Magnesium in PDB 6zhu: Yeast UBA1 in Complex with UBC3 and Atp
Enzymatic activity of Yeast UBA1 in Complex with UBC3 and Atp
All present enzymatic activity of Yeast UBA1 in Complex with UBC3 and Atp:
2.3.2.23;
6.2.1.45;
Protein crystallography data
The structure of Yeast UBA1 in Complex with UBC3 and Atp, PDB code: 6zhu
was solved by
M.Misra,
H.Schindelin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.81 /
3.18
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.636,
152.408,
252.567,
90,
90.45,
90
|
R / Rfree (%)
|
21.7 /
26.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Yeast UBA1 in Complex with UBC3 and Atp
(pdb code 6zhu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Yeast UBA1 in Complex with UBC3 and Atp, PDB code: 6zhu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6zhu
Go back to
Magnesium Binding Sites List in 6zhu
Magnesium binding site 1 out
of 4 in the Yeast UBA1 in Complex with UBC3 and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1102
b:72.3
occ:1.00
|
O
|
A:HOH1203
|
2.0
|
72.8
|
1.0
|
OD2
|
A:ASP544
|
2.3
|
53.0
|
1.0
|
O
|
A:HOH1201
|
2.4
|
75.1
|
1.0
|
O2G
|
A:ATP1101
|
2.5
|
55.5
|
1.0
|
O2A
|
A:ATP1101
|
2.8
|
54.9
|
1.0
|
HB2
|
A:ASP544
|
2.9
|
61.4
|
1.0
|
O1B
|
A:ATP1101
|
2.9
|
55.5
|
1.0
|
CG
|
A:ASP544
|
3.2
|
52.3
|
1.0
|
CB
|
A:ASP544
|
3.5
|
51.2
|
1.0
|
HD12
|
A:ILE863
|
3.7
|
58.9
|
1.0
|
HB3
|
A:ASP544
|
3.7
|
61.4
|
1.0
|
PG
|
A:ATP1101
|
3.8
|
49.4
|
1.0
|
PB
|
A:ATP1101
|
3.9
|
49.7
|
1.0
|
O3B
|
A:ATP1101
|
4.0
|
47.2
|
1.0
|
H5'2
|
A:ATP1101
|
4.1
|
64.1
|
1.0
|
PA
|
A:ATP1101
|
4.2
|
46.0
|
1.0
|
O1G
|
A:ATP1101
|
4.2
|
49.3
|
1.0
|
OD1
|
A:ASP544
|
4.3
|
53.1
|
1.0
|
O3A
|
A:ATP1101
|
4.4
|
44.2
|
1.0
|
HB
|
A:ILE863
|
4.5
|
58.4
|
1.0
|
O
|
A:ASP544
|
4.5
|
52.5
|
1.0
|
CD1
|
A:ILE863
|
4.6
|
49.1
|
1.0
|
CA
|
A:ASP544
|
4.8
|
51.2
|
1.0
|
HG13
|
A:ILE863
|
4.9
|
59.0
|
1.0
|
HD11
|
A:ILE863
|
5.0
|
58.9
|
1.0
|
O3G
|
A:ATP1101
|
5.0
|
46.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6zhu
Go back to
Magnesium Binding Sites List in 6zhu
Magnesium binding site 2 out
of 4 in the Yeast UBA1 in Complex with UBC3 and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1102
b:67.6
occ:1.00
|
O
|
E:HOH1202
|
1.7
|
69.4
|
1.0
|
O
|
E:HOH1201
|
1.8
|
68.3
|
1.0
|
OD2
|
E:ASP544
|
2.2
|
59.7
|
1.0
|
O2G
|
E:ATP1101
|
2.3
|
61.3
|
1.0
|
O1B
|
E:ATP1101
|
2.3
|
61.0
|
1.0
|
O1A
|
E:ATP1101
|
2.5
|
50.9
|
1.0
|
HB2
|
E:ASP544
|
2.8
|
65.9
|
1.0
|
CG
|
E:ASP544
|
3.1
|
58.0
|
1.0
|
CB
|
E:ASP544
|
3.3
|
54.9
|
1.0
|
HB3
|
E:ASP544
|
3.4
|
65.9
|
1.0
|
PG
|
E:ATP1101
|
3.5
|
54.7
|
1.0
|
PB
|
E:ATP1101
|
3.5
|
52.6
|
1.0
|
O3B
|
E:ATP1101
|
3.7
|
51.9
|
1.0
|
PA
|
E:ATP1101
|
3.8
|
47.3
|
1.0
|
HD12
|
E:ILE863
|
3.9
|
65.4
|
1.0
|
H5'1
|
E:ATP1101
|
3.9
|
66.7
|
1.0
|
O3A
|
E:ATP1101
|
4.0
|
47.2
|
1.0
|
O1G
|
E:ATP1101
|
4.2
|
56.4
|
1.0
|
OD1
|
E:ASP544
|
4.3
|
57.9
|
1.0
|
HB
|
E:ILE863
|
4.4
|
66.1
|
1.0
|
O
|
E:ASP544
|
4.6
|
54.5
|
1.0
|
HH21
|
E:ARG481
|
4.6
|
70.7
|
1.0
|
O3G
|
E:ATP1101
|
4.7
|
50.5
|
1.0
|
CA
|
E:ASP544
|
4.7
|
52.5
|
1.0
|
O2B
|
E:ATP1101
|
4.8
|
56.6
|
1.0
|
O5'
