Zinc in PDB 6thk: Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa

Protein crystallography data

The structure of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa, PDB code: 6thk was solved by H.M.Behrens, C.Kleanthous, E.D.Lowe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.19 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.240, 53.870, 104.800, 90.00, 95.15, 90.00
R / Rfree (%) 22.5 / 27.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa (pdb code 6thk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa, PDB code: 6thk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6thk

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Zinc binding site 1 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:47.9
occ:1.00
ND1 A:HIS501 2.2 49.0 1.0
OD1 A:ASP383 2.3 40.4 1.0
C3 A:GOL601 2.3 45.9 1.0
NE2 A:HIS503 2.3 46.8 1.0
OD2 A:ASP383 2.7 43.2 1.0
CG A:ASP383 2.8 40.8 1.0
O3 A:GOL601 2.9 40.1 1.0
CG A:HIS501 3.0 47.3 1.0
CB A:HIS501 3.1 43.4 1.0
CD2 A:HIS503 3.1 46.9 1.0
C2 A:GOL601 3.1 54.2 1.0
C1 A:GOL601 3.2 54.5 1.0
CE1 A:HIS503 3.3 46.5 1.0
CE1 A:HIS501 3.3 49.3 1.0
OG A:SER380 3.7 43.5 1.0
O1 A:GOL601 4.2 49.9 1.0
CD2 A:HIS501 4.2 49.8 1.0
CG A:HIS503 4.3 45.7 1.0
CB A:ASP383 4.3 39.7 1.0
CB A:SER380 4.3 47.8 1.0
ND1 A:HIS503 4.3 47.2 1.0
NE2 A:HIS501 4.3 49.8 1.0
O2 A:GOL601 4.4 58.6 1.0
CA A:HIS501 4.6 42.7 1.0
CA A:ASP383 4.9 38.7 1.0
N A:ASP383 5.0 40.3 1.0
CD2 A:LEU499 5.0 49.9 1.0

Zinc binding site 2 out of 8 in 6thk

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Zinc binding site 2 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:53.3
occ:1.00
NE2 A:HIS504 2.3 42.5 1.0
ND1 A:HIS502 2.3 45.7 1.0
CE1 A:HIS504 2.4 41.8 1.0
O A:HOH782 2.8 39.3 1.0
CG A:HIS502 3.1 44.0 1.0
CB A:HIS502 3.2 40.6 1.0
CE1 A:HIS502 3.4 45.1 1.0
CD2 A:HIS504 3.6 42.9 1.0
ND1 A:HIS504 3.7 42.7 1.0
CA A:HIS502 4.3 40.2 1.0
CD2 A:HIS502 4.3 45.2 1.0
CG A:HIS504 4.3 41.9 1.0
NE2 A:HIS502 4.4 45.4 1.0

Zinc binding site 3 out of 8 in 6thk

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Zinc binding site 3 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:63.7
occ:1.00
ND1 A:HIS505 2.2 57.6 1.0
O A:HOH777 2.3 58.7 1.0
CE1 A:HIS505 3.0 57.1 1.0
CG A:HIS505 3.3 56.2 1.0
CB A:HIS505 3.7 52.7 1.0
NE2 A:HIS505 4.2 57.6 1.0
CD2 A:HIS505 4.4 57.9 1.0
N A:HIS505 4.7 45.6 1.0
CA A:HIS505 4.9 52.4 1.0

Zinc binding site 4 out of 8 in 6thk

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Zinc binding site 4 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:75.0
occ:1.00
OE2 A:GLU129 2.0 92.1 1.0
OE1 A:GLU129 2.1 87.0 1.0
OD1 A:ASP127 2.1 77.6 1.0
CD A:GLU129 2.3 91.3 1.0
CG A:ASP127 2.6 74.4 1.0
OD2 A:ASP127 2.6 80.1 1.0
O A:HOH755 2.7 55.5 1.0
O A:HOH734 3.0 78.9 1.0
OH A:TYR171 3.6 68.3 1.0
CG A:GLU129 3.7 63.9 1.0
CB A:ASP127 4.0 58.1 1.0
CD A:LYS130 4.5 68.9 1.0
CA A:ASP127 4.5 55.1 1.0
NZ A:LYS130 4.5 95.1 1.0
CZ A:TYR171 4.6 65.7 1.0
CE A:LYS130 4.6 80.0 1.0
CB A:GLU129 4.7 55.5 1.0
CE2 A:TYR171 4.7 57.0 1.0
C A:ASP127 4.8 56.0 1.0
OH A:TYR172 4.9 59.4 1.0

