Magnesium in PDB 3rfu: Crystal Structure of A Copper-Transporting Pib-Type Atpase

The structure of Crystal Structure of A Copper-Transporting Pib-Type Atpase, PDB code: 3rfu was solved by P.Gourdon, X.Liu, T.Skjorringe, J.P.Morth, L.Birk Moller, B.Panyellapedersen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.150, 72.980, 329.950, 89.96, 90.04, 90.22
R / Rfree (%)	23.5 / 26.1

The structure of Crystal Structure of A Copper-Transporting Pib-Type Atpase also contains other interesting chemical elements:

Fluorine	(F)	16 atoms
Aluminium	(Al)	4 atoms
Potassium	(K)	4 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Copper-Transporting Pib-Type Atpase (pdb code 3rfu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Copper-Transporting Pib-Type Atpase, PDB code: 3rfu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg996 b:68.2 occ:1.00 OD1 A:ASP624 2.6 0.5 1.0 O A:THR428 2.6 87.2 1.0 F2 A:ALF995 2.6 60.1 1.0 F3 A:ALF995 2.8 52.0 1.0 CG A:ASP624 3.4 0.8 1.0 C A:THR428 3.5 0.0 1.0 O A:ASP624 3.5 59.1 1.0 AL A:ALF995 3.6 0.4 1.0 OD2 A:ASP624 3.6 0.3 1.0 OD2 A:ASP426 3.7 74.4 1.0 O A:GLY278 3.7 0.7 1.0 C A:ASP624 4.1 91.8 1.0 CB A:THR428 4.2 98.5 1.0 CA A:GLY278 4.2 0.2 1.0 N A:GLY429 4.3 0.6 1.0 CA A:THR428 4.4 99.1 1.0 CA A:GLY429 4.4 0.3 1.0 C A:GLY278 4.4 0.4 1.0 OD1 A:ASN627 4.6 1.0 1.0 N A:GLY625 4.6 99.5 1.0 CG A:ASP426 4.6 86.3 1.0 CB A:ASP624 4.7 0.3 1.0 CA A:GLY625 4.7 0.6 1.0 CG2 A:THR428 4.7 0.7 1.0 CA A:ASP624 4.8 1.0 1.0 OD1 A:ASP426 4.8 0.5 1.0 CG2 A:THR430 4.8 79.4 1.0 O A:THR277 4.9 0.4 1.0 N A:THR428 4.9 90.3 1.0 F4 A:ALF995 4.9 37.0 1.0 N A:ASP624 4.9 0.1 1.0 C A:GLY429 5.0 1.0 1.0 F1 A:ALF995 5.0 51.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg996 b:67.2 occ:1.00 OD1 B:ASP624 2.6 0.5 1.0 O B:THR428 2.6 86.3 1.0 F2 B:ALF995 2.6 80.2 1.0 F3 B:ALF995 2.9 63.5 1.0 CG B:ASP624 3.4 0.6 1.0 O B:ASP624 3.5 66.1 1.0 C B:THR428 3.5 0.8 1.0 OD2 B:ASP624 3.6 0.3 1.0 OD2 B:ASP426 3.6 77.1 1.0 AL B:ALF995 3.7 0.1 1.0 O B:GLY278 3.8 0.5 1.0 C B:ASP624 4.0 92.2 1.0 CB B:THR428 4.2 98.7 1.0 CA B:GLY278 4.2 0.0 1.0 N B:GLY429 4.3 0.8 1.0 CA B:THR428 4.3 99.4 1.0 CA B:GLY429 4.4 0.5 1.0 C B:GLY278 4.5 0.6 1.0 OD1 B:ASN627 4.5 0.3 1.0 CG B:ASP426 4.6 86.9 1.0 N B:GLY625 4.6 98.7 1.0 CB B:ASP624 4.6 0.7 1.0 CA B:GLY625 4.7 1.0 1.0 CG2 B:THR428 4.7 0.6 1.0 OD1 B:ASP426 4.8 0.8 1.0 CA B:ASP624 4.8 0.9 1.0 CG2 B:THR430 4.8 79.9 1.0 N B:THR428 4.8 91.6 1.0 O B:THR277 4.9 0.2 1.0 N B:ASP624 4.9 0.2 1.0 C B:GLY429 5.0 0.5 1.0 F4 B:ALF995 5.0 48.