Magnesium in PDB 4qrh: Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp

All present enzymatic activity of Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp:
2.7.4.8;

The structure of Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp, PDB code: 4qrh was solved by K.Liu, K.Krasny, A.R.Myers, K.A.Satyshur, J.L.Keck, J.D.Wnag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.26 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.486, 93.961, 85.259, 90.00, 111.09, 90.00
R / Rfree (%)	20.1 / 22.7

The structure of Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Magnesium atom in the Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp (pdb code 4qrh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp, PDB code: 4qrh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:21.8 occ:1.00 O2C B:0O2303 2.0 25.4 1.0 O2D B:0O2303 2.1 22.4 1.0 O B:HOH558 2.2 40.6 1.0 O1B B:0O2303 2.3 46.9 1.0 O3G B:0O2303 2.4 57.3 1.0 O B:HOH559 2.7 50.1 1.0 PC B:0O2303 3.1 23.8 1.0 PD B:0O2303 3.2 22.4 1.0 O3C B:0O2303 3.3 22.9 1.0 PG B:0O2303 3.4 59.0 1.0 PB B:0O2303 3.5 47.1 1.0 O3B B:0O2303 3.6 53.4 1.0 OH B:TYR78 3.6 35.8 1.0 O B:HOH560 3.8 34.6 1.0 O1D B:0O2303 3.8 21.0 1.0 O B:HOH525 3.8 40.3 1.0 O2G B:0O2303 3.9 59.1 1.0 O1C B:0O2303 4.0 24.8 1.0 N B:GLY16 4.2 22.6 1.0 O3' B:0O2303 4.4 21.8 1.0 CA B:GLY16 4.4 23.6 1.0 O3A B:0O2303 4.4 38.9 1.0 O3D B:0O2303 4.5 21.4 1.0 CZ B:TYR78 4.5 33.4 1.0 C3' B:0O2303 4.5 20.5 1.0 O2B B:0O2303 4.6 48.2 1.0 C5' B:0O2303 4.7 24.0 1.0 O1G B:0O2303 4.7 58.2 1.0 C4' B:0O2303 4.9 22.1 1.0 CE2 B:TYR78 4.9 32.7 1.0

Magnesium binding site 2 out of 3 in the Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:22.7 occ:1.00 O2C C:0O2304 1.9 22.5 1.0 O2D C:0O2304 2.3 23.2 1.0 O C:HOH542 2.3 36.8 1.0 O1B C:0O2304 2.7 42.7 1.0 O3G C:0O2304 2.8 57.0 1.0 PC C:0O2304 3.1 21.6 1.0 PD C:0O2304 3.3 22.3 1.0 O3C C:0O2304 3.4 22.2 1.0 PG C:0O2304 3.7 59.4 1.0 O2G C:0O2304 3.8 58.4 1.0 OH C:TYR78 3.8 30.7 1.0 O1D C:0O2304 3.8 20.2 1.0 PB C:0O2304 3.9 42.8 1.0 O3B C:0O2304 4.0 49.5 1.0 O C:HOH541 4.0 42.6 1.0 O1C C:0O2304 4.1 22.3 1.0 N C:GLY16 4.3 23.9 1.0 O3' C:0O2304 4.3 20.3 1.0 O3A C:0O2304 4.5 33.7 1.0 C3' C:0O2304 4.5 19.5 1.0 CA C:GLY16 4.6 25.2 1.0 O3D C:0O2304 4.6 21.0 1.0 C5' C:0O2304 4.6 21.4 1.0 CZ C:TYR78 4.6 26.9 1.0 C4' C:0O2304 4.9 20.1 1.0

Magnesium binding site 3 out of 3 in the Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:23.2 occ:1.00 O1B D:0O2306 2.0 38.3 1.0 O2C D:0O2306 2.1 22.0 1.0 O2D D:0O2306 2.1 20.0 1.0 O3G D:0O2306 2.2 55.7 1.0 PG D:0O2306 3.1 56.0 1.0 PB D:0O2306 3.1 35.9 1.0 PC D:0O2306 3.2 21.5 1.0 PD D:0O2306 3.2 18.6 1.0 O3B D:0O2306 3.2 47.6 1.0 O2G D:0O2306 3.4 57.2 1.0 O3C D:0O2306 3.4 19.8 1.0 O D:HOH506 3.8 40.1 1.0 O2B D:0O2306 3.8 42.0 1.0 O1D D:0O2306 3.8 17.7 1.0 OH D:TYR78 3.9 32.5 1.0 O D:HOH519 4.0 28.1 1.0 N D:GLY16 4.0 21.3 1.0 O1C D:0O2306 4.3 21.9 1.0 O3' D:0O2306 4.3 17.8 1.0 O3A D:0O2306 4.4 29.6 1.0 CA D:GLY16 4.4 21.9 1.0 C3' D:0O2306 4.4 16.9 1.0 C5' D:0O2306 4.4 18.3 1.0 O1G D:0O2306 4.4 55.0 1.0 O3D D:0O2306 4.5 17.8 1.0 CZ D:TYR78 4.7 26.2 1.0 C4' D:0O2306 4.8 17.1 1.0 CE2 D:TYR78 4.9 25.9 1.0 O5' D:0O2306 5.0 19.9 1.0

K.Liu, A.R.Myers, T.Pisithkul, K.R.Claas, K.A.Satyshur, D.Amador-Noguez, J.L.Keck, J.D.Wang. Molecular Mechanism and Evolution of Guanylate Kinase Regulation By (P)Ppgpp. Mol.Cell V. 57 735 2015.
ISSN: ISSN 1097-2765
PubMed: 25661490
DOI: 10.1016/J.MOLCEL.2014.12.037