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Magnesium in PDB 5ofr: Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State

Protein crystallography data

The structure of Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State, PDB code: 5ofr was solved by K.Beis, K.Bountra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.30 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 235.290, 105.040, 117.370, 90.00, 105.55, 90.00
R / Rfree (%) 25.7 / 26

Other elements in 5ofr:

The structure of Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State also contains other interesting chemical elements:

Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State (pdb code 5ofr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State, PDB code: 5ofr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5ofr

Go back to Magnesium Binding Sites List in 5ofr
Magnesium binding site 1 out of 2 in the Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:77.3
occ:1.00
OG A:SER385 1.9 1.0 1.0
O1 A:VO4603 1.9 0.7 1.0
O1B A:ADP601 1.9 0.0 1.0
OE1 A:GLN426 2.3 0.1 1.0
V A:VO4603 2.7 0.7 1.0
CB A:SER385 3.0 98.4 1.0
O2 A:VO4603 3.2 0.4 1.0
CD A:GLN426 3.3 1.0 1.0
PB A:ADP601 3.3 0.6 1.0
O3B A:ADP601 3.6 0.2 1.0
N A:SER385 3.6 97.1 1.0
NE2 A:GLN426 3.9 0.2 1.0
CA A:SER385 3.9 95.8 1.0
OD2 A:ASP505 4.0 88.1 1.0
O4 A:VO4603 4.0 0.6 1.0
OD1 A:ASP505 4.0 85.2 1.0
O1A A:ADP601 4.0 0.9 1.0
O2A A:ADP601 4.1 0.9 1.0
O3A A:ADP601 4.1 0.9 1.0
O2B A:ADP601 4.3 0.4 1.0
PA A:ADP601 4.3 0.3 1.0
CG A:GLN426 4.4 0.8 1.0
O3 A:VO4603 4.4 0.0 1.0
CG A:ASP505 4.4 85.0 1.0
OE1 A:GLU506 4.5 0.0 1.0
CB A:LYS384 4.6 0.5 1.0
CE A:LYS384 4.7 97.4 1.0
C A:LYS384 4.8 1.0 1.0
N B:GLY483 4.9 0.3 1.0
N A:LYS384 4.9 0.5 1.0

Magnesium binding site 2 out of 2 in 5ofr

Go back to Magnesium Binding Sites List in 5ofr
Magnesium binding site 2 out of 2 in the Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Antibacterial Peptide Abc Transporter Mcjd in A High Energy Outward Occluded Intermediate State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:37.9
occ:1.00
OG B:SER385 1.9 88.2 1.0
O1 B:VO4603 1.9 91.6 1.0
OE1 B:GLN426 2.3 80.2 1.0
O2B B:ADP601 2.3 68.0 1.0
CB B:SER385 3.0 84.6 1.0
V B:VO4603 3.2 91.1 1.0
CD B:GLN426 3.2 90.8 1.0
O3B B:ADP601 3.4 70.3 1.0
PB B:ADP601 3.4 68.6 1.0
N B:SER385 3.6 83.3 1.0
NE2 B:GLN426 3.7 82.1 1.0
CA B:SER385 3.8 82.7 1.0
OD2 B:ASP505 3.9 0.4 1.0
OD1 B:ASP505 3.9 0.2 1.0
O2 B:VO4603 4.0 87.8 1.0
O3A B:ADP601 4.0 66.4 1.0
O2A B:ADP601 4.1 62.9 1.0
O1A B:ADP601 4.2 64.1 1.0
CG B:GLN426 4.3 92.1 1.0
PA B:ADP601 4.3 63.2 1.0
CG B:ASP505 4.3 0.3 1.0
O4 B:VO4603 4.4 92.0 1.0
OE1 B:GLU506 4.4 0.6 1.0
O3 B:VO4603 4.6 93.2 1.0
O1B B:ADP601 4.7 68.3 1.0
CB B:LYS384 4.8 86.9 1.0
C B:LYS384 4.8 86.9 1.0
N A:GLY483 4.9 72.4 1.0
CE B:LYS384 4.9 97.9 1.0

Reference:

K.Bountra, G.Hagelueken, H.G.Choudhury, V.Corradi, K.El Omari, A.Wagner, I.Mathavan, S.Zirah, W.Yuan Wahlgren, D.P.Tieleman, O.Schiemann, S.Rebuffat, K.Beis. Structural Basis For Antibacterial Peptide Self-Immunity By the Bacterial Abc Transporter Mcjd. Embo J. V. 36 3062 2017.
ISSN: ESSN 1460-2075
PubMed: 28864543
DOI: 10.15252/EMBJ.201797278
Page generated: Mon Dec 14 20:59:48 2020

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