Magnesium in PDB 6d84: Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer
(pdb code 6d84). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer, PDB code: 6d84:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6d84
Go back to
Magnesium Binding Sites List in 6d84
Magnesium binding site 1 out
of 4 in the Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1002
b:0.2
occ:1.00
|
O2G
|
C:GTP1001
|
1.9
|
0.4
|
1.0
|
O2B
|
C:GTP1001
|
2.2
|
0.4
|
1.0
|
OG1
|
C:THR31
|
2.4
|
0.6
|
1.0
|
CG2
|
C:THR48
|
2.4
|
0.4
|
1.0
|
CG2
|
C:THR31
|
2.5
|
0.6
|
1.0
|
OG1
|
C:THR48
|
2.6
|
0.4
|
1.0
|
PG
|
C:GTP1001
|
2.8
|
0.4
|
1.0
|
O1G
|
C:GTP1001
|
2.8
|
0.4
|
1.0
|
CB
|
C:THR31
|
3.0
|
0.6
|
1.0
|
CB
|
C:THR48
|
3.1
|
0.4
|
1.0
|
O2A
|
C:GTP1001
|
3.3
|
0.4
|
1.0
|
PB
|
C:GTP1001
|
3.4
|
0.4
|
1.0
|
O3B
|
C:GTP1001
|
3.6
|
0.4
|
1.0
|
N
|
C:THR48
|
3.9
|
0.4
|
1.0
|
PA
|
C:GTP1001
|
4.0
|
0.4
|
1.0
|
O3A
|
C:GTP1001
|
4.1
|
0.4
|
1.0
|
N
|
C:THR31
|
4.1
|
0.6
|
1.0
|
O3G
|
C:GTP1001
|
4.1
|
0.4
|
1.0
|
O1A
|
C:GTP1001
|
4.1
|
0.4
|
1.0
|
CA
|
C:THR48
|
4.1
|
0.4
|
1.0
|
CA
|
C:THR31
|
4.1
|
0.6
|
1.0
|
OD2
|
C:ASP67
|
4.2
|
0.1
|
1.0
|
O
|
C:ILE46
|
4.3
|
0.4
|
1.0
|
CG2
|
C:THR45
|
4.4
|
0.4
|
1.0
|
OD1
|
C:ASN52
|
4.5
|
0.7
|
1.0
|
NZ
|
C:LYS30
|
4.6
|
0.1
|
1.0
|
O1B
|
C:GTP1001
|
4.6
|
0.4
|
1.0
|
CG
|
C:LYS30
|
4.8
|
0.1
|
1.0
|
CG
|
C:ASP67
|
4.9
|
0.1
|
1.0
|
OD1
|
C:ASP67
|
4.9
|
0.1
|
1.0
|
CE
|
C:LYS30
|
4.9
|
0.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6d84
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Magnesium Binding Sites List in 6d84
Magnesium binding site 2 out
of 4 in the Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg1002
b:0.9
occ:1.00
|
O2G
|
H:GTP1001
|
1.9
|
0.5
|
1.0
|
O1G
|
H:GTP1001
|
2.0
|
0.5
|
1.0
|
CG2
|
H:THR31
|
2.2
|
0.6
|
1.0
|
PG
|
H:GTP1001
|
2.2
|
0.5
|
1.0
|
O1B
|
H:GTP1001
|
2.2
|
0.5
|
1.0
|
OG1
|
H:THR31
|
2.3
|
0.6
|
1.0
|
OG1
|
H:THR48
|
2.6
|
0.4
|
1.0
|
CB
|
H:THR31
|
2.8
|
0.6
|
1.0
|
PB
|
H:GTP1001
|
2.9
|
0.5
|
1.0
|
O3B
|
H:GTP1001
|
2.9
|
0.5
|
1.0
|
O3A
|
H:GTP1001
|
3.2
|
0.5
|
1.0
|
O3G
|
H:GTP1001
|
3.6
|
0.5
|
1.0
|
CG2
|
H:THR48
|
3.7
|
0.4
|
1.0
|
CB
|
H:THR48
|
3.7
|
0.4
|
1.0
|
N
|
H:THR31
|
3.8
|
0.6
|
1.0
|
CA
|
H:THR31
|
3.9
|
0.6
|
1.0
|
O1A
|
H:GTP1001
|
4.0
|
0.5
|
1.0
|
N
|
H:THR48
|
4.2
|
0.4
|
1.0
|
PA
|
H:GTP1001
|
4.2
|
0.5
|
1.0
|
O2B
|
H:GTP1001
|
4.3
|
0.5
|
1.0
|
CG
|
H:LYS30
|
4.3
|
0.8
|
1.0
|
CG2
|
H:THR45
|
4.4
|
0.1
|
1.0
|
O
|
H:ILE46
|
4.5
|
0.3
|
1.0
|
CA
|
H:THR48
|
4.6
|
0.4
|
1.0
|
OD2
|
H:ASP67
|
4.8
|
0.3
|
1.0
|
C
|
H:LYS30
|
4.9
|
0.8
|
1.0
|
O2A
|
H:GTP1001
|
5.0
|
