Magnesium in PDB 6d84: Structure of the Cargo Bound Ap-1:ARF1:Tetherin-Nef (L164A, L165A) Dileucine Mutant Dimer

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 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 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 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 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

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