Magnesium in PDB 3x2s: Crystal Structure of Pyrene-Conjugated Adenylate Kinase

All present enzymatic activity of Crystal Structure of Pyrene-Conjugated Adenylate Kinase:
2.7.4.3;

The structure of Crystal Structure of Pyrene-Conjugated Adenylate Kinase, PDB code: 3x2s was solved by A.Fujii, Y.Sekiguchi, H.Matsumura, T.Inoue, W.-S.Chung, S.Hirota, T.Matsuo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.67 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.114, 58.992, 118.308, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.6

The binding sites of Magnesium atom in the Crystal Structure of Pyrene-Conjugated Adenylate Kinase (pdb code 3x2s). 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 Pyrene-Conjugated Adenylate Kinase, PDB code: 3x2s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Pyrene-Conjugated 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 Pyrene-Conjugated Adenylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:35.7 occ:1.00 O1D A:AP5303 2.0 40.9 1.0 O A:HOH408 2.0 28.7 1.0 O A:HOH406 2.1 65.4 1.0 O A:HOH401 2.2 40.3 1.0 O A:HOH407 2.3 44.4 1.0 O2G A:AP5303 2.6 30.0 1.0 PD A:AP5303 2.9 40.5 1.0 O3D A:AP5303 3.0 41.1 1.0 N A:GLY14 3.6 41.9 1.0 CA A:GLY14 3.6 40.8 1.0 PG A:AP5303 3.7 33.0 1.0 OD2 A:ASP84 3.8 54.7 1.0 O3G A:AP5303 3.8 37.9 1.0 OD1 A:ASP84 3.9 54.0 1.0 O1A A:AP5303 4.1 40.2 1.0 O3A A:AP5303 4.2 42.1 1.0 O2D A:AP5303 4.2 35.3 1.0 O3B A:AP5303 4.2 38.2 1.0 CG A:ASP84 4.3 52.4 1.0 PE A:AP5303 4.6 41.5 1.0 OG A:SER30 4.6 37.1 1.0 C A:LYS13 4.7 40.5 1.0 NH1 A:ARG156 4.7 49.3 1.0 PA A:AP5303 4.8 39.7 1.0 NH1 A:ARG123 4.8 51.5 1.0 NZ A:LYS13 4.8 41.3 1.0 OD1 A:ASP33 4.8 53.6 1.0 PB A:AP5303 4.8 42.2 1.0 OD2 A:ASP33 4.9 52.9 1.0 CB A:LYS13 4.9 38.1 1.0 O A:HOH405 5.0 27.5 1.0 O1G A:AP5303 5.0 35.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Pyrene-Conjugated 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 Pyrene-Conjugated Adenylate Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:37.1 occ:1.00 O B:HOH406 1.9 39.9 1.0 O B:HOH407 1.9 51.9 1.0 O1D B:AP5303 1.9 41.9 1.0 O B:HOH401 2.3 33.5 1.0 O2G B:AP5303 2.3 38.1 1.0 O B:HOH402 2.4 60.5 1.0 O2E B:AP5303 3.1 43.7 1.0 PD B:AP5303 3.3 40.6 1.0 PG B:AP5303 3.5 38.9 1.0 N B:GLY14 3.7 41.9 1.0 CA B:GLY14 3.7 43.2 1.0 O3G B:AP5303 3.8 41.8 1.0 OD2 B:ASP84 3.8 46.5 1.0 OD1 B:ASP84 4.0 46.3 1.0 O3B B:AP5303 4.2 43.9 1.0 PE B:AP5303 4.3 39.5 1.0 O3D B:AP5303 4.3 42.3 1.0 O2D B:AP5303 4.3 42.3 1.0 CG B:ASP84 4.3 46.1 1.0 O2A B:AP5303 4.3 49.3 1.0 NH1 B:ARG123 4.4 54.3 1.0 O1A B:AP5303 4.4 47.7 1.0 OG B:SER30 4.5 41.1 1.0 NH1 B:ARG156 4.7 49.4 1.0 O3A B:AP5303 4.7 47.6 1.0 OD1 B:ASP33 4.7 55.1 1.0 O1G B:AP5303 4.8 37.9 1.0 PA B:AP5303 4.8 47.9 1.0 C B:LYS13 4.9 41.0 1.0 NH2 B:ARG36 4.9 73.2 1.0 OD2 B:ASP33 5.0 55.8 1.0

A.Fujii, Y.Sekiguchi, H.Matsumura, T.Inoue, W.S.Chung, S.Hirota, T.Matsuo. Excimer Emission Properties on Pyrene-Labeled Protein Surface: Correlation Between Emission Spectra, Ring Stacking Modes, and Flexibilities of Pyrene Probes. Bioconjug.Chem. V. 26 537 2015.
ISSN: ISSN 1043-1802
PubMed: 25646669
DOI: 10.1021/ACS.BIOCONJCHEM.5B00026