Magnesium in PDB 7nre: Crystal Structure of E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1)

Protein crystallography data

The structure of Crystal Structure of E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1), PDB code: 7nre was solved by R.P.Jakob, H.Kaur, J.K.Marzinek, R.Green, Y.Imai, J.Bolla, C.Robinson, P.J.Bond, K.Lewis, T.Maier, S.Hiller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 2.30
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 69.995, 82.563, 94.305, 90, 108.64, 90
R / Rfree (%) 20.5 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1) (pdb code 7nre). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1), PDB code: 7nre:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7nre

Go back to Magnesium Binding Sites List in 7nre
Magnesium binding site 1 out of 2 in the Crystal Structure of E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1)


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 E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:24.9
occ:1.00
OD2 A:ASP497 2.5 34.6 1.0
O A:HOH1163 2.7 30.9 1.0
CG A:ASP497 3.4 32.9 1.0
HB2 A:ASP497 3.6 31.5 1.0
CB A:ASP497 4.0 26.3 1.0
OD1 A:ASP497 4.2 34.1 1.0
O A:HOH1176 4.3 20.8 1.0
HB3 A:ASP497 4.4 31.5 1.0
OD1 A:ASP498 4.6 47.5 1.0

Magnesium binding site 2 out of 2 in 7nre

Go back to Magnesium Binding Sites List in 7nre
Magnesium binding site 2 out of 2 in the Crystal Structure of E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1)


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 E.Coli Bama Beta-Barrel in Complex with Darobactin (Crystal Form 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1006

b:63.9
occ:1.00
HZ1 A:LYS798 2.2 74.1 1.0
OD1 A:ASP703 2.2 59.4 1.0
OD1 A:ASP704 2.9 44.6 1.0
NZ A:LYS798 3.1 61.8 1.0
CG A:ASP703 3.2 56.1 1.0
HZ3 A:LYS798 3.3 74.1 1.0
OD2 A:ASP703 3.4 60.2 1.0
HE2 A:LYS798 3.5 77.8 1.0
HZ2 A:LYS798 3.7 74.1 1.0
O A:HOH1224 3.7 56.9 1.0
CE A:LYS798 3.8 64.8 1.0
HE3 A:LYS798 3.9 77.8 1.0
CG A:ASP704 3.9 42.8 1.0
H A:ASP703 4.2 46.2 1.0
OD2 A:ASP704 4.5 43.5 1.0
C A:ASP703 4.5 35.3 1.0
CB A:ASP703 4.6 47.4 1.0
HA A:ASP704 4.6 47.2 1.0
O A:ASP703 4.6 33.3 1.0
N A:ASP704 4.7 35.2 1.0
H A:ASP704 4.9 42.3 1.0
CA A:ASP703 4.9 39.0 1.0
N A:ASP703 4.9 38.5 1.0

Reference:

H.Kaur, R.P.Jakob, J.K.Marzinek, R.Green, Y.Imai, J.R.Bolla, E.Agustoni, C.V.Robinson, P.J.Bond, K.Lewis, T.Maier, S.Hiller. The Antibiotic Darobactin Mimics A Beta-Strand to Inhibit Outer Membrane Insertasemimicking A Substrate Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03455-W
Page generated: Mon Jul 12 14:40:27 2021

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