Magnesium in PDB 4nu0: Crystal Structure of Adenylate Kinase From Streptococcus Pneumoniae with AP5A

All present enzymatic activity of Crystal Structure of Adenylate Kinase From Streptococcus Pneumoniae with AP5A:
2.7.4.3;

The structure of Crystal Structure of Adenylate Kinase From Streptococcus Pneumoniae with AP5A, PDB code: 4nu0 was solved by T.T.Thach, T.T.Luong, S.H.Lee, D.K.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.42 / 1.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.202, 48.338, 52.574, 75.30, 72.95, 88.77
R / Rfree (%)	19.3 / 23

The binding sites of Magnesium atom in the Crystal Structure of Adenylate Kinase From Streptococcus Pneumoniae with AP5A (pdb code 4nu0). 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 Adenylate Kinase From Streptococcus Pneumoniae with AP5A, PDB code: 4nu0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Adenylate Kinase From Streptococcus Pneumoniae with AP5A


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 Adenylate Kinase From Streptococcus Pneumoniae with AP5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:21.1 occ:1.00 O2B A:AP5302 2.2 19.1 1.0 O2G A:AP5302 2.3 18.5 1.0 O A:HOH452 2.4 28.4 1.0 O A:HOH442 2.6 47.8 1.0 O A:HOH416 2.6 27.9 1.0 O A:HOH402 2.7 19.7 1.0 HA3 A:GLY14 3.3 18.5 1.0 H A:GLY14 3.3 19.8 1.0 PG A:AP5302 3.3 19.3 1.0 PB A:AP5302 3.5 17.8 1.0 O3G A:AP5302 3.5 25.4 1.0 HH12 A:ARG156 3.6 20.4 1.0 O3B A:AP5302 3.8 18.5 1.0 HH12 A:ARG128 3.8 21.1 1.0 N A:GLY14 3.8 16.5 1.0 O A:HOH469 3.9 29.3 1.0 CA A:GLY14 3.9 15.4 1.0 HB2 A:LYS13 4.0 21.3 1.0 HA2 A:GLY14 4.1 18.5 1.0 HH22 A:ARG36 4.1 27.2 1.0 O1E A:AP5302 4.2 19.2 1.0 NH1 A:ARG156 4.3 17.0 1.0 HH11 A:ARG156 4.4 20.4 1.0 O3A A:AP5302 4.5 25.2 1.0 O1B A:AP5302 4.5 25.7 1.0 NH1 A:ARG128 4.5 17.6 1.0 O2A A:AP5302 4.5 22.5 1.0 HE2 A:LYS13 4.5 37.8 1.0 O A:HOH421 4.5 21.2 1.0 OD2 A:ASP85 4.6 23.4 1.0 HH11 A:ARG128 4.6 21.1 1.0 O2E A:AP5302 4.6 24.9 1.0 O1G A:AP5302 4.7 25.6 1.0 PD A:AP5302 4.8 30.1 1.0 PE A:AP5302 4.8 20.4 1.0 NH2 A:ARG36 4.8 22.7 1.0 O3D A:AP5302 4.8 26.9 1.0 PA A:AP5302 4.9 16.2 1.0 CB A:LYS13 4.9 17.7 1.0 OD1 A:ASP85 4.9 25.5 1.0 O A:HOH482 4.9 23.3 1.0 C A:LYS13 4.9 15.9 1.0 HB3 A:LYS13 5.0 21.3 1.0 O1A A:AP5302 5.0 16.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Adenylate Kinase From Streptococcus Pneumoniae with AP5A


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 Adenylate Kinase From Streptococcus Pneumoniae with AP5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:20.8 occ:1.00 O2G B:AP5302 2.1 20.7 1.0 O2B B:AP5302 2.3 20.0 1.0 O B:HOH501 2.4 27.0 1.0 O B:HOH554 2.4 22.1 1.0 O B:HOH593 2.5 35.7 1.0 O B:HOH405 2.6 17.8 1.0 PG B:AP5302 3.4 21.7 1.0 H B:GLY14 3.4 19.7 1.0 HA3 B:GLY14 3.5 19.1 1.0 HH12 B:ARG156 3.5 22.1 1.0 PB B:AP5302 3.5 18.0 1.0 HH12 B:ARG128 3.7 22.4 1.0 O B:HOH438 3.8 31.0 1.0 O3B B:AP5302 3.8 17.0 1.0 HB2 B:LYS13 3.9 33.0 1.0 N B:GLY14 4.0 16.4 1.0 O3G B:AP5302 4.0 28.8 1.0 CA B:GLY14 4.1 15.9 1.0 O B:HOH418 4.2 22.7 1.0 HH22 B:ARG36 4.2 24.4 1.0 NH1 B:ARG156 4.2 18.4 1.0 HA2 B:GLY14 4.2 19.1 1.0 HH11 B:ARG156 4.3 22.1 1.0 O1E B:AP5302 4.4 20.2 1.0 O2A B:AP5302 4.4 19.8 1.0 NH1 B:ARG128 4.4 18.6 1.0 OD2 B:ASP85 4.4 25.3 1.0 O3A B:AP5302 4.5 20.0 1.0 HH11 B:ARG128 4.5 22.4 1.0 O3D B:AP5302 4.5 66.4 1.0 O1G B:AP5302 4.6 26.7 1.0 O2E B:AP5302 4.6 31.6 1.0 O1B B:AP5302 4.6 24.3 1.0 O B:HOH445 4.7 33.6 1.0 PE B:AP5302 4.8 20.0 1.0 O B:HOH419 4.8 27.2 1.0 CB B:LYS13 4.8 27.5 1.0 PA B:AP5302 4.8 15.4 1.0 NH2 B:ARG36 4.9 20.4 1.0 HG B:SER30 4.9 23.5 1.0 HB3 B:LYS13 5.0 33.0 1.0 PD B:AP5302 5.0 46.9 1.0

T.T.Thach, T.T.Luong, S.H.Lee, D.K.Rhee. Adenylate Kinase From Streptococcus Pneumoniae Is Essential For Growth Through Its Catalytic Activity Febs Open Bio V. 4 672 2014.
ISSN: ESSN 2211-5463
PubMed: 25180151
DOI: 10.1016/J.FOB.2014.07.002