Magnesium in PDB 4xvu: Structure of GET3 Bound to the Transmembrane Domain of NYV1

The structure of Structure of GET3 Bound to the Transmembrane Domain of NYV1, PDB code: 4xvu was solved by A.Mateja, M.Paduch, H.-Y.Chang, A.Szydlowska, A.A.Kossiakoff, R.S.Hegde, R.J.Keenan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.38 / 2.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	79.440, 109.230, 111.350, 63.05, 77.74, 70.17
R / Rfree (%)	19.7 / 23.4

The structure of Structure of GET3 Bound to the Transmembrane Domain of NYV1 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of GET3 Bound to the Transmembrane Domain of NYV1 (pdb code 4xvu). 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 GET3 Bound to the Transmembrane Domain of NYV1, PDB code: 4xvu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of GET3 Bound to the Transmembrane Domain of NYV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of GET3 Bound to the Transmembrane Domain of NYV1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:31.1 occ:1.00 O A:HOH516 2.1 36.6 1.0 O A:HOH504 2.1 29.3 1.0 OG1 A:THR32 2.1 28.5 1.0 O1G A:ATP401 2.2 42.4 1.0 O A:HOH515 2.2 29.5 1.0 O1B A:ATP401 2.2 32.2 1.0 HD22 A:ASN57 3.0 42.7 1.0 HD22 A:ASN61 3.2 54.9 1.0 CB A:THR32 3.3 32.2 1.0 HB A:THR32 3.3 38.7 1.0 PG A:ATP401 3.3 42.4 1.0 H A:THR32 3.3 36.0 1.0 PB A:ATP401 3.4 38.5 1.0 O3B A:ATP401 3.5 37.5 1.0 HB2 A:LYS31 3.7 36.6 1.0 HE2 A:LYS31 3.7 37.1 1.0 ND2 A:ASN57 3.8 35.6 1.0 HB2 A:ASN61 3.8 49.0 1.0 ND2 A:ASN61 3.9 45.7 1.0 N A:THR32 3.9 30.0 1.0 HD21 A:ASN57 4.0 42.7 1.0 OD1 A:ASP166 4.0 43.9 1.0 CA A:THR32 4.1 31.0 1.0 O2G A:ATP401 4.1 43.5 1.0 OD2 A:ASP166 4.1 40.4 1.0 O2B A:ATP401 4.2 33.4 1.0 HA A:THR32 4.3 37.2 1.0 HZ1 B:LYS26 4.3 44.2 1.0 HD21 A:ASN61 4.3 54.9 1.0 O A:HOH531 4.3 34.4 1.0 HG21 A:THR32 4.4 41.9 1.0 O3G A:ATP401 4.4 39.8 1.0 O2A A:ATP401 4.4 34.4 1.0 CG2 A:THR32 4.4 34.9 1.0 CG A:ASP166 4.5 42.0 1.0 HZ3 B:LYS26 4.6 44.2 1.0 CB A:ASN61 4.6 40.8 1.0 O3A A:ATP401 4.6 33.1 1.0 CB A:LYS31 4.6 30.5 1.0 CG A:ASN61 4.7 45.0 1.0 CE A:LYS31 4.7 30.9 1.0 HG23 A:THR32 4.7 41.9 1.0 HB3 A:ASN57 4.7 44.2 1.0 HB3 A:LYS31 4.8 36.6 1.0 HB2 A:ASN57 4.8 44.2 1.0 NZ B:LYS26 4.9 36.8 1.0 HZ1 A:LYS31 4.9 37.6 1.0 CG A:ASN57 4.9 36.4 1.0 O A:THR167 4.9 38.7 1.0 C A:LYS31 4.9 32.2 1.0 PA A:ATP401 5.0 39.1 1.0 HB3 A:ASN61 5.0 49.0 1.0

