Sodium in PDB 7oje: Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa
Protein crystallography data
The structure of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa, PDB code: 7oje
was solved by
C.Pichlo,
T.Hermanns,
K.Hofmann,
U.Baumann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
51.67 /
2.05
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
151.607,
151.607,
83.751,
90,
90,
120
|
R / Rfree (%)
|
18.5 /
21.9
|
Other elements in 7oje:
The structure of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa
(pdb code 7oje). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa, PDB code: 7oje:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 7oje
Go back to
Sodium Binding Sites List in 7oje
Sodium binding site 1 out
of 3 in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa
![](/pictures/NA/pdb/oj/7oje-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/oj/7oje-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na605
b:30.7
occ:1.00
|
O
|
A:HOH823
|
2.3
|
28.2
|
1.0
|
O
|
A:ARG548
|
2.3
|
25.1
|
1.0
|
O
|
A:ARG551
|
2.3
|
25.7
|
1.0
|
O2
|
A:CIT601
|
2.4
|
39.7
|
1.0
|
O6
|
A:CIT601
|
2.4
|
32.5
|
1.0
|
O7
|
A:CIT601
|
2.5
|
34.7
|
1.0
|
C6
|
A:CIT601
|
3.0
|
41.9
|
1.0
|
C3
|
A:CIT601
|
3.2
|
39.0
|
1.0
|
C1
|
A:CIT601
|
3.3
|
46.7
|
1.0
|
C
|
A:ARG551
|
3.5
|
27.6
|
1.0
|
C
|
A:ARG548
|
3.5
|
34.2
|
1.0
|
C2
|
A:CIT601
|
3.7
|
38.7
|
1.0
|
O
|
A:HOH716
|
3.9
|
39.0
|
1.0
|
N
|
A:ARG551
|
4.0
|
22.6
|
1.0
|
O
|
A:LEU549
|
4.0
|
26.0
|
1.0
|
NZ
|
A:LYS552
|
4.0
|
25.0
|
1.0
|
O5
|
A:CIT601
|
4.0
|
42.6
|
1.0
|
CE
|
A:LYS552
|
4.1
|
27.5
|
1.0
|
CA
|
A:ARG551
|
4.1
|
24.9
|
1.0
|
C
|
A:LEU549
|
4.2
|
26.4
|
1.0
|
CD
|
A:LYS552
|
4.3
|
24.3
|
1.0
|
O4
|
A:CIT601
|
4.3
|
35.7
|
1.0
|
O1
|
A:CIT601
|
4.4
|
45.8
|
1.0
|
CB
|
A:ARG551
|
4.4
|
23.7
|
1.0
|
CA
|
A:ARG548
|
4.4
|
33.9
|
1.0
|
O
|
A:HOH785
|
4.4
|
33.5
|
1.0
|
N
|
A:LEU549
|
4.5
|
28.2
|
1.0
|
CA
|
A:LEU549
|
4.5
|
31.6
|
1.0
|
C4
|
A:CIT601
|
4.6
|
33.8
|
1.0
|
N
|
A:LYS552
|
4.6
|
21.2
|
1.0
|
C
|
A:LEU550
|
4.7
|
26.0
|
1.0
|
CB
|
A:ARG548
|
4.8
|
39.4
|
1.0
|
N
|
A:LEU550
|
4.8
|
23.1
|
1.0
|
CA
|
A:LYS552
|
4.9
|
24.7
|
1.0
|
CG
|
A:LYS552
|
4.9
|
22.1
|
1.0
|
C5
|
A:CIT601
|
4.9
|
36.1
|
1.0
|
|
Sodium binding site 2 out
of 3 in 7oje
Go back to
Sodium Binding Sites List in 7oje
Sodium binding site 2 out
of 3 in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa
![](/pictures/NA/pdb/oj/7oje-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/oj/7oje-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na606
b:34.6
occ:1.00
|
O
|
A:ASN283
|
2.3
|
40.8
|
1.0
|
O
|
A:ASN439
|
2.3
|
33.5
|
1.0
|
O
|
A:GLY285
|
2.5
|
38.6
|
1.0
|
O
|
A:HOH901
|
2.6
|
45.8
|
1.0
|
O
|
A:HOH900
|
2.6
|
47.0
|
1.0
|
O
|