Zinc binding site 5 out of 8 in 6thk

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Zinc binding site 5 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn606

b:62.3
occ:1.00
OE2 A:GLU288 2.1 66.5 1.0
OE2 A:GLU221 2.3 68.5 1.0
CD A:GLU288 3.0 61.4 1.0
OE1 A:GLU288 3.1 59.6 1.0
CD A:GLU221 3.1 83.3 1.0
OE1 A:GLU221 3.5 85.6 1.0
CE A:LYS217 3.6 87.4 1.0
CG A:LYS217 3.8 83.5 1.0
CD A:LYS217 4.3 87.2 1.0
NZ A:LYS255 4.3 73.6 1.0
CG A:GLU288 4.4 51.7 1.0
CG A:GLU221 4.4 65.9 1.0
NZ A:LYS217 4.6 93.5 1.0

Zinc binding site 6 out of 8 in 6thk

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Zinc binding site 6 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn607

b:0.4
occ:1.00
OE2 A:GLU485 2.2 85.5 1.0
NE2 A:HIS371 2.2 90.9 1.0
OE1 A:GLU489 2.3 98.9 1.0
CD2 A:HIS371 2.6 90.9 1.0
CD A:LYS370 3.2 96.8 1.0
CD A:GLU485 3.2 96.3 1.0
CD A:GLU489 3.3 0.1 1.0
CG A:GLU485 3.4 72.5 1.0
CE1 A:HIS371 3.6 90.7 1.0
CE A:LYS370 3.7 0.1 1.0
CG A:GLU489 3.8 66.3 1.0
CG A:HIS371 3.9 89.0 1.0
NZ A:LYS370 3.9 0.5 1.0
CG A:LYS370 4.3 88.1 1.0
OE1 A:GLU485 4.3 88.3 1.0
ND1 A:HIS371 4.4 91.2 1.0
OE2 A:GLU489 4.4 99.1 1.0
O A:SER367 4.6 66.1 1.0
O A:GLU485 4.7 59.6 1.0
CD2 A:LEU488 4.9 51.7 1.0
CB A:GLU485 4.9 57.4 1.0
CB A:LYS370 5.0 76.2 1.0

Zinc binding site 7 out of 8 in 6thk

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Zinc binding site 7 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn608

b:85.4
occ:1.00
OE2 A:GLU311 2.7 85.4 1.0
OE1 A:GLU311 2.9 80.0 1.0
CD A:GLU311 3.0 93.6 1.0
O A:HOH707 3.8 55.5 1.0
CG A:GLU311 4.3 75.1 1.0
CB A:ALA314 4.4 61.5 1.0
O A:HOH762 4.6 68.6 1.0
O A:HOH783 4.7 71.7 1.0
CA A:GLU311 4.8 61.2 1.0
CB A:GLU311 5.0 62.9 1.0

Zinc binding site 8 out of 8 in 6thk

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Zinc binding site 8 out of 8 in the Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Mechanism of Pyocin S5 Import Into Pseudomonas Aeruginosa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn609

b:0.9
occ:1.00
OE2 A:GLU336 2.2 0.9 1.0
OE1 A:GLU333 2.3 90.2 1.0
CD A:GLU336 2.9 99.9 1.0
OE1 A:GLU336 3.1 95.9 1.0
CD A:GLU333 3.1 97.2 1.0
OE2 A:GLU333 3.2 98.4 1.0
CG A:GLU336 4.3 66.1 1.0
CG A:GLU333 4.5 66.1 1.0
CB A:GLU336 4.6 51.9 1.0
CB A:GLU333 4.9 49.7 1.0
CA A:GLU333 4.9 47.6 1.0

Reference:

H.M.Behrens, E.D.Lowe, J.Gault, N.G.Housden, R.Kaminska, T.M.Weber, C.Thompson, G.L.A.Mislin, I.J.Schalk, D.Walker, C.V.Robinson, C.Kleanthous. Pyocin S5 Import Into Pseudomonas Aeruginosa Reveals A Generic Mode of Bacteriocin Transport Biorxiv 2019.
DOI: 10.1101/856047
Page generated: Wed Dec 16 12:53:26 2020

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