Magnesium in PDB 6ut4: Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
(pdb code 6ut4). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb, PDB code: 6ut4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6ut4
Go back to
Magnesium Binding Sites List in 6ut4
Magnesium binding site 1 out
of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg702
b:46.2
occ:1.00
|
OG1
|
A:THR222
|
2.1
|
45.1
|
1.0
|
O2B
|
A:GSP701
|
2.1
|
50.0
|
1.0
|
O2G
|
A:GSP701
|
2.5
|
50.0
|
1.0
|
OD2
|
A:ASP356
|
2.9
|
45.4
|
1.0
|
OD1
|
A:ASP356
|
2.9
|
45.4
|
1.0
|
CB
|
A:THR222
|
3.2
|
45.1
|
1.0
|
CG
|
A:ASP356
|
3.3
|
45.4
|
1.0
|
NH1
|
B:ARG425
|
3.3
|
58.7
|
1.0
|
PB
|
A:GSP701
|
3.4
|
50.0
|
1.0
|
PG
|
A:GSP701
|
3.6
|
50.0
|
1.0
|
OE2
|
A:GLU357
|
3.8
|
49.2
|
1.0
|
CG2
|
A:THR222
|
3.8
|
45.1
|
1.0
|
O3G
|
A:GSP701
|
3.9
|
50.0
|
1.0
|
O1B
|
A:GSP701
|
3.9
|
50.0
|
1.0
|
O3B
|
A:GSP701
|
3.9
|
50.0
|
1.0
|
OG1
|
A:THR408
|
4.3
|
44.9
|
1.0
|
CZ
|
B:ARG425
|
4.4
|
58.7
|
1.0
|
CA
|
A:THR222
|
4.5
|
45.1
|
1.0
|
O2A
|
A:GSP701
|
4.5
|
50.0
|
1.0
|
N
|
A:THR222
|
4.6
|
45.1
|
1.0
|
O3A
|
A:GSP701
|
4.7
|
50.0
|
1.0
|
CB
|
A:ASP356
|
4.7
|
45.4
|
1.0
|
CD
|
A:GLU357
|
4.9
|
49.2
|
1.0
|
PA
|
A:GSP701
|
5.0
|
50.0
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6ut4
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Magnesium Binding Sites List in 6ut4
Magnesium binding site 2 out
of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg702
b:36.6
occ:1.00
|
O
|
C:HOH802
|
2.1
|
35.8
|
1.0
|
OG1
|
B:THR222
|
2.1
|
40.0
|
1.0
|
O
|
B:HOH902
|
2.1
|
35.3
|
1.0
|
O2G
|
B:GSP701
|
2.1
|
40.4
|
1.0
|
O2B
|
B:GSP701
|
2.2
|
40.4
|
1.0
|
OD1
|
B:ASP356
|
2.9
|
40.1
|
1.0
|
OD2
|
B:ASP356
|
3.3
|
40.1
|
1.0
|
PG
|
B:GSP701
|
3.4
|
40.4
|
1.0
|
CB
|
B:THR222
|
3.5
|
40.0
|
1.0
|
PB
|
B:GSP701
|
3.5
|
40.4
|
1.0
|
CG
|
B:ASP356
|
3.5
|
40.1
|
1.0
|
OG1
|
B:THR408
|
3.8
|
41.4
|
1.0
|
O3B
|
B:GSP701
|
3.8
|
40.4
|
1.0
|
O3G
|
B:GSP701
|
3.9
|
40.4
|
1.0
|
N
|
B:THR222
|
4.1
|
40.0
|
1.0
|
OE2
|
B:GLU357
|
4.1
|
42.9
|
1.0
|
NH2
|
C:ARG426
|
4.1
|
33.4
|
1.0
|
O1B
|
B:GSP701
|
4.2
|
40.4
|
1.0
|
CA
|
B:THR222
|
4.3
|
40.0
|
1.0
|
CG2
|
B:THR222
|
4.4
|
40.0
|
1.0
|
CB
|
B:LYS221
|
4.6
|
39.0
|
1.0
|
CB
|
B:THR408
|
4.6
|
41.4
|
1.0
|
O2A
|
B:GSP701
|
4.6
|
40.4
|
1.0
|
O3A
|
B:GSP701
|
4.7
|
40.4
|
1.0
|
S1G
|
B:GSP701
|
4.8
|
40.4
|
1.0
|
CD
|
B:GLU357
|
5.0
|
42.9
|
1.0
|
CB
|
B:ASP356
|
5.0
|
40.1
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6ut4
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Magnesium Binding Sites List in 6ut4
