Magnesium in PDB 9cmf: Substrate Bound Dosp

All present enzymatic activity of Substrate Bound Dosp:
3.1.4.52;

The structure of Substrate Bound Dosp also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Substrate Bound Dosp (pdb code 9cmf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Substrate Bound Dosp, PDB code: 9cmf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Substrate Bound Dosp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Substrate Bound Dosp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg904 b:67.4 occ:1.00 O2P A:C2E903 1.9 83.6 1.0 OD1 A:ASN643 2.0 80.1 1.0 OE2 A:GLU584 3.1 78.6 1.0 CG A:ASN643 3.2 81.0 1.0 P1 A:C2E903 3.4 87.2 1.0 CD A:GLU584 3.8 79.8 1.0 OE1 A:GLU584 4.0 83.3 1.0 ND2 A:ASN643 4.0 80.3 1.0 O1P A:C2E903 4.0 82.7 1.0 CG A:GLU675 4.1 86.5 1.0 O5' A:C2E903 4.2 78.4 1.0 OE2 A:GLU675 4.2 91.6 1.0 CB A:ASN643 4.3 77.1 1.0 O3A A:C2E903 4.4 81.1 1.0 OD2 A:ASP705 4.6 109.9 1.0 CD A:GLU675 4.7 91.7 1.0 C2A A:C2E903 4.7 75.6 1.0 NZ A:LYS726 4.8 87.9 1.0 C3A A:C2E903 4.8 77.1 1.0 O2A A:C2E903 4.9 79.6 1.0

Magnesium binding site 2 out of 4 in the Substrate Bound Dosp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Substrate Bound Dosp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg905 b:93.8 occ:1.00 OD2 A:ASP705 2.1 109.9 1.0 CG A:ASP705 3.1 111.7 1.0 O1P A:C2E903 3.5 82.7 1.0 OD1 A:ASP728 3.7 100.9 1.0 OD1 A:ASP705 3.7 112.3 1.0 OD1 A:ASP706 4.0 117.0 1.0 CB A:ASP705 4.2 110.1 1.0 CG A:ASP728 4.3 99.1 1.0 OE1 A:GLU762 4.5 84.3 1.0 P1 A:C2E903 4.5 87.2 1.0 OD2 A:ASP706 4.6 116.9 1.0 CG A:ASP706 4.6 116.5 1.0 OD2 A:ASP728 4.6 96.4 1.0 O2P A:C2E903 4.8 83.6 1.0 O3A A:C2E903 4.9 81.1 1.0

Magnesium binding site 3 out of 4 in the Substrate Bound Dosp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Substrate Bound Dosp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg904 b:73.7 occ:1.00 O2P B:C2E903 1.9 73.0 1.0 OE2 B:GLU584 2.4 69.9 1.0 OD1 B:ASN643 2.8 78.4 1.0 P1 B:C2E903 3.1 77.3 1.0 CD B:GLU584 3.3 68.8 1.0 OE1 B:GLU584 3.5 69.7 1.0 O1P B:C2E903 3.6 77.9 1.0 O5' B:C2E903 3.7 77.2 1.0 CG B:ASN643 3.8 75.9 1.0 NZ B:LYS726 3.9 82.8 1.0 OE2 B:GLU762 4.0 88.8 1.0 ND2 B:ASN643 4.0 76.1 1.0 OE2 B:GLU675 4.1 97.4 1.0 MG B:MG905 4.2 96.8 1.0 CG B:GLU675 4.2 90.7 1.0 C5' B:C2E903 4.4 73.3 1.0 O3A B:C2E903 4.5 79.0 1.0 OD2 B:ASP705 4.6 96.7 1.0 CD B:GLU675 4.6 94.1 1.0 CG B:GLU584 4.6 61.6 1.0 OE1 B:GLU762 4.7 86.9 1.0 CD B:GLU762 4.8 86.3 1.0 CE B:LYS726 4.8 82.9 1.0 CD B:LYS726 4.8 84.7 1.0

Magnesium binding site 4 out of 4 in the Substrate Bound Dosp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Substrate Bound Dosp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg905 b:96.8 occ:1.00 OD2 B:ASP705 2.0 96.7 1.0 OE1 B:GLU762 2.0 86.9 1.0 O1P B:C2E903 2.6 77.9 1.0 CG B:ASP705 3.0 98.2 1.0 CD B:GLU762 3.1 86.3 1.0 OD1 B:ASP705 3.4 102.0 1.0 OE2 B:GLU762 3.5 88.8 1.0 P1 B:C2E903 3.8 77.3 1.0 O2P B:C2E903 4.0 73.0 1.0 MG B:MG904 4.2 73.7 1.0 CB B:ASP705 4.3 95.0 1.0 CG B:GLU762 4.3 81.6 1.0 CB B:GLU762 4.6 80.2 1.0 OD1 B:ASP728 4.7 100.3 1.0 O3A B:C2E903 4.7 79.0 1.0 OD1 B:ASP706 4.8 112.8 1.0 O5' B:C2E903 5.0 77.2 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