Magnesium in PDB 4tq3: Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+

The structure of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+, PDB code: 4tq3 was solved by H.Huang, E.J.Levin, Y.Bai, M.Zhou, New York Consortium On Membraneprotein Structure (Nycomps), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.34 / 2.41
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.605, 218.922, 65.292, 90.00, 90.13, 90.00
R / Rfree (%)	22.1 / 25.5

The binding sites of Magnesium atom in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ (pdb code 4tq3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+, PDB code: 4tq3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:46.6 occ:1.00 OD2 A:ASP72 2.0 47.6 1.0 OD1 A:ASN68 2.2 42.6 1.0 O2B A:GPP401 2.3 46.6 1.0 O1A A:GPP401 2.6 47.8 1.0 CG A:ASP72 3.1 49.0 1.0 CG A:ASN68 3.3 43.1 1.0 PB A:GPP401 3.5 48.4 1.0 OD2 A:ASP76 3.7 54.9 1.0 CB A:ASP72 3.7 46.5 1.0 O3B A:GPP401 3.8 52.0 1.0 ND2 A:ASN68 3.8 42.1 1.0 PA A:GPP401 3.8 50.9 1.0 NH1 A:ARG22 3.9 45.3 1.0 OD1 A:ASP76 4.0 56.5 1.0 O3A A:GPP401 4.1 49.5 1.0 OD1 A:ASP72 4.2 49.1 1.0 CG A:ASP76 4.3 59.8 1.0 CD1 A:LEU88 4.3 62.5 1.0 NZ A:LYS146 4.4 47.2 1.0 O A:ASN68 4.5 45.3 1.0 CB A:ASN68 4.5 40.4 1.0 C1 A:GPP401 4.6 42.6 1.0 O1 A:GPP401 4.6 46.8 1.0 C A:ASN68 4.6 43.1 1.0 O1B A:GPP401 4.8 49.1 1.0 N A:ALA69 5.0 44.6 1.0

Magnesium binding site 2 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:56.0 occ:1.00 O A:HOH508 2.0 38.8 1.0 O A:HOH509 2.0 46.9 1.0 OD2 A:ASP198 2.1 48.4 1.0 O A:HOH510 2.4 46.4 1.0 OD1 A:ASP202 2.8 50.8 1.0 CG A:ASP198 3.3 47.1 1.0 OD2 A:ASP202 3.5 46.9 1.0 O2A A:GPP401 3.5 48.4 1.0 CG A:ASP202 3.5 47.8 1.0 O3B A:GPP401 4.0 52.0 1.0 CB A:ASP198 4.1 45.9 1.0 O3A A:GPP401 4.1 49.5 1.0 OD1 A:ASP198 4.3 44.2 1.0 O A:HOH504 4.3 49.0 1.0 PA A:GPP401 4.5 50.9 1.0 PB A:GPP401 4.6 48.4 1.0 CD1 A:LEU207 4.8 45.4 1.0 CD2 A:PHE201 4.9 56.2 1.0 ND2 A:ASN209 4.9 36.2 1.0

Magnesium binding site 3 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:49.5 occ:1.00 OD2 B:ASP72 1.9 46.1 1.0 OD1 B:ASN68 2.0 45.3 1.0 O2B B:GPP401 2.2 45.5 1.0 O1A B:GPP401 2.5 48.3 1.0 CG B:ASN68 3.0 43.4 1.0 CG B:ASP72 3.0 49.2 1.0 PB B:GPP401 3.4 50.4 1.0 ND2 B:ASN68 3.4 39.3 1.0 CB B:ASP72 3.6 49.3 1.0 PA B:GPP401 3.7 50.0 1.0 O3B B:GPP401 3.8 50.2 1.0 OD2 B:ASP76 3.9 60.9 1.0 O3A B:GPP401 4.0 49.9 1.0 OD1 B:ASP72 4.1 46.5 1.0 NH1 B:ARG22 4.2 47.9 1.0 NZ B:LYS146 4.2 41.1 1.0 OD1 B:ASP76 4.2 59.4 1.0 CD1 B:LEU88 4.3 59.7 1.0 O B:ASN68 4.3 36.4 1.0 CB B:ASN68 4.3 34.9 1.0 C1 B:GPP401 4.4 46.0 1.0 O1 B:GPP401 4.4 50.3 1.0 CG B:ASP76 4.5 63.1 1.0 C B:ASN68 4.5 39.1 1.0 O1B B:GPP401 4.7 47.2 1.0 O2A B:GPP401 5.0 60.1 1.0 N B:ALA69 5.0 38.1 1.0 CA B:ASN68 5.0 36.4 1.0

Magnesium binding site 4 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:61.2 occ:1.00 OD2 B:ASP198 2.5 51.5 1.0 OD1 B:ASP202 3.0 54.9 1.0 O2A B:GPP401 3.2 60.1 1.0 OD2 B:ASP202 3.6 47.6 1.0 CG B:ASP198 3.6 56.6 1.0 CG B:ASP202 3.7 50.4 1.0 O3A B:GPP401 3.8 49.9 1.0 O3B B:GPP401 4.1 50.2 1.0 PA B:GPP401 4.2 50.0 1.0 CB B:ASP198 4.3 47.2 1.0 CD1 B:LEU207 4.5 49.5 1.0 OD1 B:ASP198 4.6 59.5 1.0 PB B:GPP401 4.7 50.4 1.0 ND2 B:ASN209 4.8 45.1 1.0 CD2 B:PHE201 4.9 63.3 1.0

