Magnesium in PDB 6ofr: The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli

Protein crystallography data

The structure of The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli, PDB code: 6ofr was solved by R.Grinter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.520, 76.520, 412.750, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli (pdb code 6ofr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli, PDB code: 6ofr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ofr

Go back to Magnesium Binding Sites List in 6ofr
Magnesium binding site 1 out of 2 in the The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:53.2
occ:1.00
O A:GLN539 2.2 51.3 1.0
O A:LEU478 2.2 47.1 1.0
O A:HOH1063 2.3 50.1 1.0
O A:HOH980 2.4 44.4 1.0
O A:HOH1126 2.5 69.8 1.0
C A:LEU478 3.4 44.3 1.0
C A:GLN539 3.4 50.8 1.0
CA A:ASP540 4.0 48.1 1.0
OD1 A:ASN480 4.0 47.5 1.0
CA A:LEU478 4.0 37.3 1.0
N A:ASP540 4.1 48.0 1.0
O A:HOH1107 4.3 55.2 1.0
N A:SER479 4.4 38.8 1.0
CA A:GLN539 4.5 44.6 1.0
O A:HOH979 4.5 43.9 1.0
C A:ASP540 4.5 49.3 1.0
CB A:LEU478 4.5 35.3 1.0
CB A:SER479 4.5 41.4 1.0
O A:SER479 4.6 46.6 1.0
O A:LEU541 4.6 41.7 1.0
C A:SER479 4.7 44.1 1.0
CA A:SER479 4.8 38.8 1.0
CB A:GLN539 4.8 46.2 1.0
O A:ASP540 4.9 50.1 1.0
N A:LEU541 4.9 42.6 1.0
CG A:ASN480 5.0 51.9 1.0
OG A:SER479 5.0 46.1 1.0

Magnesium binding site 2 out of 2 in 6ofr

Go back to Magnesium Binding Sites List in 6ofr
Magnesium binding site 2 out of 2 in the The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Outer Membrane Transporter Yddb From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg809

b:63.1
occ:1.00
O A:HOH1124 2.2 59.0 1.0
O A:LEU193 2.2 54.8 1.0
O A:HOH1118 2.8 54.3 1.0
O A:SER190 3.0 54.9 1.0
C A:LEU193 3.5 52.9 1.0
N A:SER195 4.0 50.4 1.0
CA A:THR194 4.1 48.0 1.0
C A:SER190 4.2 53.9 1.0
N A:THR194 4.2 46.8 1.0
C A:THR194 4.4 53.1 1.0
O3 A:BOG802 4.4 79.1 1.0
CA A:LEU193 4.5 48.1 1.0
CD1 A:LEU193 4.6 53.1 1.0
N A:LEU193 4.6 48.5 1.0
CB A:SER195 4.6 51.7 1.0
OG A:SER195 4.8 52.3 1.0
CB A:LEU193 4.8 47.4 1.0
CA A:SER195 5.0 50.1 1.0
O A:ASP191 5.0 53.6 1.0

Reference:

R.Grinter, P.M.Leung, L.C.Wijeyewickrema, D.Littler, S.Beckham, R.N.Pike, D.Walker, C.Greening, T.Lithgow. Protease-Associated Import Systems Are Widespread in Gram-Negative Bacteria. Plos Genet. V. 15 08435 2019.
ISSN: ESSN 1553-7404
PubMed: 31613892
DOI: 10.1371/JOURNAL.PGEN.1008435
Page generated: Mon Dec 14 23:43:05 2020

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