|
E:ATP1101
|
4.8
|
54.2
|
1.0
|
O2A
|
E:ATP1101
|
4.8
|
43.5
|
1.0
|
CD1
|
E:ILE863
|
4.8
|
54.5
|
1.0
|
C5'
|
E:ATP1101
|
4.8
|
55.6
|
1.0
|
H3'
|
E:ATP1101
|
5.0
|
61.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6zhu
Go back to
Magnesium Binding Sites List in 6zhu
Magnesium binding site 3 out
of 4 in the Yeast UBA1 in Complex with UBC3 and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1102
b:69.0
occ:1.00
|
O
|
C:HOH1201
|
1.8
|
69.4
|
1.0
|
O
|
C:HOH1202
|
2.1
|
72.2
|
1.0
|
O2G
|
C:ATP1101
|
2.2
|
59.5
|
1.0
|
O2B
|
C:ATP1101
|
2.8
|
58.0
|
1.0
|
O2A
|
C:ATP1101
|
2.9
|
51.7
|
1.0
|
OD2
|
C:ASP544
|
3.0
|
61.0
|
1.0
|
HB2
|
C:ASP544
|
3.1
|
71.5
|
1.0
|
PG
|
C:ATP1101
|
3.3
|
48.9
|
1.0
|
HD12
|
C:ILE863
|
3.6
|
63.7
|
1.0
|
O1G
|
C:ATP1101
|
3.7
|
44.5
|
1.0
|
O3B
|
C:ATP1101
|
3.7
|
47.7
|
1.0
|
CG
|
C:ASP544
|
3.7
|
60.9
|
1.0
|
PB
|
C:ATP1101
|
3.8
|
50.6
|
1.0
|
CB
|
C:ASP544
|
3.8
|
59.6
|
1.0
|
HB
|
C:ILE863
|
4.0
|
61.6
|
1.0
|
HB3
|
C:ASP544
|
4.0
|
71.5
|
1.0
|
PA
|
C:ATP1101
|
4.2
|
45.6
|
1.0
|
O3A
|
C:ATP1101
|
4.4
|
46.3
|
1.0
|
CD1
|
C:ILE863
|
4.5
|
53.0
|
1.0
|
H5'1
|
C:ATP1101
|
4.5
|
62.8
|
1.0
|
H
|
C:ILE863
|
4.6
|
58.0
|
1.0
|
O3G
|
C:ATP1101
|
4.6
|
47.3
|
1.0
|
HG13
|
C:ILE863
|
4.7
|
61.2
|
1.0
|
HH21
|
C:ARG481
|
4.7
|
71.6
|
1.0
|
CB
|
C:ILE863
|
4.8
|
51.3
|
1.0
|
HD11
|
C:ILE863
|
4.9
|
63.7
|
1.0
|
OD1
|
C:ASP544
|
4.9
|
61.1
|
1.0
|
O
|
C:ASP544
|
4.9
|
60.2
|
1.0
|
CG1
|
C:ILE863
|
4.9
|
51.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6zhu
Go back to
Magnesium Binding Sites List in 6zhu
Magnesium binding site 4 out
of 4 in the Yeast UBA1 in Complex with UBC3 and Atp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Yeast UBA1 in Complex with UBC3 and Atp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg1102
b:62.5
occ:1.00
|
O
|
G:HOH1201
|
1.8
|
73.6
|
1.0
|
OD2
|
G:ASP544
|
2.0
|
77.8
|
1.0
|
O2A
|
G:ATP1101
|
2.4
|
66.3
|
1.0
|
O1G
|
G:ATP1101
|
2.5
|
71.5
|
1.0
|
O2B
|
G:ATP1101
|
2.6
|
67.5
|
1.0
|
HB2
|
G:ASP544
|
2.6
|
84.5
|
1.0
|
O
|
G:HOH1202
|
2.8
|
80.7
|
1.0
|
CG
|
G:ASP544
|
2.9
|
70.2
|
1.0
|
CB
|
G:ASP544
|
3.1
|
70.4
|
1.0
|
HB3
|
G:ASP544
|
3.3
|
84.5
|
1.0
|
PB
|
G:ATP1101
|
3.6
|
64.2
|
1.0
|
PG
|
G:ATP1101
|
3.7
|
67.7
|
1.0
|
PA
|
G:ATP1101
|
3.7
|
65.2
|
1.0
|
H5'2
|
G:ATP1101
|
3.8
|
81.6
|
1.0
|
O3B
|
G:ATP1101
|
3.8
|
65.1
|
1.0
|
OD1
|
G:ASP544
|
4.0
|
70.9
|
1.0
|
O3A
|
G:ATP1101
|
4.1
|
64.1
|
1.0
|
O3G
|
G:ATP1101
|
4.2
|
67.5
|
1.0
|
O
|
G:ASP544
|
4.5
|
70.5
|
1.0
|
CA
|
G:ASP544
|
4.5
|
71.3
|
1.0
|
HD12
|
G:ILE863
|
4.6
|
79.8
|
1.0
|
C5'
|
G:ATP1101
|
4.7
|
68.0
|
1.0
|
HB
|
G:ILE863
|
4.7
|
78.7
|
1.0
|
O5'
|
G:ATP1101
|
4.7
|
67.8
|
1.0
|
O1A
|
G:ATP1101
|
4.8
|
69.7
|
1.0
|
HH21
|
G:ARG481
|
4.9
|
88.6
|
1.0
|
H3'
|
G:ATP1101
|
4.9
|
78.3
|
1.0
|
HA
|
G:ASP544
|
4.9
|
85.5
|
1.0
|
C
|
G:ASP544
|
5.0
|
71.2
|
1.0
|
|
Reference:
M.Misra,
A.Schaefer,
M.Kuhn,
L.Pluska,
I.Tessmer,
T.Sommer,
H.Schindelin.
Atp Induced Conformational Changes Facilitate E1-E2 Disulfide Bridging in the Ubiquitin System To Be Published.
Page generated: Wed Oct 2 02:19:09 2024
|