Sodium in PDB 6s98: Crystal Structure of the Catalytic Domain of UBE2S Wt.
Enzymatic activity of Crystal Structure of the Catalytic Domain of UBE2S Wt.
All present enzymatic activity of Crystal Structure of the Catalytic Domain of UBE2S Wt.:
2.3.2.23;
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of UBE2S Wt., PDB code: 6s98
was solved by
A.K.L.Liess,
S.Lorenz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.15 /
1.55
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.812,
49.050,
71.926,
90.00,
106.03,
90.00
|
R / Rfree (%)
|
16.1 /
18.4
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of the Catalytic Domain of UBE2S Wt.
(pdb code 6s98). 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 Catalytic Domain of UBE2S Wt., PDB code: 6s98:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 6s98
Go back to
Sodium Binding Sites List in 6s98
Sodium binding site 1 out
of 3 in the Crystal Structure of the Catalytic Domain of UBE2S Wt.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of the Catalytic Domain of UBE2S Wt. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na201
b:17.7
occ:1.00
|
OD1
|
A:ASN124
|
2.2
|
15.7
|
1.0
|
OD1
|
B:ASN124
|
2.3
|
17.6
|
1.0
|
O
|
B:PRO123
|
2.3
|
15.5
|
1.0
|
O
|
A:PRO123
|
2.3
|
15.2
|
1.0
|
O
|
B:HOH345
|
2.5
|
17.2
|
1.0
|
HA
|
A:ASN124
|
2.9
|
18.3
|
1.0
|
HA
|
B:ASN124
|
2.9
|
18.1
|
1.0
|
C
|
A:PRO123
|
3.3
|
16.8
|
1.0
|
C
|
B:PRO123
|
3.3
|
15.9
|
1.0
|
HB3
|
A:HIS122
|
3.4
|
15.9
|
1.0
|
HB3
|
B:HIS122
|
3.4
|
15.2
|
1.0
|
CG
|
A:ASN124
|
3.4
|
15.0
|
1.0
|
CG
|
B:ASN124
|
3.4
|
18.7
|
1.0
|
O
|
A:HIS122
|
3.5
|
15.2
|
1.0
|
CA
|
A:ASN124
|
3.7
|
15.3
|
1.0
|
CA
|
B:ASN124
|
3.7
|
15.0
|
1.0
|
O
|
B:HIS122
|
3.7
|
15.6
|
1.0
|
N
|
A:ASN124
|
3.8
|
14.4
|
1.0
|
HD2
|
B:PRO125
|
3.8
|
21.2
|
1.0
|
HD2
|
A:PRO125
|
3.8
|
23.5
|
1.0
|
N
|
B:ASN124
|
3.8
|
13.1
|
1.0
|
C
|
A:HIS122
|
3.9
|
15.8
|
1.0
|
O
|
A:HOH319
|
3.9
|
16.9
|
1.0
|
O
|
B:HOH349
|
4.0
|
20.1
|
1.0
|
CB
|
A:ASN124
|
4.1
|
14.1
|
1.0
|
CB
|
B:ASN124
|
4.1
|
16.1
|
1.0
|
C
|
B:HIS122
|
4.1
|
15.7
|
1.0
|
CB
|
A:HIS122
|
4.2
|
13.2
|
1.0
|
CB
|
B:HIS122
|
4.3
|
12.7
|
1.0
|
HB3
|
B:ASN124
|
4.3
|
19.4
|
1.0
|
HB3
|
A:ASN124
|
4.4
|
17.0
|
1.0
|
HB2
|
A:HIS122
|
4.4
|
15.9
|
1.0
|
N
|
A:PRO123
|
4.4
|
15.1
|
1.0
|
CA
|
A:PRO123
|
4.4
|
15.4
|
1.0
|
ND2
|
A:ASN124
|
4.5
|
18.2
|
1.0
|
HB2
|
B:HIS122
|
4.5
|
15.2
|
1.0
|
HD3
|
B:PRO125
|
4.5
|
21.2
|
1.0
|
ND2
|
B:ASN124
|
4.5
|
19.1
|
1.0
|
