Calcium in PDB 5ud6: Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound

The structure of Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound, PDB code: 5ud6 was solved by S.Watkin, J.R.Keown, F.G.Pearce, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.93 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.630, 74.700, 97.550, 90.00, 103.31, 90.00
R / Rfree (%)	21.2 / 25.5

The binding sites of Calcium atom in the Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound (pdb code 5ud6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound, PDB code: 5ud6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:36.2 occ:1.00 O A:HOH544 2.1 27.0 1.0 O A:ALA52 2.3 28.4 1.0 O A:GLY87 2.4 28.3 1.0 OG A:SER58 2.5 28.0 1.0 OE1 A:GLU66 2.5 33.9 1.0 OE2 A:GLU66 2.6 33.7 1.0 O A:HOH572 2.9 39.5 1.0 CD A:GLU66 2.9 32.9 1.0 C A:GLY87 3.4 26.9 1.0 CB A:SER58 3.4 26.8 1.0 C A:ALA52 3.5 27.8 1.0 CB A:ALA52 4.0 28.5 1.0 CA A:GLY87 4.1 26.7 1.0 CA A:SER58 4.2 25.9 1.0 N A:ALA88 4.3 26.9 1.0 CA A:ALA52 4.4 27.4 1.0 CG A:GLU66 4.4 32.0 1.0 N A:GLY53 4.5 27.9 1.0 O A:HOH504 4.5 26.1 1.0 CA A:GLY53 4.6 28.7 1.0 NZ A:LYS402 4.7 36.5 1.0 CZ3 A:TRP63 4.7 40.2 1.0 CA A:ALA88 4.7 27.1 1.0 CH2 A:TRP63 4.9 41.3 1.0 C A:SER58 4.9 26.2 1.0 O A:SER58 4.9 27.1 1.0 O A:VAL51 5.0 28.1 1.0 N A:GLY87 5.0 27.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:35.1 occ:1.00 O B:HOH558 2.1 29.7 1.0 OG B:SER58 2.4 24.0 1.0 O B:GLY87 2.4 27.5 1.0 O B:ALA52 2.5 28.1 1.0 OE1 B:GLU66 2.6 30.6 1.0 OE2 B:GLU66 2.6 30.2 1.0 O B:HOH566 2.8 30.0 1.0 CD B:GLU66 2.9 30.6 1.0 CB B:SER58 3.4 23.8 1.0 C B:GLY87 3.4 26.9 1.0 C B:ALA52 3.7 27.8 1.0 CB B:ALA52 4.1 30.0 1.0 CA B:GLY87 4.2 26.3 1.0 CA B:SER58 4.2 24.9 1.0 O B:HOH517 4.4 26.5 1.0 CG B:GLU66 4.4 32.2 1.0 N B:ALA88 4.4 27.1 1.0 CA B:ALA52 4.6 28.9 1.0 CZ3 B:TRP63 4.6 32.4 1.0 NZ B:LYS402 4.6 33.1 1.0 N B:GLY53 4.6 26.7 1.0 CA B:GLY53 4.7 25.6 1.0 CA B:ALA88 4.8 27.5 1.0 CH2 B:TRP63 4.8 31.6 1.0 O B:SER58 4.9 26.3 1.0 C B:SER58 4.9 25.3 1.0 O B:GLY89 4.9 24.5 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:51.9 occ:1.00 OG C:SER58 2.3 42.0 1.0 O C:ALA52 2.3 42.8 1.0 O C:GLY87 2.4 44.3 1.0 OE1 C:GLU66 2.5 48.2 1.0 OE2 C:GLU66 2.8 50.9 1.0 CD C:GLU66 3.1 49.3 1.0 CB C:SER58 3.2 40.1 1.0 C C:GLY87 3.4 44.6 1.0 C C:ALA52 3.5 41.4 1.0 CA C:GLY87 4.1 42.4 1.0 CA C:SER58 4.1 39.7 1.0 CB C:ALA52 4.1 42.9 1.0 NZ C:LYS402 4.3 60.1 1.0 N C:ALA88 4.4 47.1 1.0 N C:GLY53 4.4 40.9 1.0 CA C:ALA52 4.4 41.0 1.0 CA C:GLY53 4.5 40.8 1.0 CG C:GLU66 4.6 49.4 1.0 CA C:ALA88 4.7 49.6 1.0 CZ3 C:TRP63 4.8 53.8 1.0 C C:SER58 4.9 40.3 1.0 O C:GLY89 4.9 39.0 1.0 O C:SER58 5.0 41.5 1.0 CH2 C:TRP63 5.0 54.5 1.0 N C:GLY89 5.0 39.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:45.4 occ:1.00 O D:GLY87 2.3 36.1 1.0 OE1 D:GLU66 2.3 37.0 1.0 O D:ALA52 2.4 36.7 1.0 OG D:SER58 2.5 34.2 1.0 OE2 D:GLU66 2.5 36.8 1.0 CD D:GLU66 2.8 37.4 1.0 O D:HOH547 3.1 24.7 1.0 C D:GLY87 3.3 35.4 1.0 CB D:SER58 3.5 33.1 1.0 C D:ALA52 3.6 34.9 1.0 CB D:ALA52 4.0 36.1 1.0 CA D:GLY87 4.0 35.1 1.0 N D:ALA88 4.3 35.0 1.0 CA D:SER58 4.3 33.6 1.0 NZ D:LYS402 4.3 46.0 1.0 CG D:GLU66 4.3 38.4 1.0 CA D:ALA52 4.5 35.0 1.0 CZ3 D:TRP63 4.5 42.6 1.0 N D:GLY53 4.6 34.1 1.0 CA D:ALA88 4.6 35.7 1.0 CA D:GLY53 4.7 33.3 1.0 CH2 D:TRP63 4.8 42.8 1.0 O D:GLY89 4.9 34.6 1.0 N D:GLY87 5.0 36.3 1.0 N D:GLY89 5.0 34.5 1.0 O D:VAL51 5.0 34.8 1.0

S.Watkin, J.R.Keown, F.G.Pearce. Crystal Structure of Dhdps From Cyanidioschyzon Merolae with Lysine Bound To Be Published.