Magnesium in PDB 5ycd: Crystal Structure of Poecilia Reticulata Adenylate Kinase

The structure of Crystal Structure of Poecilia Reticulata Adenylate Kinase, PDB code: 5ycd was solved by E.Bae, J.Kim, S.Moon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.18 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.790, 81.505, 120.123, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of Poecilia Reticulata Adenylate Kinase (pdb code 5ycd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Poecilia Reticulata Adenylate Kinase, PDB code: 5ycd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Poecilia Reticulata Adenylate Kinase


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 Poecilia Reticulata Adenylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.2 occ:1.00 O A:HOH357 2.2 33.3 1.0 O2D A:AP5201 2.3 19.4 1.0 O A:HOH303 2.3 33.2 1.0 O A:HOH345 2.5 44.6 1.0 O A:HOH315 2.5 38.9 1.0 O1G A:AP5201 2.7 28.2 1.0 O3B A:AP5201 3.1 47.2 1.0 PG A:AP5201 3.3 23.7 1.0 PD A:AP5201 3.4 22.2 1.0 O3G A:AP5201 3.7 20.0 1.0 N A:GLY22 4.1 16.9 1.0 CA A:GLY22 4.1 17.2 1.0 O2E A:AP5201 4.2 23.8 1.0 O A:HOH301 4.3 23.4 1.0 O1A A:AP5201 4.4 24.1 1.0 O3D A:AP5201 4.5 20.7 1.0 O1D A:AP5201 4.5 26.1 1.0 PB A:AP5201 4.5 27.6 1.0 OD2 A:ASP93 4.6 27.9 1.0 O3A A:AP5201 4.7 71.1 1.0 O2G A:AP5201 4.8 23.6 1.0 PE A:AP5201 4.8 20.0 1.0 PA A:AP5201 4.9 27.1 1.0 OD1 A:ASP93 4.9 30.6 1.0 NH1 A:ARG138 5.0 30.4 1.0 NH2 A:ARG44 5.0 22.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Poecilia Reticulata Adenylate Kinase


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 Poecilia Reticulata Adenylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:39.5 occ:1.00 O B:HOH306 2.2 33.1 1.0 O B:HOH366 2.2 31.7 1.0 O B:HOH335 2.3 29.5 1.0 O2D B:AP5201 2.3 20.2 1.0 O B:HOH385 2.4 34.8 1.0 O2G B:AP5201 2.8 25.9 1.0 O3B B:AP5201 3.3 38.1 1.0 PG B:AP5201 3.4 22.1 1.0 PD B:AP5201 3.5 20.5 1.0 O3G B:AP5201 3.7 19.8 1.0 N B:GLY22 3.9 17.6 1.0 CA B:GLY22 4.0 19.1 1.0 O1E B:AP5201 4.1 20.7 1.0 O B:HOH361 4.3 41.9 1.0 O2A B:AP5201 4.4 17.9 1.0 O3D B:AP5201 4.5 20.3 1.0 O B:HOH301 4.5 27.1 1.0 O1D B:AP5201 4.6 19.7 1.0 PB B:AP5201 4.6 24.3 1.0 OD2 B:ASP93 4.6 26.9 1.0 PE B:AP5201 4.7 20.4 1.0 O3A B:AP5201 4.7 44.1 1.0 NH2 B:ARG138 4.8 27.4 1.0 O1G B:AP5201 4.9 25.7 1.0 O2E B:AP5201 4.9 19.3 1.0 OD1 B:ASP93 5.0 25.8 1.0 PA B:AP5201 5.0 23.5 1.0

E.Bae, J.Kim, S.Moon. Crystal Structure of Poecilia Reticulata Adenylate Kinase To Be Published.