Magnesium binding site 2 out of 4 in the Structure of GET3 Bound to the Transmembrane Domain of NYV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of GET3 Bound to the Transmembrane Domain of NYV1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:35.8 occ:1.00 O B:HOH542 1.9 35.6 1.0 O B:HOH519 2.1 30.8 1.0 OG1 B:THR32 2.1 30.1 1.0 O3G B:ATP401 2.2 32.5 1.0 O2B B:ATP401 2.2 29.1 1.0 O B:HOH518 2.2 26.6 1.0 PG B:ATP401 3.2 36.6 1.0 CB B:THR32 3.3 28.9 1.0 HB B:THR32 3.3 34.6 1.0 H B:THR32 3.3 32.1 1.0 PB B:ATP401 3.3 37.4 1.0 HD22 B:ASN57 3.4 40.7 1.0 O3B B:ATP401 3.5 30.1 1.0 O B:HOH575 3.5 42.9 1.0 HB2 B:ASN61 3.6 43.4 1.0 HB2 B:LYS31 3.7 32.7 1.0 N B:THR32 3.8 26.7 1.0 HE2 B:LYS31 3.9 33.7 1.0 O1G B:ATP401 3.9 35.8 1.0 OD1 B:ASN61 4.0 42.8 1.0 OD1 B:ASP166 4.0 31.0 1.0 CA B:THR32 4.1 27.0 1.0 O1A B:ATP401 4.1 25.6 1.0 ND2 B:ASN57 4.1 33.9 1.0 HZ1 A:LYS26 4.1 53.4 1.0 OD2 B:ASP166 4.2 32.8 1.0 O1B B:ATP401 4.2 29.4 1.0 O B:HOH543 4.2 27.6 1.0 HD21 B:ASN57 4.3 40.7 1.0 HA B:THR32 4.3 32.4 1.0 HG21 B:THR32 4.3 33.1 1.0 CG2 B:THR32 4.4 27.6 1.0 CB B:ASN61 4.4 36.2 1.0 O2G B:ATP401 4.4 27.6 1.0 O3A B:ATP401 4.5 28.8 1.0 CG B:ASP166 4.5 31.0 1.0 HZ3 A:LYS26 4.6 53.4 1.0 CG B:ASN61 4.6 39.9 1.0 CB B:LYS31 4.6 27.2 1.0 HZ1 B:LYS31 4.7 35.7 1.0 HG23 B:THR32 4.7 33.1 1.0 HB3 B:ASN61 4.7 43.4 1.0 O2A B:ATP401 4.7 31.9 1.0 PA B:ATP401 4.7 36.4 1.0 NZ A:LYS26 4.8 44.5 1.0 CE B:LYS31 4.8 28.1 1.0 HB3 B:LYS31 4.8 32.7 1.0 HZ3 B:LYS31 4.8 35.7 1.0 C B:LYS31 4.9 25.5 1.0 H B:LYS31 4.9 32.4 1.0 HB3 B:ASN57 4.9 40.8 1.0 HE2 A:LYS26 4.9 53.0 1.0 NZ B:LYS31 5.0 29.8 1.0

Magnesium binding site 3 out of 4 in the Structure of GET3 Bound to the Transmembrane Domain of NYV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of GET3 Bound to the Transmembrane Domain of NYV1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:42.4 occ:1.00 O G:HOH521 2.1 35.1 1.0 O3G G:ATP401 2.1 60.7 1.0 OG1 G:THR32 2.1 31.5 1.0 O G:HOH554 2.2 28.8 1.0 O2B G:ATP401 2.2 51.4 1.0 O G:HOH581 2.3 32.2 1.0 PG G:ATP401 3.2 62.1 1.0 CB G:THR32 3.3 30.4 1.0 HB G:THR32 3.3 36.5 1.0 H G:THR32 3.3 36.1 1.0 PB G:ATP401 3.4 53.4 1.0 O3B G:ATP401 3.5 68.1 1.0 HD22 G:ASN57 3.5 47.8 1.0 HB2 G:LYS31 3.7 32.9 1.0 HB2 G:ASN61 3.7 51.1 1.0 HE2 G:LYS31 3.8 35.5 1.0 N G:THR32 3.8 30.1 1.0 O1G G:ATP401 3.9 61.1 1.0 CA G:THR32 4.0 29.1 1.0 OD2 G:ASP166 4.0 31.9 1.0 ND2 G:ASN57 4.1 39.9 1.0 O1A G:ATP401 4.1 40.2 1.0 OD1 G:ASP166 4.1 35.5 1.0 OD1 G:ASN61 4.2 48.4 1.0 HZ1 H:LYS26 4.2 58.8 1.0 HD21 G:ASN57 4.2 47.8 1.0 O1B G:ATP401 4.3 54.1 1.0 HA G:THR32 4.3 34.9 1.0 O2G G:ATP401 4.3 60.9 1.0 O G:HOH518 4.4 28.3 1.0 HG21 G:THR32 4.4 35.8 1.0 CG2 G:THR32 4.4 29.8 1.0 CG G:ASP166 4.5 32.4 1.0 CB G:LYS31 4.5 27.4 1.0 CB G:ASN61 4.5 42.6 1.0 O3A G:ATP401 4.6 49.3 1.0 HB3 G:LYS31 4.7 32.9 1.0 CE G:LYS31 4.7 29.6 1.0 HZ3 H:LYS26 4.7 58.8 1.0 CG G:ASN61 4.7 45.7 1.0 HG23 G:THR32 4.7 35.8 1.0 PA G:ATP401 4.8 43.6 1.0 HB3 G:ASN61 4.8 51.1 1.0 C G:LYS31 4.8 28.4 1.0 HZ1 G:LYS31 4.8 35.5 1.0 NZ H:LYS26 4.9 49.0 1.0 O2A G:ATP401 4.9 42.4 1.0 HE2 H:LYS26 4.9 57.8 1.0 H G:LYS31 4.9 33.9 1.0 HB2 G:ASN57 5.0 43.8 1.0 HB3 G:ASN57 5.0 43.8 1.0 HZ3 G:LYS31 5.0 35.5 1.0

