Magnesium in PDB 9clo: Dosp R97A with C-Di-Gmp

All present enzymatic activity of Dosp R97A with C-Di-Gmp:
3.1.4.52;

The structure of Dosp R97A with C-Di-Gmp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Dosp R97A with C-Di-Gmp (pdb code 9clo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dosp R97A with C-Di-Gmp, PDB code: 9clo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dosp R97A with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dosp R97A with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:35.4 occ:1.00 O2P A:C2E902 2.1 50.7 1.0 OE2 A:GLU584 2.3 49.2 1.0 OD1 A:ASN643 3.1 38.3 1.0 P1 A:C2E902 3.3 63.5 1.0 CD A:GLU584 3.4 55.3 1.0 NZ A:LYS726 3.5 70.7 1.0 O5' A:C2E902 3.6 60.9 1.0 OE1 A:GLU584 3.8 54.2 1.0 OE2 A:GLU762 3.8 70.0 1.0 CG A:ASN643 3.9 41.8 1.0 O1P A:C2E902 4.0 56.7 1.0 ND2 A:ASN643 4.0 44.5 1.0 C5' A:C2E902 4.4 56.1 1.0 CG A:GLU675 4.4 54.7 1.0 OD2 A:ASP705 4.5 83.4 1.0 O3A A:C2E902 4.6 50.4 1.0 OE2 A:GLU675 4.6 54.5 1.0 CG A:GLU584 4.6 50.5 1.0 CE A:LYS726 4.7 71.5 1.0 CD A:GLU762 4.8 71.4 1.0 CD A:LYS726 4.8 70.4 1.0 MG A:MG904 4.9 53.7 1.0 CD A:GLU675 4.9 58.2 1.0 CD2 A:LEU586 4.9 39.8 1.0 OE1 A:GLU762 4.9 71.8 1.0 C3A A:C2E902 5.0 46.0 1.0

Magnesium binding site 2 out of 4 in the Dosp R97A with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dosp R97A with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:53.7 occ:1.00 OE1 A:GLU762 2.2 71.8 1.0 OD2 A:ASP705 2.6 83.4 1.0 O1P A:C2E902 2.8 56.7 1.0 OD1 A:ASP728 3.1 82.1 1.0 CD A:GLU762 3.4 71.4 1.0 CG A:ASP705 3.7 84.7 1.0 OE2 A:GLU762 3.8 70.0 1.0 P1 A:C2E902 3.9 63.5 1.0 CG A:ASP728 3.9 78.9 1.0 OD1 A:ASP705 4.1 88.4 1.0 O2P A:C2E902 4.1 50.7 1.0 OD1 A:ASP706 4.4 89.0 1.0 OD2 A:ASP728 4.5 78.7 1.0 CG A:GLU762 4.6 69.5 1.0 CA A:ASP728 4.6 74.9 1.0 O3A A:C2E902 4.7 50.4 1.0 CB A:GLU762 4.7 66.2 1.0 N A:LYS729 4.7 73.3 1.0 CB A:ASP728 4.7 74.8 1.0 MG A:MG903 4.9 35.4 1.0 CB A:ASP705 5.0 81.4 1.0

Magnesium binding site 3 out of 4 in the Dosp R97A with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dosp R97A with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:18.7 occ:1.00 O2P B:C2E901 2.1 53.2 1.0 OD1 B:ASN643 2.3 53.6 1.0 OE2 B:GLU584 2.8 46.0 1.0 CG B:ASN643 3.4 46.8 1.0 P1 B:C2E901 3.5 46.9 1.0 CD B:GLU584 3.7 44.8 1.0 ND2 B:ASN643 3.9 49.1 1.0 CG B:GLU675 3.9 64.6 1.0 OE1 B:GLU584 4.0 50.9 1.0 OE2 B:GLU675 4.1 65.1 1.0 O5' B:C2E901 4.2 47.0 1.0 O1P B:C2E901 4.3 57.3 1.0 CD B:GLU675 4.4 68.1 1.0 OD2 B:ASP705 4.5 82.2 1.0 O3A B:C2E901 4.6 53.9 1.0 NZ B:LYS726 4.6 66.5 1.0 CB B:ASN643 4.7 40.4 1.0 OE2 B:GLU762 4.8 70.9 1.0 CB B:GLU675 4.8 59.2 1.0 C2A B:C2E901 4.9 58.1 1.0 CG B:GLU584 5.0 36.3 1.0 C3A B:C2E901 5.0 54.6 1.0

Magnesium binding site 4 out of 4 in the Dosp R97A with C-Di-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dosp R97A with C-Di-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:59.3 occ:1.00 OD2 B:ASP705 2.7 82.2 1.0 OD1 B:ASP728 2.9 81.7 1.0 O1P B:C2E901 3.0 57.3 1.0 CG B:ASP728 3.4 80.2 1.0 OD1 B:ASP706 3.5 92.6 1.0 OD2 B:ASP728 3.6 79.1 1.0 CG B:ASP705 3.6 83.8 1.0 OE1 B:GLU762 3.9 65.9 1.0 OD1 B:ASP705 4.0 83.8 1.0 P1 B:C2E901 4.3 46.9 1.0 CG B:ASP706 4.4 94.3 1.0 CB B:ASP728 4.6 74.8 1.0 OD2 B:ASP706 4.6 92.7 1.0 O2P B:C2E901 4.8 53.2 1.0 CB B:ASP705 4.8 84.7 1.0 O3A B:C2E901 4.9 53.9 1.0

W.Wu, P.Kumar, C.A.Brautigam, S.C.Tso, H.R.Baniasadi, D.L.Kober, M.A.Gilles-Gonzalez. Structures of the Multi-Domain Oxygen Sensor Dosp: Remote Control of A C-Di-Gmp Phosphodiesterase By A Regulatory Pas Domain Nat Commun V. 15 9653 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-53942-7