Magnesium in PDB 1t9s: Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp:
3.1.4.17;

The structure of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp, PDB code: 1t9s was solved by K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D.Hsieh, J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.-H.Kim, J.Schlessinger, G.Bollag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.01 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.969, 90.872, 68.991, 90.00, 98.07, 90.00
R / Rfree (%)	17.5 / 21.2

The structure of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp (pdb code 1t9s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp, PDB code: 1t9s:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2 b:11.5 occ:1.00 OD1 A:ASP654 2.2 8.7 1.0 O A:HOH1151 2.2 12.7 1.0 O A:HOH1153 2.2 10.6 1.0 O1P A:5GP859 2.2 13.8 1.0 O A:HOH1154 2.2 11.9 1.0 O A:HOH1152 2.2 10.4 1.0 CG A:ASP654 3.1 7.6 1.0 OD2 A:ASP654 3.2 9.2 1.0 P A:5GP859 3.3 16.3 1.0 ZN A:ZN1 3.6 13.6 1.0 O2P A:5GP859 3.7 11.9 1.0 O5' A:5GP859 3.8 16.3 1.0 O A:HOH862 3.9 12.6 1.0 CD2 A:HIS653 4.0 7.2 1.0 OE2 A:GLU682 4.0 8.8 1.0 OG1 A:THR723 4.1 9.1 1.0 O A:HIS653 4.2 6.4 1.0 NE2 A:HIS685 4.2 4.5 1.0 O A:THR723 4.4 7.5 1.0 CE1 A:HIS657 4.4 6.6 1.0 CD2 A:HIS685 4.4 6.5 1.0 ND1 A:HIS657 4.4 9.2 1.0 CB A:ASP654 4.4 6.3 1.0 NE2 A:HIS653 4.5 9.3 1.0 O3P A:5GP859 4.5 15.4 1.0 CB A:THR723 4.6 8.6 1.0 OD2 A:ASP764 4.6 8.4 1.0 CA A:ASP654 4.8 6.2 1.0 CD A:GLU682 4.9 8.7 1.0 O A:HOH929 5.0 14.8 1.0 CD2 A:HIS613 5.0 9.0 1.0 CG A:GLU682 5.0 6.0 1.0 C A:HIS653 5.0 6.1 1.0

Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:11.1 occ:1.00 OD1 B:ASP654 2.1 6.6 1.0 O B:HOH1136 2.1 12.2 1.0 O1P B:5GP859 2.2 13.2 1.0 O B:HOH1133 2.2 13.1 1.0 O B:HOH1135 2.2 11.6 1.0 O B:HOH1134 2.2 10.6 1.0 CG B:ASP654 3.1 6.3 1.0 OD2 B:ASP654 3.3 8.7 1.0 P B:5GP859 3.3 18.4 1.0 ZN B:ZN1 3.6 14.3 1.0 O2P B:5GP859 3.7 13.7 1.0 O5' B:5GP859 3.9 17.2 1.0 O B:HOH863 3.9 14.3 1.0 CD2 B:HIS653 4.1 8.7 1.0 OE2 B:GLU682 4.1 8.9 1.0 OG1 B:THR723 4.1 9.0 1.0 NE2 B:HIS685 4.2 3.9 1.0 O B:HIS653 4.2 6.2 1.0 CD2 B:HIS685 4.4 5.3 1.0 O B:THR723 4.4 9.6 1.0 NE2 B:HIS653 4.5 9.1 1.0 CB B:ASP654 4.5 6.3 1.0 O3P B:5GP859 4.5 16.1 1.0 ND1 B:HIS657 4.5 8.3 1.0 CE1 B:HIS657 4.5 7.8 1.0 CB B:THR723 4.6 8.9 1.0 OD2 B:ASP764 4.6 8.8 1.0 CA B:ASP654 4.8 6.2 1.0 O B:HOH1027 4.9 19.5 1.0 CG B:GLU682 4.9 7.9 1.0 CD B:GLU682 4.9 8.5 1.0

K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D.Hsieh, J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.-H.Kim, J.Schlessinger, G.Bollag. A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases Mol.Cell V. 15 279 2004.
ISSN: ISSN 1097-2765
PubMed: 15260978
DOI: 10.1016/J.MOLCEL.2004.07.005