Magnesium in PDB 5m1t: Pamucr Phosphodiesterase, C-Di-Gmp Complex

The structure of Pamucr Phosphodiesterase, C-Di-Gmp Complex, PDB code: 5m1t was solved by A.Hutchin, I.Tews, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.27 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.370, 116.110, 52.140, 90.00, 102.52, 90.00
R / Rfree (%)	19.5 / 23.8

The binding sites of Magnesium atom in the Pamucr Phosphodiesterase, C-Di-Gmp Complex (pdb code 5m1t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Pamucr Phosphodiesterase, C-Di-Gmp Complex, PDB code: 5m1t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Pamucr Phosphodiesterase, C-Di-Gmp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pamucr Phosphodiesterase, C-Di-Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:13.9 occ:1.00 O2P A:C2E701 2.1 20.8 1.0 OE1 A:GLU560 2.1 25.7 1.0 O A:HOH825 2.2 24.7 1.0 OD2 A:ASP590 2.2 26.3 1.0 OE2 A:GLU469 2.2 19.8 1.0 OD1 A:ASN528 2.2 19.6 1.0 CG A:ASP590 3.0 26.4 1.0 CG A:ASN528 3.2 19.2 1.0 CD A:GLU469 3.2 21.2 1.0 CD A:GLU560 3.3 25.9 1.0 P1 A:C2E701 3.4 22.2 1.0 OD1 A:ASP590 3.4 26.5 1.0 ND2 A:ASN528 3.4 18.6 1.0 OE1 A:GLU469 3.7 21.2 1.0 O5' A:C2E701 3.9 22.3 1.0 MG A:MG703 4.0 26.4 1.0 O1P A:C2E701 4.0 23.3 1.0 OE2 A:GLU560 4.1 26.4 1.0 CB A:GLU560 4.2 24.2 1.0 O A:HOH837 4.2 19.8 1.0 CB A:ASP590 4.3 25.2 1.0 CG A:GLU560 4.4 25.4 1.0 O A:HOH868 4.4 29.4 1.0 CG A:GLU469 4.4 21.6 1.0 NZ A:LYS611 4.4 25.0 1.0 CB A:ASN528 4.6 19.7 1.0 OE2 A:GLU647 4.6 33.0 1.0 O3A A:C2E701 4.7 23.5 1.0 C5' A:C2E701 4.8 23.5 1.0 C2A A:C2E701 4.9 22.8 1.0 CD A:LYS611 4.9 23.8 1.0

Magnesium binding site 2 out of 4 in the Pamucr Phosphodiesterase, C-Di-Gmp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pamucr Phosphodiesterase, C-Di-Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:26.4 occ:1.00 O A:HOH801 2.2 14.9 1.0 OD1 A:ASP590 2.2 26.5 1.0 OD1 A:ASP591 2.4 27.9 1.0 O1P A:C2E701 2.4 23.3 1.0 OE1 A:GLU647 2.5 33.1 1.0 OE2 A:GLU647 2.5 33.0 1.0 CD A:GLU647 2.8 33.6 1.0 O A:HOH825 3.1 24.7 1.0 CG A:ASP590 3.2 26.4 1.0 P1 A:C2E701 3.6 22.2 1.0 N A:ASP591 3.6 24.1 1.0 OD2 A:ASP590 3.6 26.3 1.0 CG A:ASP591 3.6 27.1 1.0 O2P A:C2E701 3.7 20.8 1.0 MG A:MG702 4.0 13.9 1.0 CA A:ASP591 4.0 24.8 1.0 CG A:GLU647 4.3 32.4 1.0 O A:HOH837 4.4 19.8 1.0 O5' A:C2E701 4.4 22.3 1.0 CB A:ASP591 4.4 25.9 1.0 CB A:ASP590 4.5 25.2 1.0 OD1 A:ASP613 4.5 25.7 1.0 OD2 A:ASP591 4.5 27.8 1.0 C5' A:C2E701 4.5 23.5 1.0 NH1 A:ARG614 4.6 38.2 1.0 C A:ASP590 4.6 24.3 1.0 O3A A:C2E701 4.7 23.5 1.0 CA A:ASP590 4.8 24.4 1.0 CB A:LYS611 5.0 22.6 1.0

