Magnesium in PDB 1u3d: Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound

The structure of Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound, PDB code: 1u3d was solved by C.A.Brautigam, B.S.Smith, Z.Ma, M.Palnitkar, D.R.Tomchick, M.Machius, J.Deisenhofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.45
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.213, 169.213, 104.521, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 25.3

The structure of Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound (pdb code 1u3d). 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 the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound, PDB code: 1u3d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound


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 the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg514 b:81.7 occ:1.00 N3B A:ANP511 2.2 1.0 0.8 O2A A:ANP511 2.3 0.0 0.8 PB A:ANP511 3.1 0.0 0.8 O2B A:ANP511 3.2 0.9 0.8 PA A:ANP511 3.2 0.1 0.8 O3A A:ANP511 3.3 0.7 0.8 PG A:ANP511 3.4 0.8 0.8 O1G A:ANP511 3.5 0.2 0.8 O1A A:ANP511 4.0 0.2 0.8 O3G A:ANP511 4.2 0.5 0.8 O1B A:ANP511 4.5 0.6 0.8 O5' A:ANP511 4.6 0.8 0.8 O2G A:ANP511 4.7 0.3 0.8 C5' A:ANP511 4.9 97.3 0.8

Magnesium binding site 2 out of 4 in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound


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 the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg515 b:66.4 occ:1.00 O A:ASN238 2.6 70.9 1.0 OG1 A:THR246 2.6 63.1 1.0 CA A:ARG239 2.9 82.9 1.0 NE2 A:HIS358 3.1 45.3 1.0 C A:ASN238 3.1 68.6 1.0 N A:ARG239 3.3 72.2 1.0 O A:HOH592 3.5 60.4 1.0 C A:ARG239 3.6 82.3 1.0 CB A:ARG239 3.7 89.8 1.0 CB A:THR246 3.7 69.8 1.0 CG2 A:THR247 3.8 36.1 1.0 MG A:MG516 3.8 84.0 1.0 O A:LYS241 3.9 81.6 1.0 O A:ARG239 3.9 81.3 1.0 CE1 A:HIS358 3.9 43.0 1.0 CD2 A:HIS358 4.1 46.7 1.0 N A:LYS241 4.2 74.2 1.0 CB A:LYS241 4.3 76.8 1.0 CB A:ASN238 4.3 68.5 1.0 CA A:ASN238 4.4 67.5 1.0 N A:ARG240 4.6 82.0 1.0 CA A:LYS241 4.6 77.0 1.0 C A:LYS241 4.7 77.8 1.0 C A:THR246 4.7 56.1 1.0 CG2 A:THR246 4.7 71.0 1.0 O A:THR246 4.7 58.8 1.0 O A:TYR235 4.8 44.6 1.0 CA A:THR246 4.8 62.3 1.0 CG A:ARG239 4.9 92.5 1.0 CG A:LYS241 5.0 74.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound


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 the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg516 b:84.0 occ:1.00 OG1 A:THR246 2.4 63.1 1.0 O A:SER244 2.5 68.0 1.0 N A:SER244 2.8 68.9 1.0 CB A:SER244 3.0 63.1 1.0 CA A:SER244 3.1 66.7 1.0 C A:SER244 3.1 64.6 1.0 O A:LYS241 3.2 81.6 1.0 CB A:LYS241 3.4 76.8 1.0 CB A:THR246 3.6 69.8 1.0 OG A:SER244 3.7 64.3 1.0 C A:LYS241 3.7 77.8 1.0 CG2 A:THR246 3.8 71.0 1.0 N A:THR246 3.8 59.5 1.0 MG A:MG515 3.8 66.4 1.0 CD2 A:HIS358 3.9 46.7 1.0 C A:ASP243 4.0 73.6 1.0 CA A:LYS241 4.2 77.0 1.0 NE2 A:HIS358 4.2 45.3 1.0 CA A:THR246 4.2 62.3 1.0 N A:ASP243 4.3 69.7 1.0 N A:ALA245 4.3 59.1 1.0 C A:ALA242 4.5 69.1 1.0 N A:ALA242 4.5 77.5 1.0 CA A:ASP243 4.6 71.0 1.0 O A:ASN238 4.6 70.9 1.0 CG A:LYS241 4.6 74.1 1.0 C A:ALA245 4.8 64.7 1.0 O A:ALA242 4.9 73.3 1.0 CA A:ALA242 5.0 69.1 1.0 C A:THR246 5.0 56.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound


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 the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana with Amppnp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg517 b:68.3 occ:1.00 O1 A:NDS512 2.2 61.0 1.0 CE A:LYS222 2.5 82.1 1.0 O A:ASN219 2.9 45.8 1.0 CD A:LYS222 3.1 77.8 1.0 NZ A:LYS222 3.3 65.2 1.0 CG A:LYS222 3.5 57.9 1.0 S1 A:NDS512 3.6 50.2 1.0 CB A:LYS222 3.6 44.0 1.0 C A:ASN219 3.7 38.3 1.0 N A:ALA223 3.8 40.3 1.0 CB A:ASN219 3.8 47.1 1.0 CA A:ASN219 3.9 37.3 1.0 O2 A:NDS512 4.0 62.5 1.0 CB A:ALA223 4.2 37.3 1.0 OD1 A:ASN219 4.2 54.7 1.0 CA A:ALA223 4.3 39.1 1.0 C A:LYS222 4.3 42.6 1.0 C4 A:NDS512 4.3 59.9 1.0 CA A:LYS222 4.5 43.6 1.0 CG A:ASN219 4.5 56.8 1.0 O3 A:NDS512 4.7 49.6 1.0 O A:HOH529 4.9 44.4 1.0 N A:GLY220 4.9 37.7 1.0

C.A.Brautigam, B.S.Smith, Z.Ma, M.Palnitkar, D.R.Tomchick, M.Machius, J.Deisenhofer. Structure of the Photolyase-Like Domain of Cryptochrome 1 From Arabidopsis Thaliana. Proc.Natl.Acad.Sci.Usa V. 101 12142 2004.
ISSN: ISSN 0027-8424
PubMed: 15299148
DOI: 10.1073/PNAS.0404851101