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

Protein crystallography data

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

Magnesium Binding Sites:

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 6ybu

Go back to Magnesium Binding Sites List in 6ybu
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 6ybu

Go back to Magnesium Binding Sites List in 6ybu
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 6ybu

Go back to Magnesium Binding Sites List in 6ybu
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 6ybu

Go back to Magnesium Binding Sites List in 6ybu
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

Reference:

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
Page generated: Wed Mar 3 14:59:04 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy