Magnesium in PDB 4tq4: Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp and MG2+

The structure of Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp and MG2+, PDB code: 4tq4 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)	39.08 / 2.50
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 (%)	21.5 / 25.5

The binding sites of Magnesium atom in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp and MG2+ (pdb code 4tq4). 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 Dmapp and MG2+, PDB code: 4tq4:
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 Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:56.1 occ:1.00 O A:HOH511 2.1 53.0 1.0 OD2 A:ASP72 2.2 55.2 1.0 O2A A:DMA403 2.3 51.5 1.0 OD1 A:ASN68 2.3 45.9 1.0 O3B A:DMA403 2.3 57.1 1.0 O A:HOH512 2.4 59.2 1.0 PB A:DMA403 3.2 55.7 1.0 O1B A:DMA403 3.3 52.5 1.0 CG A:ASN68 3.3 47.7 1.0 CG A:ASP72 3.3 52.4 1.0 PA A:DMA403 3.6 52.6 1.0 ND2 A:ASN68 3.8 47.8 1.0 O3A A:DMA403 3.8 44.7 1.0 CB A:ASP72 3.8 54.0 1.0 NH1 A:ARG22 3.9 52.5 1.0 OD2 A:ASP76 4.0 61.3 1.0 OD1 A:ASP76 4.1 63.4 1.0 OD1 A:ASP72 4.4 49.8 1.0 O1 A:DMA403 4.4 47.0 1.0 NZ A:LYS146 4.4 50.2 1.0 CG A:ASP76 4.5 63.1 1.0 CD1 A:LEU88 4.5 60.6 1.0 C1 A:DMA403 4.6 46.8 1.0 O2B A:DMA403 4.6 52.9 1.0 CB A:ASN68 4.6 46.2 1.0 O A:ASN68 4.6 48.8 1.0 O1A A:DMA403 4.8 54.6 1.0 O A:HOH507 4.8 58.5 1.0 C A:ASN68 4.8 44.3 1.0

Magnesium binding site 2 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:54.4 occ:1.00 O A:HOH508 1.9 48.0 1.0 OD2 A:ASP198 2.2 55.8 1.0 O A:HOH507 2.2 58.5 1.0 OD1 A:ASP202 2.2 58.8 1.0 O A:HOH510 2.3 50.0 1.0 O A:HOH509 2.4 54.8 1.0 CG A:ASP202 3.0 58.2 1.0 OD2 A:ASP202 3.1 57.0 1.0 O1A A:DMA403 3.3 54.6 1.0 CG A:ASP198 3.4 56.1 1.0 CB A:ASP198 4.1 52.4 1.0 O3A A:DMA403 4.2 44.7 1.0 CD1 A:LEU207 4.3 48.7 1.0 OD1 A:ASP198 4.3 54.7 1.0 PA A:DMA403 4.4 52.6 1.0 O1B A:DMA403 4.4 52.5 1.0 CB A:ASP202 4.5 49.9 1.0 CD2 A:PHE201 4.5 63.1 1.0 NZ A:LYS84 4.7 62.8 1.0 O A:ASP198 4.8 50.6 1.0 ND2 A:ASN209 4.9 50.7 1.0 CE2 A:PHE201 5.0 60.5 1.0 CA A:ASP202 5.0 54.8 1.0 PB A:DMA403 5.0 55.7 1.0

Magnesium binding site 3 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:60.7 occ:1.00 OD2 B:ASP72 2.0 53.0 1.0 OD1 B:ASN68 2.1 47.8 1.0 O3B B:DMA403 2.6 64.6 1.0 O2A B:DMA403 2.7 63.2 1.0 CG B:ASP72 3.1 55.6 1.0 CG B:ASN68 3.1 47.2 1.0 CB B:ASP72 3.5 60.4 1.0 OD2 B:ASP76 3.6 74.6 1.0 ND2 B:ASN68 3.6 51.3 1.0 PB B:DMA403 3.8 65.4 1.0 PA B:DMA403 3.9 56.9 1.0 O1B B:DMA403 3.9 63.4 1.0 OD1 B:ASP76 4.0 75.3 1.0 NZ B:LYS146 4.1 52.2 1.0 OD1 B:ASP72 4.2 53.8 1.0 CG B:ASP76 4.2 75.2 1.0 O B:ASN68 4.2 44.6 1.0 NH1 B:ARG22 4.2 54.5 1.0 O1 B:DMA403 4.2 60.6 1.0 O3A B:DMA403 4.3 67.1 1.0 CB B:ASN68 4.4 46.7 1.0 C B:ASN68 4.5 44.6 1.0 CD1 B:LEU88 4.7 77.2 1.0 N B:ALA69 4.9 49.1 1.0 CA B:ASN68 5.0 44.3 1.0 CA B:ASP72 5.0 61.1 1.0

Magnesium binding site 4 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:71.8 occ:1.00 OD1 B:ASP202 2.4 69.8 1.0 OD2 B:ASP198 2.6 72.4 1.0 OD2 B:ASP202 3.1 60.1 1.0 CG B:ASP202 3.1 66.3 1.0 O1A B:DMA403 3.6 68.6 1.0 CG B:ASP198 3.8 76.6 1.0 NZ B:LYS84 4.2 85.2 1.0 O1B B:DMA403 4.2 63.4 1.0 CD1 B:LEU207 4.4 56.5 1.0 CB B:ASP198 4.4 65.7 1.0 ND2 B:ASN209 4.5 55.1 1.0 PA B:DMA403 4.5 56.9 1.0 CB B:ASP202 4.6 61.5 1.0 O3A B:DMA403 4.7 67.1 1.0 OD1 B:ASP198 4.8 78.9 1.0 CD2 B:PHE201 4.9 76.7 1.0 O2A B:DMA403 4.9 63.2 1.0

