone PAC4
 Mono view
 Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of Human Proteasome-Assembling Chaperone PAC4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni201
b:31.8
occ:1.00
|
NE2
|
D:HIS29
|
2.0
|
29.5
|
1.0
|
O
|
D:HOH320
|
2.1
|
30.1
|
1.0
|
NE2
|
D:HIS46
|
2.2
|
27.9
|
1.0
|
O
|
D:HOH345
|
2.2
|
33.3
|
1.0
|
NE2
|
D:HIS27
|
2.2
|
38.5
|
1.0
|
CD2
|
D:HIS29
|
2.9
|
31.7
|
1.0
|
CE1
|
D:HIS29
|
3.0
|
31.8
|
1.0
|
CE1
|
D:HIS46
|
3.1
|
28.1
|
1.0
|
CD2
|
D:HIS27
|
3.1
|
36.3
|
1.0
|
CD2
|
D:HIS46
|
3.2
|
27.6
|
1.0
|
CE1
|
D:HIS27
|
3.3
|
40.1
|
1.0
|
CG
|
D:HIS29
|
4.1
|
28.2
|
1.0
|
ND1
|
D:HIS29
|
4.1
|
31.8
|
1.0
|
O
|
D:LEU68
|
4.1
|
32.4
|
1.0
|
ND1
|
D:HIS46
|
4.2
|
26.1
|
1.0
|
CG
|
D:HIS27
|
4.3
|
40.8
|
1.0
|
CG
|
D:HIS46
|
4.3
|
26.4
|
1.0
|
ND1
|
D:HIS27
|
4.3
|
40.3
|
1.0
|
O
|
D:HOH371
|
4.4
|
49.6
|
1.0
|
O
|
D:HOH378
|
4.4
|
40.4
|
1.0
|
O
|
D:HOH374
|
4.6
|
37.8
|
1.0
|
OG1
|
D:THR44
|
4.7
|
37.5
|
1.0
|
CB
|
D:ASN16
|
4.9
|
52.4
|
1.0
|
CG
|
D:ASN16
|
5.0
|
50.3
|
1.0
|
|
Reference:
E.Kurimoto,
T.Satoh,
Y.Ito,
E.Ishihara,
K.Okamoto,
M.Yagi-Utsumi,
K.Tanaka,
K.Kato.
Crystal Structure of Human Proteasome Assembly Chaperone PAC4 Involved in Proteasome Formation Protein Sci. V. 26 1080 2017.
ISSN: ESSN 1469-896X
PubMed: 28263418
DOI: 10.1002/PRO.3153
Page generated: Thu Oct 10 08:09:45 2024
|