Magnesium binding site 3 out
of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg702
b:21.9
occ:1.00
|
O
|
C:HOH801
|
2.1
|
23.2
|
1.0
|
O2B
|
C:GSP701
|
2.1
|
27.5
|
1.0
|
O
|
D:HOH803
|
2.2
|
26.1
|
1.0
|
O2G
|
C:GSP701
|
2.2
|
27.5
|
1.0
|
OG1
|
C:THR222
|
2.3
|
23.1
|
1.0
|
OD1
|
C:ASP356
|
3.0
|
23.2
|
1.0
|
NH2
|
D:ARG426
|
3.2
|
21.8
|
1.0
|
CB
|
C:THR222
|
3.3
|
23.1
|
1.0
|
PB
|
C:GSP701
|
3.5
|
27.5
|
1.0
|
PG
|
C:GSP701
|
3.5
|
27.5
|
1.0
|
CG
|
C:ASP356
|
3.8
|
23.2
|
1.0
|
O3B
|
C:GSP701
|
3.9
|
27.5
|
1.0
|
OD2
|
C:ASP356
|
3.9
|
23.2
|
1.0
|
CG2
|
C:THR222
|
4.0
|
23.1
|
1.0
|
O2A
|
C:GSP701
|
4.2
|
27.5
|
1.0
|
O3G
|
C:GSP701
|
4.3
|
27.5
|
1.0
|
O1B
|
C:GSP701
|
4.3
|
27.5
|
1.0
|
OE1
|
C:GLU357
|
4.4
|
24.8
|
1.0
|
NZ
|
D:LYS378
|
4.5
|
26.6
|
1.0
|
CG2
|
D:THR372
|
4.5
|
23.6
|
1.0
|
CZ
|
D:ARG426
|
4.5
|
21.8
|
1.0
|
O3A
|
C:GSP701
|
4.5
|
27.5
|
1.0
|
CA
|
C:THR222
|
4.6
|
23.1
|
1.0
|
N
|
C:THR222
|
4.7
|
23.1
|
1.0
|
S1G
|
C:GSP701
|
4.7
|
27.5
|
1.0
|
CD
|
C:GLU357
|
4.8
|
24.8
|
1.0
|
NH1
|
D:ARG425
|
4.8
|
22.7
|
1.0
|
PA
|
C:GSP701
|
4.8
|
27.5
|
1.0
|
OG1
|
C:THR408
|
4.9
|
21.9
|
1.0
|
CG
|
C:GLU357
|
4.9
|
24.8
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6ut4
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Magnesium Binding Sites List in 6ut4
Magnesium binding site 4 out
of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg702
b:29.4
occ:1.00
|
O2B
|
D:GSP701
|
2.1
|
40.5
|
1.0
|
O
|
D:HOH802
|
2.1
|
23.5
|
1.0
|
OG1
|
D:THR222
|
2.1
|
22.8
|
1.0
|
O
|
D:HOH801
|
2.1
|
30.2
|
1.0
|
O2G
|
D:GSP701
|
2.2
|
40.5
|
1.0
|
OD2
|
D:ASP356
|
2.9
|
21.8
|
1.0
|
OD1
|
D:ASP356
|
3.0
|
21.8
|
1.0
|
OE2
|
D:GLU357
|
3.1
|
23.2
|
1.0
|
CB
|
D:THR222
|
3.3
|
22.8
|
1.0
|
CG
|
D:ASP356
|
3.4
|
21.8
|
1.0
|
PB
|
D:GSP701
|
3.4
|
40.5
|
1.0
|
PG
|
D:GSP701
|
3.6
|
40.5
|
1.0
|
NH2
|
E:ARG426
|
3.6
|
21.3
|
1.0
|
O1B
|
D:GSP701
|
3.8
|
40.5
|
1.0
|
CG2
|
D:THR222
|
3.9
|
22.8
|
1.0
|
O3B
|
D:GSP701
|
4.0
|
40.5
|
1.0
|
CD
|
D:GLU357
|
4.2
|
23.2
|
1.0
|
OG1
|
D:THR408
|
4.2
|
19.6
|
1.0
|
O3G
|
D:GSP701
|
4.3
|
40.5
|
1.0
|
CA
|
D:THR222
|
4.5
|
22.8
|
1.0
|
O1A
|
D:GSP701
|
4.6
|
40.5
|
1.0
|
N
|
D:THR222
|
4.6
|
22.8
|
1.0
|
CG
|
D:GLU357
|
4.6
|
23.2
|
1.0
|
O3A
|
D:GSP701
|
4.7
|
40.5
|
1.0
|
OG1
|
E:THR372
|
4.7
|
21.9
|
1.0
|
S1G
|
D:GSP701
|
4.7
|
40.5
|
1.0
|
NZ
|
E:LYS378
|
4.8
|
28.2
|
1.0
|
CZ
|
E:ARG426
|
4.9
|
21.3
|
1.0
|
CB
|
D:ASP356
|
4.9
|
21.8
|
1.0
|
O2A
|
D:GSP701
|
5.0
|
40.5
|
1.0
|
PA
|
D:GSP701
|
5.0
|
40.5