Magnesium binding site 3 out of 4 in the Pamucr Phosphodiesterase, C-Di-Gmp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pamucr Phosphodiesterase, C-Di-Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:31.1 occ:1.00 OE1 B:GLU647 2.2 38.1 1.0 O11 B:C2E701 2.2 28.6 1.0 OD1 B:ASP591 2.3 27.5 1.0 OD1 B:ASP590 2.4 27.6 1.0 O B:HOH802 2.4 28.2 1.0 O B:HOH844 2.5 50.7 1.0 OE2 B:GLU647 2.7 36.7 1.0 CD B:GLU647 2.7 36.3 1.0 CG B:ASP590 3.3 28.2 1.0 O B:HOH830 3.3 25.9 1.0 P11 B:C2E701 3.5 29.8 1.0 OD2 B:ASP590 3.5 31.0 1.0 CG B:ASP591 3.6 27.1 1.0 O21 B:C2E701 3.7 26.4 1.0 N B:ASP591 3.8 25.4 1.0 CA B:ASP591 4.2 26.0 1.0 CG B:GLU647 4.2 34.5 1.0 MG B:MG703 4.3 16.5 1.0 OD2 B:ASP591 4.4 26.8 1.0 O5A B:C2E701 4.4 30.2 1.0 C5A B:C2E701 4.5 30.3 1.0 CB B:ASP591 4.5 26.5 1.0 OD1 B:ASP613 4.5 29.8 1.0 O B:HOH813 4.5 26.4 1.0 O3' B:C2E701 4.6 31.6 1.0 CB B:ASP590 4.6 27.6 1.0 C B:ASP590 4.8 25.5 1.0 CB B:GLU647 5.0 30.9 1.0

Magnesium binding site 4 out of 4 in the Pamucr Phosphodiesterase, C-Di-Gmp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pamucr Phosphodiesterase, C-Di-Gmp Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg703 b:16.5 occ:1.00 O21 B:C2E701 2.1 26.4 1.0 OD2 B:ASP590 2.1 31.0 1.0 OE1 B:GLU560 2.1 32.3 1.0 O B:HOH830 2.1 25.9 1.0 OE2 B:GLU469 2.2 32.2 1.0 OD1 B:ASN528 2.3 28.8 1.0 CG B:ASP590 3.1 28.2 1.0 CG B:ASN528 3.2 29.1 1.0 CD B:GLU469 3.2 33.4 1.0 CD B:GLU560 3.3 32.5 1.0 P11 B:C2E701 3.5 29.8 1.0 ND2 B:ASN528 3.5 29.1 1.0 OD1 B:ASP590 3.6 27.6 1.0 OE1 B:GLU469 3.7 32.3 1.0 O5A B:C2E701 4.0 30.2 1.0 OE2 B:GLU560 4.1 32.2 1.0 O11 B:C2E701 4.1 28.6 1.0 CB B:GLU560 4.2 32.5 1.0 CB B:ASP590 4.2 27.6 1.0 MG B:MG702 4.3 31.1 1.0 CG B:GLU560 4.3 33.0 1.0 O B:HOH820 4.3 42.4 1.0 O B:HOH813 4.4 26.4 1.0 CG B:GLU469 4.4 34.1 1.0 CB B:ASN528 4.6 30.1 1.0 NZ B:LYS611 4.6 27.7 1.0 OE2 B:GLU647 4.7 36.7 1.0 O3' B:C2E701 4.7 31.6 1.0 CD B:LYS611 4.9 27.5 1.0 C2' B:C2E701 5.0 32.5 1.0

D.Bellini, S.Horrell, A.Hutchin, C.W.Phippen, R.W.Strange, Y.Cai, A.Wagner, J.S.Webb, I.Tews, M.A.Walsh. Dimerisation Induced Formation of the Active Site and the Identification of Three Metal Sites in Eal-Phosphodiesterases. Sci Rep V. 7 42166 2017.
ISSN: ESSN 2045-2322
PubMed: 28186120
DOI: 10.1038/SREP42166