Magnesium in PDB 1u3c: Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana

The structure of Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana, PDB code: 1u3c 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)	34.60 / 2.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.430, 169.430, 104.245, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 25.4

The structure of Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana 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 (pdb code 1u3c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana, PDB code: 1u3c:
Jump to Magnesium binding site number: 1; 2; 3;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg514 b:75.7 occ:1.00 O6 A:HEZ518 2.0 37.0 0.5 O A:HOH580 2.6 39.8 1.0 OD2 A:ASP359 3.0 46.0 1.0 O A:HOH579 3.1 49.5 1.0 OD1 A:ASP359 3.1 41.0 1.0 CG A:ASP359 3.4 42.1 1.0 C6 A:HEZ518 3.4 28.4 0.5 N6A A:FAD510 3.4 24.6 1.0 CG2 A:VAL363 4.1 22.3 1.0 C5 A:HEZ518 4.2 46.7 0.5 C5 A:HEZ518 4.3 40.4 0.5 C4 A:HEZ518 4.4 48.5 0.5 C4 A:HEZ518 4.4 53.8 0.5 C8M A:FAD510 4.5 32.1 1.0 C6 A:HEZ518 4.7 39.7 0.5 C6A A:FAD510 4.8 29.5 1.0 CB A:ASP359 4.9 36.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Phr Domain of Cryptochrome 1 From Arabidopsis Thaliana


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg515 b:72.3 occ:1.00 O A:ASN238 2.2 68.4 1.0 OG1 A:THR246 2.5 54.7 1.0 NE2 A:HIS358 3.0 36.9 1.0 C A:ASN238 3.2 67.8 1.0 CB A:THR246 3.6 61.5 1.0 MG A:MG516 3.7 78.2 1.0 O A:HOH573 3.7 55.5 1.0 CG2 A:THR247 3.7 28.6 1.0 O A:LYS241 3.8 78.5 1.0 CA A:ARG239 3.9 72.6 1.0 CE1 A:HIS358 3.9 36.9 1.0 CB A:ASN238 3.9 69.5 1.0 N A:ARG239 4.0 67.6 1.0 CD2 A:HIS358 4.0 36.3 1.0 CB A:LYS241 4.2 77.4 1.0 C A:ARG239 4.2 73.1 1.0 CA A:ASN238 4.2 67.6 1.0 N A:LYS241 4.3 75.4 1.0 C A:THR246 4.5 51.4 1.0 O A:ARG239 4.5 66.4 1.0 CG2 A:THR246 4.5 65.0 1.0 O A:THR246 4.5 54.6 1.0 CA A:THR246 4.6 59.0 1.0 CA A:LYS241 4.7 77.3 1.0 C A:LYS241 4.7 77.6 1.0 N A:ARG240 4.7 76.9 1.0 CG A:LYS241 4.9 81.7 1.0 N A:THR247 4.9 44.1 1.0 O A:TYR235 4.9 40.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg516 b:78.2 occ:1.00 OG1 A:THR246 2.4 54.7 1.0 O A:SER244 2.5 68.6 1.0 N A:SER244 2.9 71.5 1.0 CB A:SER244 3.0 72.0 1.0 O A:LYS241 3.0 78.5 1.0 C A:SER244 3.1 68.1 1.0 CA A:SER244 3.1 70.6 1.0 CB A:LYS241 3.3 77.4 1.0 CB A:THR246 3.5 61.5 1.0 C A:LYS241 3.6 77.6 1.0 CG2 A:THR246 3.7 65.0 1.0 MG A:MG515 3.7 72.3 1.0 OG A:SER244 3.8 77.4 1.0 N A:THR246 3.8 58.1 1.0 CD2 A:HIS358 3.8 36.3 1.0 CA A:LYS241 4.1 77.3 1.0 C A:ASP243 4.1 75.8 1.0 NE2 A:HIS358 4.1 36.9 1.0 CA A:THR246 4.2 59.0 1.0 N A:ALA245 4.3 65.0 1.0 N A:ASP243 4.3 72.8 1.0 CG A:LYS241 4.5 81.7 1.0 N A:ALA242 4.5 76.4 1.0 C A:ALA242 4.5 70.8 1.0 CA A:ASP243 4.6 73.6 1.0 O A:ASN238 4.8 68.4 1.0 C A:ALA245 4.8 64.1 1.0 O A:ALA242 4.8 71.3 1.0 N A:LYS241 4.9 75.4 1.0 CA A:ALA242 5.0 69.9 1.0 C A:THR246 5.0 51.4 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