0.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6d84
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Magnesium Binding Sites List in 6d84
Magnesium binding site 3 out
of 4 in the Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Mg1002
b:0.1
occ:1.00
|
O2G
|
I:GTP1001
|
1.9
|
0.0
|
1.0
|
CG2
|
I:THR48
|
2.1
|
0.5
|
1.0
|
O1B
|
I:GTP1001
|
2.2
|
0.0
|
1.0
|
OG1
|
I:THR31
|
2.4
|
0.7
|
1.0
|
CG2
|
I:THR31
|
2.6
|
0.7
|
1.0
|
OG1
|
I:THR48
|
2.6
|
0.5
|
1.0
|
PG
|
I:GTP1001
|
2.9
|
0.0
|
1.0
|
CB
|
I:THR48
|
2.9
|
0.5
|
1.0
|
O3G
|
I:GTP1001
|
3.0
|
0.0
|
1.0
|
CB
|
I:THR31
|
3.0
|
0.7
|
1.0
|
PB
|
I:GTP1001
|
3.4
|
0.0
|
1.0
|
O1A
|
I:GTP1001
|
3.6
|
0.0
|
1.0
|
O3B
|
I:GTP1001
|
3.6
|
0.0
|
1.0
|
N
|
I:THR48
|
3.9
|
0.5
|
1.0
|
O3A
|
I:GTP1001
|
3.9
|
0.0
|
1.0
|
CA
|
I:THR48
|
4.0
|
0.5
|
1.0
|
PA
|
I:GTP1001
|
4.1
|
0.0
|
1.0
|
O1G
|
I:GTP1001
|
4.2
|
0.0
|
1.0
|
N
|
I:THR31
|
4.2
|
0.7
|
1.0
|
O
|
I:ILE46
|
4.2
|
0.2
|
1.0
|
CA
|
I:THR31
|
4.2
|
0.7
|
1.0
|
O2A
|
I:GTP1001
|
4.2
|
0.0
|
1.0
|
CG2
|
I:THR45
|
4.2
|
0.3
|
1.0
|
OD2
|
I:ASP67
|
4.3
|
0.9
|
1.0
|
OD1
|
I:ASN52
|
4.6
|
0.0
|
1.0
|
O2B
|
I:GTP1001
|
4.6
|
0.0
|
1.0
|
NZ
|
I:LYS30
|
4.9
|
0.6
|
1.0
|
CG
|
I:LYS30
|
4.9
|
0.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6d84
Go back to
Magnesium Binding Sites List in 6d84
Magnesium binding site 4 out
of 4 in the Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Mg1002
b:0.6
occ:1.01
|
O3G
|
N:GTP1001
|
1.9
|
0.9
|
1.0
|
O2G
|
N:GTP1001
|
1.9
|
0.9
|
1.0
|
CG2
|
N:THR31
|
2.1
|
0.1
|
1.0
|
PG
|
N:GTP1001
|
2.1
|
0.9
|
1.0
|
O2B
|
N:GTP1001
|
2.2
|
0.9
|
1.0
|
OG1
|
N:THR31
|
2.3
|
0.1
|
1.0
|
OG1
|
N:THR48
|
2.6
|
0.0
|
1.0
|
CB
|
N:THR31
|
2.7
|
0.1
|
1.0
|
PB
|
N:GTP1001
|
2.9
|
0.9
|
1.0
|
O3B
|
N:GTP1001
|
2.9
|
0.9
|
1.0
|
O3A
|
N:GTP1001
|
3.2
|
0.9
|
1.0
|
O1G
|
N:GTP1001
|
3.5
|
0.9
|
1.0
|
CG2
|
N:THR48
|
3.6
|
0.0
|
1.0
|
CB
|
N:THR48
|
3.7
|
0.0
|
1.0
|
N
|
N:THR31
|
3.9
|
0.1
|
1.0
|
CA
|
N:THR31
|
3.9
|
0.1
|
1.0
|
CG2
|
N:THR45
|
4.2
|
0.7
|
1.0
|
O2A
|
N:GTP1001
|
4.2
|
0.9
|
1.0
|
N
|
N:THR48
|
4.3
|
0.0
|
1.0
|
O1B
|
N:GTP1001
|
4.3
|
0.9
|
1.0
|
PA
|
N:GTP1001
|
4.4
|
0.9
|
1.0
|
O
|
N:ILE46
|
4.5
|
0.7
|
1.0
|
CG
|
N:LYS30
|
4.5
|
0.8
|
1.0
|
CA
|
N:THR48
|
4.6
|
0.0
|
1.0
|
OD2
|
N:ASP67
|
4.8
|
0.3
|
1.0
|
|
Reference:
K.L.Morris,
C.Z.Buffalo,
C.M.Sturzel,
E.Heusinger,
F.Kirchhoff,
X.Ren,
J.H.Hurley.
Hiv-1 Nefs Are Cargo-Sensitive Ap-1 Trimerization Switches in Tetherin Downregulation. Cell V. 174 659 2018.
ISSN: ISSN 1097-4172
PubMed: 30053425
DOI: 10.1016/J.CELL.2018.07.004
Page generated: Mon Sep 30 22:56:08 2024
|