Magnesium binding site 5 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:73.3 occ:1.00 O C:HOH507 2.5 64.4 1.0 OD2 C:ASP198 2.8 70.2 1.0 OD1 C:ASP202 2.8 62.6 1.0 O2A C:DMA403 3.2 68.0 1.0 CG C:ASP202 3.6 63.0 1.0 OD2 C:ASP202 3.6 68.7 1.0 O2B C:DMA403 3.8 68.4 1.0 PA C:DMA403 4.0 67.6 1.0 CG C:ASP198 4.0 68.8 1.0 O3A C:DMA403 4.2 59.0 1.0 CD1 C:LEU207 4.3 55.8 1.0 O1A C:DMA403 4.3 63.6 1.0 CB C:ASP198 4.7 64.1 1.0 PB C:DMA403 4.7 64.1 1.0 ND2 C:ASN209 4.9 47.5 1.0 OD1 C:ASP198 4.9 67.0 1.0 CE C:LYS146 5.0 53.3 1.0

Magnesium binding site 6 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:56.4 occ:1.00 OD2 C:ASP72 2.1 54.6 1.0 OD1 C:ASN68 2.1 52.6 1.0 O3B C:DMA403 2.3 67.2 1.0 O C:HOH506 2.3 54.8 1.0 O1A C:DMA403 2.4 63.6 1.0 CG C:ASN68 3.1 48.7 1.0 CG C:ASP72 3.2 53.9 1.0 PB C:DMA403 3.4 64.1 1.0 ND2 C:ASN68 3.4 51.8 1.0 PA C:DMA403 3.5 67.6 1.0 O2B C:DMA403 3.6 68.4 1.0 CB C:ASP72 3.8 57.6 1.0 O3A C:DMA403 3.8 59.0 1.0 O1 C:DMA403 3.8 62.5 1.0 OD2 C:ASP76 4.0 70.0 1.0 NH1 C:ARG22 4.0 58.3 1.0 NZ C:LYS146 4.1 52.3 1.0 OD1 C:ASP76 4.2 71.4 1.0 OD1 C:ASP72 4.2 53.3 1.0 O C:ASN68 4.3 47.2 1.0 CB C:ASN68 4.4 46.4 1.0 CG C:ASP76 4.5 72.5 1.0 CD1 C:LEU88 4.6 70.6 1.0 C C:ASN68 4.7 44.8 1.0 O C:HOH507 4.7 64.4 1.0 O1B C:DMA403 4.7 57.3 1.0 O2A C:DMA403 4.9 68.0 1.0

Magnesium binding site 7 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:56.5 occ:1.00 O D:HOH505 2.1 58.2 1.0 OD2 D:ASP72 2.1 56.1 1.0 O1A D:DMA403 2.3 56.1 1.0 O1B D:DMA403 2.7 61.3 1.0 O3B D:DMA403 3.0 65.2 1.0 OD1 D:ASN68 3.1 49.4 1.0 CG D:ASP72 3.1 54.1 1.0 PB D:DMA403 3.3 61.8 1.0 OD1 D:ASP76 3.4 72.0 1.0 OD2 D:ASP76 3.6 75.8 1.0 PA D:DMA403 3.7 59.1 1.0 NZ D:LYS146 3.7 53.5 1.0 CB D:ASP72 3.8 59.5 1.0 CG D:ASP76 3.9 75.6 1.0 O3A D:DMA403 4.0 55.3 1.0 CD1 D:LEU88 4.0 78.2 1.0 OD1 D:ASP72 4.1 51.0 1.0 CG D:ASN68 4.1 47.4 1.0 ND2 D:ASN68 4.3 45.0 1.0 O1 D:DMA403 4.5 56.3 1.0 NH1 D:ARG22 4.6 51.7 1.0 O2B D:DMA403 4.7 65.2 1.0 O2A D:DMA403 4.8 65.5 1.0 CE D:LYS146 4.9 55.3 1.0 CE2 D:PHE201 5.0 75.5 1.0

Magnesium binding site 8 out of 8 in the Structure of A Ubia Homolog From Archaeoglobus Fulgidus Bound to Dmapp 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 Dmapp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:69.6 occ:1.00 OD2 D:ASP198 2.0 72.4 1.0 OD1 D:ASP202 2.5 71.6 1.0 O D:HOH506 2.6 63.2 1.0 CG D:ASP198 3.3 70.3 1.0 CG D:ASP202 3.4 68.1 1.0 OD2 D:ASP202 3.5 66.6 1.0 O2A D:DMA403 3.7 65.5 1.0 O3B D:DMA403 3.8 65.2 1.0 O3A D:DMA403 4.0 55.3 1.0 CB D:ASP198 4.2 62.6 1.0 OD1 D:ASP198 4.2 72.7 1.0 NZ D:LYS84 4.3 72.9 1.0 PA D:DMA403 4.3 59.1 1.0 CD2 D:PHE201 4.5 75.3 1.0 PB D:DMA403 4.6 61.8 1.0 CD1 D:LEU207 4.6 55.1 1.0 CE D:LYS84 4.7 72.2 1.0 CE2 D:PHE201 4.7 75.5 1.0 CB D:ASP202 4.8 62.5 1.0 O1A D:DMA403 4.9 56.1 1.0 O D:ASP198 5.0 59.2 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