A:HOH866
|
2.6
|
48.0
|
1.0
|
C
|
A:GLY285
|
3.4
|
40.2
|
1.0
|
N
|
A:GLY285
|
3.4
|
40.7
|
1.0
|
C
|
A:ASN439
|
3.5
|
34.8
|
1.0
|
C
|
A:ASN283
|
3.5
|
41.9
|
1.0
|
C
|
A:GLN284
|
3.9
|
43.3
|
1.0
|
NH2
|
A:ARG436
|
3.9
|
38.0
|
1.0
|
CA
|
A:GLY285
|
3.9
|
42.3
|
1.0
|
CA
|
A:THR440
|
4.0
|
31.1
|
1.0
|
CA
|
A:GLN284
|
4.1
|
41.5
|
1.0
|
N
|
A:THR440
|
4.2
|
31.4
|
1.0
|
N
|
A:GLN284
|
4.2
|
43.6
|
1.0
|
N
|
A:ASN286
|
4.4
|
37.0
|
1.0
|
CB
|
A:ASN286
|
4.5
|
36.9
|
1.0
|
CA
|
A:ASN283
|
4.5
|
40.7
|
1.0
|
ND2
|
A:ASN286
|
4.6
|
39.2
|
1.0
|
CA
|
A:ASN439
|
4.6
|
36.0
|
1.0
|
CB
|
A:ASN439
|
4.6
|
35.0
|
1.0
|
CB
|
A:ASN283
|
4.6
|
38.1
|
1.0
|
O
|
A:GLN284
|
4.6
|
37.9
|
1.0
|
O
|
A:HOH962
|
4.8
|
52.5
|
1.0
|
CG2
|
A:THR440
|
4.8
|
31.6
|
1.0
|
CA
|
A:ASN286
|
4.8
|
39.1
|
1.0
|
CB
|
A:THR440
|
4.9
|
33.6
|
1.0
|
|
Sodium binding site 3 out
of 3 in 7oje
Go back to
Sodium Binding Sites List in 7oje
Sodium binding site 3 out
of 3 in the Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa
![](/pictures/NA/pdb/oj/7oje-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/oj/7oje-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Covalent Complex Between Tribolium Castaneum Deubiquitinase Zup and Ubiquitin-Pa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na603
b:63.3
occ:1.00
|
O
|
C:ARG548
|
2.1
|
60.0
|
1.0
|
O
|
C:ARG551
|
2.3
|
54.7
|
1.0
|
O5
|
C:CIT601
|
2.5
|
61.6
|
1.0
|
O7
|
C:CIT601
|
2.5
|
65.0
|
1.0
|
O3
|
C:CIT601
|
2.6
|
69.8
|
1.0
|
C6
|
C:CIT601
|
3.2
|
71.7
|
1.0
|
C3
|
C:CIT601
|
3.3
|
64.5
|
1.0
|
C
|
C:ARG548
|
3.4
|
66.2
|
1.0
|
C
|
C:ARG551
|
3.4
|
56.6
|
1.0
|
C5
|
C:CIT601
|
3.6
|
75.9
|
1.0
|
O
|
C:LEU549
|
3.8
|
61.2
|
1.0
|
N
|
C:ARG551
|
3.8
|
62.0
|
1.0
|
C4
|
C:CIT601
|
3.9
|
67.3
|
1.0
|
CE
|
C:LYS552
|
3.9
|
57.9
|
1.0
|
NZ
|
C:LYS552
|
3.9
|
55.6
|
1.0
|
C
|
C:LEU549
|
4.0
|
61.6
|
1.0
|
CA
|
C:ARG551
|
4.0
|
57.0
|
1.0
|
CD
|
C:LYS552
|
4.2
|
53.0
|
1.0
|
CA
|
C:LEU549
|
4.2
|
63.5
|
1.0
|
N
|
C:LEU549
|
4.3
|
62.7
|
1.0
|
CB
|
C:ARG551
|
4.3
|
57.3
|
1.0
|
O6
|
C:CIT601
|
4.3
|
73.8
|
1.0
|
CA
|
C:ARG548
|
4.3
|
70.0
|
1.0
|
O1
|
C:CIT601
|
4.3
|
62.0
|
1.0
|
C
|
C:LEU550
|
4.5
|
54.7
|
1.0
|
N
|
C:LYS552
|
4.5
|
58.4
|
1.0
|
C2
|
C:CIT601
|
4.6
|
64.7
|
1.0
|
N
|
C:LEU550
|
4.6
|
56.3
|
1.0
|
O4
|
C:CIT601
|
4.7
|
80.9
|
1.0
|
CG
|
C:LYS552
|
4.8
|
53.2
|
1.0
|
CB
|
C:ARG548
|
4.8
|
70.5
|
1.0
|
CA
|
C:LYS552
|
4.9
|
59.9
|
1.0
|
C1
|
C:CIT601
|
4.9
|
67.0
|
1.0
|
|
Reference:
T.Hermanns,
C.Pichlo,
U.Baumann,
K.Hofmann.
A Structural Basis For the Diverse Linkage Specificities Within the Zufsp Deubiquitinase Family. Nat Commun V. 13 401 2022.
ISSN: ESSN 2041-1723
PubMed: 35058438
DOI: 10.1038/S41467-022-28049-6
Page generated: Fri Apr 7 15:23:45 2023
|