Magnesium in PDB 1xf9: Structure of NBD1 From Murine Cftr- F508S Mutant

The structure of Structure of NBD1 From Murine Cftr- F508S Mutant, PDB code: 1xf9 was solved by P.H.Thibodeau, C.A.Brautigam, M.Machius, P.J.Thomas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.40 / 2.70
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	170.449, 170.449, 109.065, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.3

The binding sites of Magnesium atom in the Structure of NBD1 From Murine Cftr- F508S Mutant (pdb code 1xf9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Structure of NBD1 From Murine Cftr- F508S Mutant, PDB code: 1xf9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg13 b:47.2 occ:1.00 O A:HOH149 2.0 61.3 1.0 OG1 A:THR465 2.0 40.7 1.0 O A:HOH89 2.3 61.0 1.0 O2G A:ATP1 2.4 54.2 1.0 O2B A:ATP1 2.5 41.5 1.0 OE1 A:GLN493 2.8 55.4 1.0 CB A:THR465 3.3 33.7 1.0 PG A:ATP1 3.6 52.9 1.0 O3B A:ATP1 3.6 45.4 1.0 PB A:ATP1 3.6 42.3 1.0 OD2 A:ASP572 3.7 38.8 1.0 CD A:GLN493 4.0 62.1 1.0 N A:THR465 4.0 43.0 1.0 O1A A:ATP1 4.2 53.1 1.0 CA A:THR465 4.2 41.3 1.0 OD1 A:ASP572 4.2 45.1 1.0 CG2 A:THR465 4.3 29.1 1.0 O3G A:ATP1 4.4 57.8 1.0 CG A:ASP572 4.4 45.2 1.0 O1G A:ATP1 4.6 49.8 1.0 O3A A:ATP1 4.6 46.3 1.0 NE2 A:GLN493 4.7 65.2 1.0 O1B A:ATP1 4.8 38.9 1.0 NZ A:LYS464 4.8 30.9 1.0 CB A:LYS464 4.9 41.6 1.0 CB A:GLN493 4.9 42.6 1.0 PA A:ATP1 5.0 50.9 1.0

Magnesium binding site 2 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg11 b:47.2 occ:1.00 O B:HOH174 1.8 56.5 1.0 OG1 B:THR465 1.9 37.2 1.0 O B:HOH87 2.0 56.5 1.0 O2G B:ATP2 2.3 53.6 1.0 O2B B:ATP2 2.4 41.2 1.0 OE1 B:GLN493 2.9 58.6 1.0 CB B:THR465 3.2 27.5 1.0 PG B:ATP2 3.5 47.0 1.0 PB B:ATP2 3.6 42.2 1.0 O3B B:ATP2 3.8 43.4 1.0 OD2 B:ASP572 4.0 39.9 1.0 O3G B:ATP2 4.0 51.6 1.0 CD B:GLN493 4.0 62.0 1.0 OD1 B:ASP572 4.1 42.8 1.0 CG2 B:THR465 4.1 23.8 1.0 N B:THR465 4.2 33.7 1.0 CA B:THR465 4.2 30.2 1.0 O1A B:ATP2 4.4 40.5 1.0 O B:HOH137 4.5 51.7 1.0 CG B:ASP572 4.5 40.9 1.0 O3A B:ATP2 4.6 42.0 1.0 NE2 B:GLN493 4.7 59.5 1.0 O1G B:ATP2 4.7 42.4 1.0 O1B B:ATP2 4.8 34.8 1.0 CB B:GLN493 5.0 50.0 1.0 NZ B:LYS464 5.0 46.9 1.0 PA B:ATP2 5.0 47.4 1.0

Magnesium binding site 3 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg15 b:65.0 occ:1.00 O B:ALA596 2.2 42.9 1.0 O B:GLY451 2.4 39.4 1.0 C B:ALA596 3.3 37.9 1.0 C B:GLY451 3.4 38.8 1.0 CA B:GLY451 4.1 41.4 1.0 CA B:ALA596 4.2 38.1 1.0 N B:ASN597 4.3 36.2 1.0 CA B:ASN597 4.3 38.3 1.0 NH1 B:ARG600 4.3 24.8 1.0 N B:GLU452 4.4 38.3 1.0 NH2 B:ARG600 4.4 27.8 1.0 OD1 B:ASN597 4.6 35.8 1.0 O C:HOH83 4.6 41.8 1.0 CB B:ALA596 4.6 37.9 1.0 CA B:GLU452 4.7 39.7 1.0 OD2 B:ASP614 4.8 47.8 1.0 CZ B:ARG600 4.9 31.7 1.0