CA
|
B:PRO123
|
4.5
|
11.5
|
1.0
|
HD3
|
A:PRO125
|
4.5
|
23.5
|
1.0
|
N
|
B:PRO123
|
4.5
|
12.7
|
1.0
|
HD21
|
A:ASN124
|
4.5
|
21.9
|
1.0
|
HD21
|
B:ASN124
|
4.6
|
22.9
|
1.0
|
CD
|
B:PRO125
|
4.6
|
17.7
|
1.0
|
CD
|
A:PRO125
|
4.6
|
19.5
|
1.0
|
CA
|
A:HIS122
|
4.6
|
13.3
|
1.0
|
H
|
A:ASN124
|
4.6
|
17.3
|
1.0
|
H
|
B:ASN124
|
4.6
|
15.7
|
1.0
|
CA
|
B:HIS122
|
4.7
|
13.0
|
1.0
|
HA
|
A:HIS122
|
4.7
|
16.0
|
1.0
|
OE1
|
B:GLU126
|
4.7
|
19.9
|
1.0
|
OE2
|
A:GLU126
|
4.8
|
18.5
|
1.0
|
HA
|
B:HIS122
|
4.8
|
15.6
|
1.0
|
HB2
|
A:ASN124
|
4.9
|
17.0
|
1.0
|
HB2
|
B:ASN124
|
4.9
|
19.4
|
1.0
|
HA
|
A:PRO123
|
4.9
|
18.5
|
1.0
|
C
|
B:ASN124
|
5.0
|
16.4
|
1.0
|
C
|
A:ASN124
|
5.0
|
19.1
|
1.0
|
OE1
|
A:GLU126
|
5.0
|
21.8
|
1.0
|
HA
|
B:PRO123
|
5.0
|
13.8
|
1.0
|
|
Sodium binding site 2 out
of 3 in 6s98
Go back to
Sodium Binding Sites List in 6s98
Sodium binding site 2 out
of 3 in the Crystal Structure of the Catalytic Domain of UBE2S Wt.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of the Catalytic Domain of UBE2S Wt. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:36.5
occ:1.00
|
O
|
A:HOH369
|
2.6
|
28.8
|
1.0
|
HB2
|
A:ARG101
|
2.7
|
17.9
|
1.0
|
O
|
B:HOH365
|
2.7
|
16.9
|
1.0
|
O
|
A:VAL98
|
2.8
|
23.4
|
1.0
|
HE1
|
B:HIS122
|
2.8
|
15.8
|
1.0
|
HG13
|
A:VAL98
|
3.1
|
53.2
|
1.0
|
O
|
B:HOH301
|
3.3
|
12.4
|
1.0
|
HD2
|
A:ARG101
|
3.3
|
24.2
|
1.0
|
HG21
|
A:THR115
|
3.4
|
20.0
|
1.0
|
CE1
|
B:HIS122
|
3.5
|
13.1
|
1.0
|
HG23
|
A:THR115
|
3.5
|
20.0
|
1.0
|
CB
|
A:ARG101
|
3.6
|
15.0
|
1.0
|
C
|
A:VAL98
|
3.8
|
25.8
|
1.0
|
HG12
|
A:VAL98
|
3.8
|
53.2
|
1.0
|
HB3
|
A:ARG101
|
3.8
|
17.9
|
1.0
|
ND1
|
B:HIS122
|
3.9
|
14.1
|
1.0
|
HG22
|
B:ILE121
|
3.9
|
16.6
|
1.0
|
CG1
|
A:VAL98
|
3.9
|
44.3
|
1.0
|
O
|
B:HOH342
|
3.9
|
18.2
|
1.0
|
CG2
|
A:THR115
|
3.9
|
16.6
|
1.0
|
HD3
|
A:ARG101
|
4.0
|
24.2
|
1.0
|
CD
|
A:ARG101
|
4.0
|
20.3
|
1.0
|
HG23
|
B:ILE121
|
4.0
|
16.6
|
1.0
|
O
|
A:ARG101
|
4.1
|
16.0
|
1.0
|
H
|
A:ARG101
|
4.1
|
19.4
|
1.0
|
O
|
B:ILE121
|
4.2
|
13.1
|
1.0
|
HA
|
A:LEU99
|
4.2
|
23.1
|
1.0
|
HA
|
A:VAL98
|
4.3
|
32.1
|
1.0
|
HG22
|
A:THR115
|
4.3
|
20.0
|
1.0
|
CG
|
A:ARG101
|
4.4
|
18.0
|
1.0
|
CG2
|
B:ILE121
|
4.4
|
13.8
|
1.0
|
HG11
|
A:VAL98
|
4.5
|
53.2
|
1.0
|
HH11
|
A:ARG101
|
4.5
|
32.2
|
1.0
|
CA
|
A:ARG101
|
4.5
|
14.2
|
1.0
|
NE2
|
B:HIS122
|
4.6
|
15.6
|
1.0
|
CA
|
A:VAL98
|
4.6
|
26.8
|
1.0
|
N
|
A:ARG101
|
4.6
|
16.1
|
1.0
|
HG3
|
A:ARG101
|
4.6
|
21.5
|
1.0
|
O
|