Magnesium binding site 4 out of 4 in the Structure of GET3 Bound to the Transmembrane Domain of NYV1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of GET3 Bound to the Transmembrane Domain of NYV1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg402 b:37.9 occ:1.00 O H:HOH518 2.0 43.2 1.0 O H:HOH546 2.0 40.6 1.0 OG1 H:THR32 2.1 40.0 1.0 O1G H:ATP401 2.2 39.7 1.0 O1B H:ATP401 2.3 36.7 1.0 O H:HOH515 2.3 36.3 1.0 HD22 H:ASN57 3.2 42.5 1.0 HZ2 H:LYS31 3.3 58.7 1.0 PG H:ATP401 3.3 40.5 1.0 CB H:THR32 3.3 37.6 1.0 PB H:ATP401 3.4 37.7 1.0 H H:THR32 3.4 42.0 1.0 HB H:THR32 3.5 45.1 1.0 O3B H:ATP401 3.5 42.6 1.0 HB2 H:ASN61 3.8 49.3 1.0 HZ1 H:LYS31 3.8 58.7 1.0 O H:HOH579 3.8 53.1 1.0 NZ H:LYS31 3.8 48.9 1.0 HZ3 H:LYS31 3.9 58.7 1.0 OD1 H:ASN61 3.9 43.9 1.0 O2G H:ATP401 3.9 41.1 1.0 ND2 H:ASN57 4.0 35.4 1.0 HB2 H:LYS31 4.0 46.0 1.0 N H:THR32 4.0 35.0 1.0 OD2 H:ASP166 4.1 39.0 1.0 OD1 H:ASP166 4.1 40.1 1.0 O2A H:ATP401 4.2 36.9 1.0 CA H:THR32 4.2 35.5 1.0 HD21 H:ASN57 4.2 42.5 1.0 O H:HOH526 4.3 25.8 1.0 O2B H:ATP401 4.3 35.7 1.0 HG21 H:THR32 4.3 44.0 1.0 HA H:THR32 4.4 42.6 1.0 CG2 H:THR32 4.4 36.6 1.0 O3G H:ATP401 4.5 38.8 1.0 CG H:ASP166 4.5 39.1 1.0 CB H:ASN61 4.6 41.1 1.0 O3A H:ATP401 4.6 35.8 1.0 HZ1 G:LYS26 4.6 53.8 1.0 HG23 H:THR32 4.6 44.0 1.0 CG H:ASN61 4.7 43.4 1.0 HE2 G:LYS26 4.7 53.9 1.0 PA H:ATP401 4.8 38.0 1.0 O1A H:ATP401 4.8 37.4 1.0 CB H:LYS31 4.9 38.4 1.0 HB2 H:ASN57 4.9 42.5 1.0 HB3 H:ASN57 4.9 42.5 1.0 O H:THR167 4.9 37.8 1.0 HB3 H:ASN61 5.0 49.3 1.0

A.Mateja, M.Paduch, H.Y.Chang, A.Szydlowska, A.A.Kossiakoff, R.S.Hegde, R.J.Keenan. Protein Targeting. Structure of the GET3 Targeting Factor in Complex with Its Membrane Protein Cargo. Science V. 347 1152 2015.
ISSN: ESSN 1095-9203
PubMed: 25745174
DOI: 10.1126/SCIENCE.1261671