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6ut4
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Magnesium Binding Sites List in 6ut4
Magnesium binding site 5 out
of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg702
b:24.0
occ:1.00
|
O
|
E:HOH801
|
2.1
|
21.0
|
1.0
|
OG1
|
E:THR222
|
2.1
|
21.1
|
1.0
|
O2G
|
E:GSP701
|
2.1
|
27.6
|
1.0
|
O
|
F:HOH801
|
2.2
|
24.6
|
1.0
|
OD2
|
E:ASP356
|
2.6
|
21.5
|
1.0
|
O2B
|
E:GSP701
|
2.8
|
27.6
|
1.0
|
OE2
|
E:GLU357
|
3.3
|
22.7
|
1.0
|
CB
|
E:THR222
|
3.3
|
21.1
|
1.0
|
NH2
|
F:ARG426
|
3.4
|
26.1
|
1.0
|
CG
|
E:ASP356
|
3.6
|
21.5
|
1.0
|
PG
|
E:GSP701
|
3.6
|
27.6
|
1.0
|
OD1
|
E:ASP356
|
3.8
|
21.5
|
1.0
|
CG2
|
E:THR222
|
4.0
|
21.1
|
1.0
|
PB
|
E:GSP701
|
4.1
|
27.6
|
1.0
|
O3G
|
E:GSP701
|
4.3
|
27.6
|
1.0
|
O3B
|
E:GSP701
|
4.3
|
27.6
|
1.0
|
CD
|
E:GLU357
|
4.4
|
22.7
|
1.0
|
O2A
|
E:GSP701
|
4.5
|
27.6
|
1.0
|
CA
|
E:THR222
|
4.5
|
21.1
|
1.0
|
N
|
E:THR222
|
4.5
|
21.1
|
1.0
|
CZ
|
F:ARG426
|
4.6
|
26.1
|
1.0
|
CG
|
E:GLU357
|
4.6
|
22.7
|
1.0
|
CG2
|
F:THR372
|
4.7
|
24.4
|
1.0
|
OG1
|
E:THR408
|
4.7
|
20.1
|
1.0
|
S1G
|
E:GSP701
|
4.7
|
27.6
|
1.0
|
CB
|
E:ASP356
|
5.0
|
21.5
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6ut4
Go back to
Magnesium Binding Sites List in 6ut4
Magnesium binding site 6 out
of 6 in the Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Cryo-Em Structure of the Asymmetric Aaa+ Domain Hexamer From Thermococcus Gammatolerans Mcrb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg702
b:32.9
occ:1.00
|
OG1
|
F:THR222
|
2.1
|
31.8
|
1.0
|
O2G
|
F:GSP701
|
2.1
|
36.6
|
1.0
|
O2B
|
F:GSP701
|
2.2
|
36.6
|
1.0
|
OD1
|
F:ASP356
|
2.8
|
31.2
|
1.0
|
OD2
|
F:ASP356
|
3.1
|
31.2
|
1.0
|
CG
|
F:ASP356
|
3.3
|
31.2
|
1.0
|
CB
|
F:THR222
|
3.3
|
31.8
|
1.0
|
PG
|
F:GSP701
|
3.4
|
36.6
|
1.0
|
PB
|
F:GSP701
|
3.5
|
36.6
|
1.0
|
O3B
|
F:GSP701
|
3.8
|
36.6
|
1.0
|
O3G
|
F:GSP701
|
3.8
|
36.6
|
1.0
|
CG2
|
F:THR222
|
4.0
|
31.8
|
1.0
|
O2A
|
F:GSP701
|
4.1
|
36.6
|
1.0
|
O1B
|
F:GSP701
|
4.3
|
36.6
|
1.0
|
OG1
|
F:THR408
|
4.4
|
29.2
|
1.0
|
N
|
F:THR222
|
4.5
|
31.8
|
1.0
|
CA
|
F:THR222
|
4.5
|
31.8
|
1.0
|
CG
|
F:GLU357
|
4.6
|
34.6
|
1.0
|
O3A
|
F:GSP701
|
4.6
|
36.6
|
1.0
|
PA
|
F:GSP701
|
4.7
|
36.6
|
1.0
|
S1G
|
F:GSP701
|
4.7
|
36.6
|
1.0
|
O1A
|
F:GSP701
|
4.7
|
36.6
|
1.0
|
CB
|
F:ASP356
|
4.8
|
31.2
|
1.0
|
|
Reference:
Y.Niu,
H.Suzuki,
C.J.Hosford,
T.Walz,
J.S.Chappie.
Structural Asymmetry Governs the Assembly and Gtpase Activity of Mcrbc Restriction Complexes To Be Published.
Page generated: Tue Oct 1 21:16:34 2024
|