A:HOH336
|
4.6
|
24.6
|
1.0
|
HG21
|
B:ILE121
|
4.7
|
16.6
|
1.0
|
C
|
A:ARG101
|
4.7
|
15.8
|
1.0
|
N
|
A:LEU99
|
4.7
|
21.7
|
1.0
|
O
|
B:HOH334
|
4.8
|
17.9
|
1.0
|
CA
|
A:LEU99
|
4.8
|
19.2
|
1.0
|
HE2
|
B:HIS122
|
4.9
|
18.7
|
1.0
|
HD21
|
A:ASN124
|
4.9
|
21.9
|
1.0
|
CB
|
A:VAL98
|
4.9
|
40.6
|
1.0
|
|
Sodium binding site 3 out
of 3 in 6s98
Go back to
Sodium Binding Sites List in 6s98
Sodium binding site 3 out
of 3 in the Crystal Structure of the Catalytic Domain of UBE2S Wt.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of the Catalytic Domain of UBE2S Wt. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na203
b:78.0
occ:1.00
|
O
|
A:ILE121
|
2.2
|
14.9
|
1.0
|
O
|
B:HOH387
|
2.3
|
33.4
|
1.0
|
O
|
A:HOH352
|
2.4
|
23.7
|
1.0
|
O
|
A:HOH301
|
2.6
|
28.2
|
1.0
|
O
|
B:HOH361
|
2.6
|
19.0
|
1.0
|
C
|
A:ILE121
|
3.4
|
12.9
|
1.0
|
HG23
|
A:ILE121
|
3.7
|
20.9
|
1.0
|
HG22
|
A:ILE121
|
3.7
|
20.9
|
1.0
|
HA
|
A:ILE121
|
3.7
|
15.8
|
1.0
|
O
|
A:HOH349
|
3.8
|
19.8
|
1.0
|
HD3
|
B:ARG101
|
3.8
|
63.2
|
1.0
|
HG22
|
A:THR53
|
3.8
|
23.4
|
1.0
|
HH11
|
B:ARG101
|
3.8
|
59.1
|
1.0
|
HB3
|
B:ARG101
|
3.9
|
37.4
|
1.0
|
HB2
|
B:ARG101
|
3.9
|
37.4
|
1.0
|
HD2
|
B:ARG101
|
4.0
|
63.2
|
1.0
|
HA
|
A:HIS122
|
4.0
|
16.0
|
1.0
|
OD2
|
B:ASP102
|
4.0
|
29.0
|
1.0
|
OH
|
A:TYR141
|
4.1
|
28.6
|
1.0
|
CA
|
A:ILE121
|
4.1
|
13.1
|
1.0
|
CG2
|
A:ILE121
|
4.1
|
17.4
|
1.0
|
HH
|
A:TYR141
|
4.2
|
34.4
|
1.0
|
HD3
|
A:PRO123
|
4.3
|
17.8
|
1.0
|
ND1
|
A:HIS122
|
4.3
|
16.3
|
1.0
|
CD
|
B:ARG101
|
4.3
|
52.7
|
1.0
|
CB
|
B:ARG101
|
4.4
|
31.1
|
1.0
|
HD2
|
A:PRO123
|
4.5
|
17.8
|
1.0
|
N
|
A:HIS122
|
4.5
|
13.5
|
1.0
|
HA
|
A:THR53
|
4.5
|
24.4
|
1.0
|
O
|
A:GLY52
|
4.5
|
26.4
|
1.0
|
HE1
|
A:HIS122
|
4.6
|
22.7
|
1.0
|
HD3
|
A:PRO54
|
4.7
|
27.7
|
1.0
|
CE1
|
A:HIS122
|
4.7
|
18.9
|
1.0
|
NH1
|
B:ARG101
|
4.7
|
49.3
|
1.0
|
CG2
|
A:THR53
|
4.7
|
19.5
|
1.0
|
CA
|
A:HIS122
|
4.7
|
13.3
|
1.0
|
CB
|
A:ILE121
|
4.8
|
15.2
|
1.0
|
O
|
B:ARG101
|
4.8
|
24.9
|
1.0
|
HB
|
A:THR53
|
4.8
|
22.0
|
1.0
|
CD
|
A:PRO123
|
4.8
|
14.8
|
1.0
|
HG21
|
A:THR53
|
4.9
|
23.4
|
1.0
|
HG21
|
A:ILE121
|
4.9
|
20.9
|
1.0
|
|
Reference:
A.K.L.Liess,
A.Kucerova,
K.Schweimer,
D.Schlesinger,
O.Dybkov,
H.Urlaub,
J.Mansfeld,
S.Lorenz.
Dimerization Regulates the Human Apc/C-Associated Ubiquitin-Conjugating Enzyme UBE2S. Sci.Signal. V. 13 2020.
ISSN: ESSN 1937-9145
PubMed: 33082289
DOI: 10.1126/SCISIGNAL.ABA8208
Page generated: Tue Oct 8 13:24:00 2024
|