Magnesium in PDB 6ybu: Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound

The structure of Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound, PDB code: 6ybu was solved by W.Abidi, S.Zouhir, S.Roche, P.V.Krasteva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	107.99, 72.57, 161.25, 90, 98.37, 90
R / Rfree (%)	18.1 / 22.5

The binding sites of Magnesium atom in the Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound (pdb code 6ybu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound, PDB code: 6ybu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:41.6 occ:1.00 O2G A:ATP301 2.0 53.6 1.0 O A:HOH429 2.1 47.3 1.0 OG1 A:THR16 2.1 63.0 1.0 O A:HOH424 2.1 48.3 1.0 O A:HOH413 2.2 42.3 1.0 O2B A:ATP301 2.3 48.8 1.0 PG A:ATP301 3.2 49.7 1.0 O3B A:ATP301 3.4 49.9 1.0 PB A:ATP301 3.4 47.4 1.0 CB A:THR16 3.4 55.7 1.0 O3G A:ATP301 4.0 50.2 1.0 N A:THR16 4.0 47.6 1.0 OD2 A:ASP124 4.1 58.1 1.0 CA A:THR16 4.3 50.7 1.0 O1B A:ATP301 4.3 46.2 1.0 O A:HOH415 4.3 49.6 1.0 OD1 A:ASP124 4.3 59.0 1.0 O1G A:ATP301 4.4 52.3 1.0 CG2 A:THR16 4.4 54.5 1.0 O1A A:ATP301 4.5 42.3 1.0 O3A A:ATP301 4.6 49.8 1.0 CG A:ASP124 4.7 54.4 1.0 SG A:CYS39 4.7 63.9 1.0 CB A:THR15 4.8 47.1 1.0 CD1 A:LEU43 4.8 53.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:45.7 occ:1.00 O3G B:ATP301 2.0 51.9 1.0 O B:HOH413 2.1 48.6 1.0 O B:HOH410 2.1 41.4 1.0 OG1 B:THR16 2.2 54.3 1.0 O B:HOH432 2.2 63.9 1.0 O2B B:ATP301 2.3 47.8 1.0 PG B:ATP301 3.2 51.6 1.0 CB B:THR16 3.4 50.9 1.0 PB B:ATP301 3.5 46.1 1.0 O3B B:ATP301 3.6 55.0 1.0 O2G B:ATP301 3.7 47.0 1.0 OD2 B:ASP124 3.9 55.1 1.0 N B:THR16 4.1 42.1 1.0 CA B:THR16 4.3 46.1 1.0 OD1 B:ASP124 4.3 57.0 1.0 O1B B:ATP301 4.3 44.4 1.0 CG2 B:THR16 4.4 48.4 1.0 O1G B:ATP301 4.5 50.4 1.0 CG B:ASP124 4.6 55.4 1.0 O1A B:ATP301 4.6 41.1 1.0 CD1 B:LEU43 4.6 53.5 1.0 O3A B:ATP301 4.6 55.4 1.0 SG B:CYS39 4.7 63.1 1.0 CB B:THR15 4.9 40.7 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg302 b:44.0 occ:1.00 O3G G:ATP301 2.0 47.2 1.0 O G:HOH423 2.0 39.8 1.0 O2B G:ATP301 2.2 42.7 1.0 OG1 G:THR16 2.2 49.2 1.0 O G:HOH429 2.3 40.9 1.0 O G:HOH426 2.3 52.7 1.0 PG G:ATP301 3.1 44.9 1.0 O3B G:ATP301 3.2 47.2 1.0 PB G:ATP301 3.3 40.1 1.0 CB G:THR16 3.3 44.6 1.0 O2G G:ATP301 3.6 46.3 1.0 N G:THR16 4.0 44.2 1.0 OD2 G:ASP124 4.1 56.6 1.0 O1A G:ATP301 4.2 38.2 1.0 O1B G:ATP301 4.2 41.3 1.0 O G:HOH409 4.3 47.6 1.0 CA G:THR16 4.3 42.4 1.0 O3A G:ATP301 4.4 42.7 1.0 O1G G:ATP301 4.4 46.0 1.0 CG2 G:THR16 4.4 30.8 1.0 CD1 G:LEU43 4.7 38.0 1.0 OD1 G:ASP124 4.7 58.3 1.0 PA G:ATP301 4.8 44.3 1.0 SG G:CYS39 4.8 63.2 1.0 CG G:ASP124 4.8 52.5 1.0 ND2 H:ASN152 4.9 48.3 1.0 CB G:THR15 5.0 41.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Native Bcse (349-523) Rq Complex with C-Di-Gmp and Atp Bound within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg302 b:46.2 occ:1.00 OG1 H:THR16 2.0 55.1 1.0 O3G H:ATP301 2.1 48.9 1.0 O H:HOH425 2.2 48.1 1.0 O H:HOH428 2.2 51.6 1.0 O2B H:ATP301 2.2 44.5 1.0 O H:HOH422 2.3 47.7 1.0 PG H:ATP301 3.2 47.0 1.0 CB H:THR16 3.2 37.0 1.0 PB H:ATP301 3.4 42.4 1.0 O3B H:ATP301 3.4 53.4 1.0 O2G H:ATP301 3.6 46.4 1.0 N H:THR16 4.0 44.4 1.0 OD2 H:ASP124 4.1 50.9 1.0 CA H:THR16 4.2 40.8 1.0 CG2 H:THR16 4.2 34.5 1.0 O1B H:ATP301 4.3 46.2 1.0 O1A H:ATP301 4.4 44.6 1.0 OD1 H:ASP124 4.5 54.3 1.0 O3A H:ATP301 4.5 46.6 1.0 O1G H:ATP301 4.5 48.1 1.0 CG H:ASP124 4.7 52.3 1.0 CD1 H:LEU43 4.7 54.9 1.0 SG H:CYS39 4.7 72.7 1.0 PA H:ATP301 4.9 44.0 1.0 CB H:THR15 4.9 43.6 1.0

W.Abidi, S.Zouhir, M.Caleechurn, S.Roche, P.V.Krasteva. Architecture and Regulation of An Enterobacterial Cellulose Secretion System. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33563593
DOI: 10.1126/SCIADV.ABD8049