Magnesium binding site 5 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:55.6 occ:1.00 O C:HOH501 2.4 45.1 1.0 OD2 C:ASP198 2.4 49.2 1.0 OD1 C:ASP202 2.7 49.7 1.0 O2A C:GPP401 3.0 54.2 1.0 OD2 C:ASP202 3.4 51.2 1.0 CG C:ASP202 3.4 49.6 1.0 CG C:ASP198 3.6 50.8 1.0 CB C:ASP198 4.2 44.5 1.0 PA C:GPP401 4.3 40.6 1.0 O3A C:GPP401 4.3 49.0 1.0 O3B C:GPP401 4.3 55.5 1.0 CD1 C:LEU207 4.5 43.8 1.0 ND2 C:ASN209 4.5 37.2 1.0 OD1 C:ASP198 4.6 54.8 1.0 CB C:ASP202 4.9 49.0 1.0

Magnesium binding site 6 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:48.8 occ:1.00 OD2 C:ASP72 1.9 46.8 1.0 OD1 C:ASN68 2.0 39.4 1.0 O2B C:GPP401 2.1 50.8 1.0 O1A C:GPP401 2.4 49.1 1.0 CG C:ASN68 3.0 38.3 1.0 CG C:ASP72 3.1 48.9 1.0 PB C:GPP401 3.4 49.4 1.0 ND2 C:ASN68 3.5 40.0 1.0 PA C:GPP401 3.6 40.6 1.0 CB C:ASP72 3.7 47.8 1.0 O3B C:GPP401 3.8 55.5 1.0 O3A C:GPP401 3.8 49.0 1.0 OD2 C:ASP76 3.9 57.6 1.0 NH1 C:ARG22 4.0 49.0 1.0 OD1 C:ASP72 4.1 46.1 1.0 OD1 C:ASP76 4.1 53.1 1.0 NZ C:LYS146 4.1 45.1 1.0 CD1 C:LEU88 4.3 62.8 1.0 O C:ASN68 4.3 40.7 1.0 CB C:ASN68 4.3 36.5 1.0 C1 C:GPP401 4.4 41.8 1.0 O1 C:GPP401 4.4 44.9 1.0 CG C:ASP76 4.5 58.3 1.0 C C:ASN68 4.6 39.6 1.0 O1B C:GPP401 4.6 48.6 1.0 O2A C:GPP401 4.8 54.2 1.0

Magnesium binding site 7 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:45.1 occ:1.00 OD2 D:ASP72 2.1 49.3 1.0 O2B D:GPP401 2.1 52.3 1.0 OD1 D:ASN68 2.2 43.4 1.0 O1A D:GPP401 2.6 41.6 1.0 CG D:ASP72 3.1 47.4 1.0 CG D:ASN68 3.2 44.8 1.0 PB D:GPP401 3.5 51.4 1.0 CB D:ASP72 3.7 46.4 1.0 ND2 D:ASN68 3.7 40.2 1.0 PA D:GPP401 3.8 43.1 1.0 O3B D:GPP401 3.9 56.1 1.0 NH1 D:ARG22 3.9 47.1 1.0 OD2 D:ASP76 3.9 57.1 1.0 OD1 D:ASP76 4.0 59.2 1.0 CD1 D:LEU88 4.0 63.9 1.0 O3A D:GPP401 4.1 46.5 1.0 OD1 D:ASP72 4.2 45.2 1.0 NZ D:LYS146 4.2 41.9 1.0 O D:ASN68 4.4 42.1 1.0 CG D:ASP76 4.4 62.7 1.0 C1 D:GPP401 4.4 43.3 1.0 O1 D:GPP401 4.5 48.9 1.0 CB D:ASN68 4.5 42.3 1.0 O1B D:GPP401 4.7 44.5 1.0 C D:ASN68 4.7 45.1 1.0

Magnesium binding site 8 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Gpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:63.7 occ:1.00 OD2 D:ASP198 2.1 58.0 1.0 OD1 D:ASP202 2.4 59.3 1.0 CG D:ASP202 3.2 54.6 1.0 CG D:ASP198 3.3 57.8 1.0 O2A D:GPP401 3.3 52.7 1.0 OD2 D:ASP202 3.4 57.7 1.0 O3B D:GPP401 3.6 56.1 1.0 O3A D:GPP401 4.1 46.5 1.0 CD1 D:LEU207 4.1 47.4 1.0 OD1 D:ASP198 4.2 58.8 1.0 PA D:GPP401 4.2 43.1 1.0 CB D:ASP198 4.3 49.9 1.0 CD2 D:PHE201 4.5 62.6 1.0 PB D:GPP401 4.5 51.4 1.0 O D:HOH502 4.6 40.5 1.0 CE2 D:PHE201 4.6 67.1 1.0 CB D:ASP202 4.6 52.8 1.0 O1A D:GPP401 4.8 41.6 1.0 ND2 D:ASN209 4.8 39.0 1.0

H.Huang, E.J.Levin, S.Liu, Y.Bai, S.W.Lockless, M.Zhou. Structure of A Membrane-Embedded Prenyltransferase Homologous to UBIAD1. Plos Biol. V. 12 01911 2014.
ISSN: ESSN 1545-7885
PubMed: 25051182
DOI: 10.1371/JOURNAL.PBIO.1001911