Magnesium binding site 4 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg12 b:60.7 occ:1.00 O C:HOH155 1.7 65.9 1.0 OG1 C:THR465 2.0 31.0 1.0 O C:HOH88 2.2 49.6 1.0 O2B C:ATP3 2.2 52.0 1.0 O2G C:ATP3 2.3 56.5 1.0 CB C:THR465 3.0 29.2 1.0 OE1 C:GLN493 3.1 53.9 1.0 PB C:ATP3 3.3 47.7 1.0 PG C:ATP3 3.4 51.5 1.0 O3B C:ATP3 3.4 51.3 1.0 N C:THR465 3.9 38.5 1.0 O1A C:ATP3 3.9 49.6 1.0 CA C:THR465 4.0 38.3 1.0 CG2 C:THR465 4.1 19.2 1.0 OD2 C:ASP572 4.1 41.1 1.0 OD1 C:ASP572 4.1 49.0 1.0 O3G C:ATP3 4.2 58.0 1.0 CD C:GLN493 4.3 59.6 1.0 O3A C:ATP3 4.4 53.0 1.0 O1G C:ATP3 4.4 51.1 1.0 O1B C:ATP3 4.5 47.8 1.0 CG C:ASP572 4.5 47.8 1.0 PA C:ATP3 4.7 53.8 1.0 NZ C:LYS464 4.8 34.5 1.0 NE2 C:GLN493 5.0 59.8 1.0

Magnesium binding site 5 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg16 b:69.6 occ:1.00 O C:ALA596 2.1 43.0 1.0 O C:HOH160 2.2 51.7 1.0 O C:GLY451 2.3 45.6 1.0 O C:HOH168 2.5 54.9 1.0 O C:HOH159 2.5 79.9 1.0 O B:HOH102 2.7 40.9 1.0 C C:ALA596 3.3 41.7 1.0 C C:GLY451 3.3 40.1 1.0 CA C:GLY451 3.9 38.2 1.0 CA C:ALA596 4.2 43.8 1.0 N C:ASN597 4.2 38.6 1.0 CA C:ASN597 4.2 45.5 1.0 N C:GLU452 4.3 41.7 1.0 NH1 C:ARG600 4.4 38.9 1.0 NH2 C:ARG600 4.4 33.4 1.0 OD1 C:ASN597 4.5 50.7 1.0 CB C:ALA596 4.6 37.1 1.0 CA C:GLU452 4.6 42.8 1.0 OD2 C:ASP614 4.9 42.2 1.0 CZ C:ARG600 4.9 32.5 1.0 C C:ASN597 5.0 43.6 1.0

Magnesium binding site 6 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg14 b:57.8 occ:1.00 O D:HOH173 1.8 70.5 1.0 OG1 D:THR465 2.1 42.7 1.0 O D:HOH90 2.2 73.4 1.0 O2G D:ATP4 2.3 69.4 1.0 O2B D:ATP4 2.4 68.1 1.0 OE1 D:GLN493 2.8 60.1 1.0 CB D:THR465 3.4 38.8 1.0 PG D:ATP4 3.5 67.6 1.0 PB D:ATP4 3.6 67.5 1.0 O3B D:ATP4 3.6 66.2 1.0 CD D:GLN493 3.7 64.0 1.0 OD1 D:ASP572 3.8 48.2 1.0 OD2 D:ASP572 4.0 49.9 1.0 N D:THR465 4.0 44.3 1.0 NE2 D:GLN493 4.2 63.6 1.0 CA D:THR465 4.2 44.2 1.0 O1G D:ATP4 4.2 59.3 1.0 CG D:ASP572 4.3 52.3 1.0 NZ D:LYS464 4.5 57.3 1.0 CG2 D:THR465 4.5 35.9 1.0 O3G D:ATP4 4.5 64.8 1.0 O1B D:ATP4 4.5 63.9 1.0 OG D:SER573 4.5 48.2 1.0 O1A D:ATP4 4.7 81.0 1.0 CB D:LYS464 4.8 56.5 1.0 O3A D:ATP4 4.8 75.2 1.0 CG D:GLN493 4.9 55.9 1.0 CB D:GLN493 4.9 48.2 1.0

Magnesium binding site 7 out of 7 in the Structure of NBD1 From Murine Cftr- F508S Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of NBD1 From Murine Cftr- F508S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg17 b:0.0 occ:1.00 O D:GLY451 1.9 56.5 1.0 O D:HOH170 2.0 63.9 1.0 O D:HOH169 2.1 69.4 1.0 O D:HOH171 2.1 60.4 1.0 O D:ALA596 2.3 46.0 1.0 C D:GLY451 3.0 57.6 1.0 C D:ALA596 3.5 44.6 1.0 CA D:GLY451 3.7 58.9 1.0 CA D:ASN597 3.9 44.0 1.0 NH1 D:ARG600 4.0 38.2 1.0 N D:GLU452 4.0 57.9 1.0 N D:ASN597 4.2 43.1 1.0 CA D:GLU452 4.3 56.5 1.0 OD1 D:ASN597 4.3 47.0 1.0 NH2 D:ARG600 4.6 37.6 1.0 CA D:ALA596 4.6 44.2 1.0 C D:ASN597 4.6 46.4 1.0 CZ D:ARG600 4.8 40.4 1.0 OD2 D:ASP614 4.9 64.1 1.0 N D:LYS598 5.0 47.0 1.0 CB D:ASN597 5.0 46.9 1.0

P.H.Thibodeau, C.A.Brautigam, M.Machius, P.J.Thomas. Side Chain and Backbone Contributions of PHE508 to Cftr Folding. Nat.Struct.Mol.Biol. V. 12 10 2005.
ISSN: ISSN 1545-9993
PubMed: 15619636
DOI: 10.1038/NSMB881