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Vanadium 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:

Magnesium (Mg) 2 atoms

Vanadium Binding Sites:

The binding sites of Vanadium 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 Vanadium atom.
In total 2 binding sites of Vanadium 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 Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 5ofr

Go back to Vanadium Binding Sites List in 5ofr
Vanadium 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 Vanadium with other atoms in the V 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:V603

b:0.7
occ:1.00
V A:VO4603 0.0 0.7 1.0
O2 A:VO4603 1.9 0.4 1.0
O4 A:VO4603 1.9 0.6 1.0
O3 A:VO4603 1.9 0.0 1.0
O1 A:VO4603 1.9 0.7 1.0
MG A:MG602 2.7 77.3 1.0
O3B A:ADP601 2.7 0.2 1.0
O1B A:ADP601 3.2 0.0 1.0
OE1 A:GLU506 3.3 0.0 1.0
PB A:ADP601 3.5 0.6 1.0
NE2 A:GLN426 3.7 0.2 1.0
OE1 A:GLN426 3.7 0.1 1.0
CE A:LYS384 4.0 97.4 1.0
CD A:GLN426 4.0 1.0 1.0
O B:ALA510 4.3 0.6 1.0
OG A:SER380 4.3 1.0 1.0
O2B A:ADP601 4.3 0.4 1.0
CD A:GLU506 4.3 0.3 1.0
NZ A:LYS384 4.4 0.6 1.0
CE1 A:HIS537 4.4 0.8 1.0
N B:GLY484 4.5 0.7 1.0
N B:GLY483 4.6 0.3 1.0
OG A:SER385 4.6 1.0 1.0
CA A:SER380 4.6 0.7 1.0
CB A:SER380 4.7 0.2 1.0
OE2 A:GLU506 4.7 0.7 1.0
O3A A:ADP601 4.8 0.9 1.0
CB B:SER482 4.8 0.2 1.0
OG B:SER482 4.9 0.8 1.0
CA B:GLY483 4.9 0.4 1.0

Vanadium binding site 2 out of 2 in 5ofr

Go back to Vanadium Binding Sites List in 5ofr
Vanadium 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 Vanadium with other atoms in the V 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:V603

b:91.1
occ:1.00
V B:VO4603 0.0 91.1 1.0
O1 B:VO4603 1.9 91.6 1.0
O2 B:VO4603 1.9 87.8 1.0
O4 B:VO4603 1.9 92.0 1.0
O3 B:VO4603 1.9 93.2 1.0
O3B B:ADP601 2.2 70.3 1.0
MG B:MG602 3.2 37.9 1.0
PB B:ADP601 3.5 68.6 1.0
OE1 B:GLU506 3.6 0.6 1.0
OG B:SER380 3.6 0.8 1.0
O2B B:ADP601 3.7 68.0 1.0
NE2 B:GLN426 3.7 82.1 1.0
CB B:SER380 4.1 96.9 1.0
N A:GLY484 4.1 66.6 1.0
OE1 B:GLN426 4.2 80.2 1.0
O A:ALA510 4.2 93.0 1.0
CD B:GLN426 4.3 90.8 1.0
CE B:LYS384 4.3 97.9 1.0
CA B:SER380 4.3 94.8 1.0
N A:GLY483 4.3 72.4 1.0
O1B B:ADP601 4.4 68.3 1.0
NE2 B:HIS537 4.4 0.8 1.0
CB A:SER482 4.5 68.4 1.0
OG A:SER482 4.5 70.6 1.0
O3A B:ADP601 4.5 66.4 1.0
CD B:GLU506 4.5 0.9 1.0
NZ B:LYS384 4.6 0.4 1.0
CA A:GLY483 4.6 71.3 1.0
OE2 B:GLU506 4.8 0.1 1.0
CA A:GLY484 4.9 65.4 1.0
C A:GLY483 4.9 71.1 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: Thu Oct 29 07:05:57 2020

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