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg996 b:58.3 occ:1.00 O C:THR428 2.6 83.0 1.0 F2 C:ALF995 2.6 61.7 1.0 OD1 C:ASP624 2.6 0.1 1.0 F3 C:ALF995 2.9 57.9 1.0 CG C:ASP624 3.4 0.5 1.0 C C:THR428 3.5 0.5 1.0 O C:ASP624 3.5 63.4 1.0 AL C:ALF995 3.6 0.9 1.0 OD2 C:ASP426 3.7 80.3 1.0 OD2 C:ASP624 3.7 0.7 1.0 O C:GLY278 3.7 0.5 1.0 CB C:THR428 4.1 98.0 1.0 C C:ASP624 4.1 91.2 1.0 CA C:GLY278 4.2 0.1 1.0 N C:GLY429 4.3 0.4 1.0 CA C:THR428 4.3 99.3 1.0 CA C:GLY429 4.4 0.8 1.0 C C:GLY278 4.4 0.4 1.0 OD1 C:ASN627 4.5 0.0 1.0 CG C:ASP426 4.6 86.8 1.0 N C:GLY625 4.6 97.5 1.0 CG2 C:THR428 4.7 0.9 1.0 CA C:GLY625 4.7 0.7 1.0 CB C:ASP624 4.7 0.7 1.0 OD1 C:ASP426 4.7 0.1 1.0 O C:THR277 4.8 0.6 1.0 N C:THR428 4.8 93.1 1.0 CG2 C:THR430 4.8 80.1 1.0 CA C:ASP624 4.8 0.3 1.0 F4 C:ALF995 4.9 45.2 1.0 N C:ASP624 4.9 0.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Copper-Transporting Pib-Type Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Copper-Transporting Pib-Type Atpase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg996 b:77.5 occ:1.00 F2 D:ALF995 2.5 80.5 1.0 OD1 D:ASP624 2.6 0.6 1.0 O D:THR428 2.6 88.1 1.0 F3 D:ALF995 2.9 62.6 1.0 CG D:ASP624 3.4 0.8 1.0 O D:ASP624 3.5 59.7 1.0 C D:THR428 3.5 0.6 1.0 OD2 D:ASP426 3.6 75.5 1.0 AL D:ALF995 3.6 0.5 1.0 OD2 D:ASP624 3.7 0.5 1.0 O D:GLY278 3.8 0.6 1.0 C D:ASP624 4.0 92.3 1.0 CB D:THR428 4.2 98.6 1.0 CA D:GLY278 4.2 0.7 1.0 N D:GLY429 4.3 0.8 1.0 CA D:THR428 4.4 99.0 1.0 CA D:GLY429 4.4 0.3 1.0 C D:GLY278 4.5 0.9 1.0 OD1 D:ASN627 4.5 1.0 1.0 CG D:ASP426 4.5 87.2 1.0 N D:GLY625 4.6 0.3 1.0 CA D:GLY625 4.6 0.0 1.0 CB D:ASP624 4.7 0.6 1.0 OD1 D:ASP426 4.7 0.7 1.0 CA D:ASP624 4.8 0.5 1.0 CG2 D:THR428 4.8 0.8 1.0 CG2 D:THR430 4.8 78.8 1.0 O D:THR277 4.8 0.9 1.0 N D:THR428 4.8 92.5 1.0 N D:ASP624 4.9 0.5 1.0 F4 D:ALF995 4.9 57.8 1.0

P.Gourdon, X.Y.Liu, T.Skjorringe, J.P.Morth, L.B.Moller, B.P.Pedersen, P.Nissen. Crystal Structure of A Copper-Transporting Pib-Type Atpase. Nature V. 475 59 2011.
ISSN: ISSN 0028-0836
PubMed: 21716286
DOI: 10.1038/NATURE10191