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Zinc in PDB 5tsh: Pilb From Geobacter Metallireducens Bound to Amp-Pnp

Protein crystallography data

The structure of Pilb From Geobacter Metallireducens Bound to Amp-Pnp, PDB code: 5tsh was solved by M.Mccallum, S.Tammam, A.Khan, L.Burrows, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.76 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.320, 99.960, 109.790, 112.99, 106.60, 88.91
R / Rfree (%) 18.4 / 21.8

Other elements in 5tsh:

The structure of Pilb From Geobacter Metallireducens Bound to Amp-Pnp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp (pdb code 5tsh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp, PDB code: 5tsh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5tsh

Go back to Zinc Binding Sites List in 5tsh
Zinc binding site 1 out of 6 in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pilb From Geobacter Metallireducens Bound to Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:37.4
occ:1.00
SG A:CYS461 2.3 51.6 1.0
SG A:CYS496 2.3 39.2 1.0
SG A:CYS493 2.3 51.7 1.0
SG A:CYS458 2.3 45.7 1.0
CB A:CYS458 3.1 48.1 1.0
CB A:CYS496 3.2 43.1 1.0
CB A:CYS461 3.3 40.6 1.0
N A:CYS493 3.4 39.5 1.0
CB A:CYS493 3.5 42.2 1.0
N A:CYS461 3.8 44.0 1.0
CA A:CYS493 3.9 39.8 1.0
N A:CYS496 3.9 41.0 1.0
C A:GLY492 4.1 40.5 1.0
CA A:CYS496 4.2 40.6 1.0
CA A:CYS461 4.2 46.4 1.0
O A:CYS493 4.3 41.5 1.0
C A:CYS493 4.4 40.5 1.0
CA A:GLY492 4.4 50.0 1.0
CB A:GLU460 4.5 50.7 1.0
CA A:CYS458 4.6 48.2 1.0
N A:GLY492 4.7 50.6 1.0
CA A:GLY500 4.8 44.0 1.0
C A:GLU460 4.8 46.9 1.0
C A:LYS495 4.9 47.3 1.0
O A:GLY492 4.9 53.0 1.0
N A:GLY500 4.9 43.4 1.0
N A:GLU460 4.9 45.3 1.0
C A:CYS458 5.0 50.0 1.0

Zinc binding site 2 out of 6 in 5tsh

Go back to Zinc Binding Sites List in 5tsh
Zinc binding site 2 out of 6 in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pilb From Geobacter Metallireducens Bound to Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:41.5
occ:1.00
SG B:CYS461 2.3 42.5 1.0
SG B:CYS496 2.3 41.4 1.0
SG B:CYS493 2.3 55.4 1.0
SG B:CYS458 2.4 46.6 1.0
CB B:CYS458 3.1 43.7 1.0
N B:CYS493 3.2 56.2 1.0
CB B:CYS493 3.3 49.7 1.0
CB B:CYS496 3.3 41.8 1.0
CB B:CYS461 3.4 41.6 1.0
CA B:CYS493 3.7 54.5 1.0
N B:CYS461 3.8 52.5 1.0
N B:CYS496 4.0 51.1 1.0
CA B:CYS461 4.2 46.8 1.0
C B:GLY492 4.2 54.6 1.0
C B:CYS493 4.3 58.9 1.0
CA B:CYS496 4.3 44.3 1.0
O B:CYS493 4.4 55.7 1.0
CA B:GLY492 4.4 48.5 1.0
CB B:GLU460 4.5 62.0 1.0
CA B:CYS458 4.6 44.8 1.0
N B:GLY492 4.6 47.6 1.0
C B:GLU460 4.7 56.1 1.0
CA B:GLY500 4.7 45.3 1.0
C B:LYS495 4.8 59.4 1.0
N B:GLU460 4.9 52.4 1.0
CA B:GLU460 5.0 55.4 1.0
N B:GLY500 5.0 38.8 1.0
C B:CYS458 5.0 47.8 1.0
N B:LYS495 5.0 59.6 1.0

Zinc binding site 3 out of 6 in 5tsh

Go back to Zinc Binding Sites List in 5tsh
Zinc binding site 3 out of 6 in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pilb From Geobacter Metallireducens Bound to Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:78.2
occ:1.00
SG C:CYS461 2.1 59.3 1.0
SG C:CYS493 2.3 58.9 1.0
SG C:CYS496 2.3 53.1 1.0
SG C:CYS458 2.4 53.5 1.0
CB C:CYS458 3.1 47.9 1.0
CB C:CYS496 3.1 47.8 1.0
CB C:CYS461 3.1 55.4 1.0
CB C:CYS493 3.4 53.1 1.0
N C:CYS493 3.6 56.4 1.0
N C:CYS461 3.7 63.1 1.0
N C:CYS496 3.9 53.6 1.0
CA C:CYS461 3.9 60.9 1.0
CA C:CYS493 4.0 52.9 1.0
CA C:CYS496 4.1 47.6 1.0
O C:CYS493 4.3 51.5 1.0
C C:GLY492 4.4 56.0 1.0
C C:CYS493 4.4 54.5 1.0
CB C:GLU460 4.5 58.4 1.0
CA C:CYS458 4.6 47.4 1.0
C C:GLU460 4.6 58.7 1.0
CA C:GLY492 4.7 52.2 1.0
CA C:GLY500 4.8 48.5 1.0
C C:LYS495 4.8 55.7 1.0
N C:GLY492 4.9 52.6 1.0
N C:GLY500 4.9 51.0 1.0
CB C:LYS495 4.9 54.6 1.0
CA C:GLU460 5.0 56.2 1.0

Zinc binding site 4 out of 6 in 5tsh

Go back to Zinc Binding Sites List in 5tsh
Zinc binding site 4 out of 6 in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pilb From Geobacter Metallireducens Bound to Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:48.7
occ:1.00
SG D:CYS461 2.3 41.0 1.0
SG D:CYS458 2.3 44.0 1.0
SG D:CYS493 2.4 54.9 1.0
SG D:CYS496 2.4 45.2 1.0
CB D:CYS458 3.1 40.0 1.0
CB D:CYS493 3.3 50.9 1.0
CB D:CYS461 3.5 41.9 1.0
N D:CYS493 3.5 50.1 1.0
CB D:CYS496 3.5 48.6 1.0
CA D:CYS493 3.8 51.9 1.0
N D:CYS461 3.8 52.1 1.0
N D:CYS496 4.2 59.8 1.0
CA D:CYS461 4.3 50.9 1.0
C D:GLY492 4.3 54.6 1.0
C D:CYS493 4.4 58.9 1.0
CB D:GLU460 4.4 60.0 1.0
CA D:CYS496 4.5 53.1 1.0
O D:CYS493 4.5 65.3 1.0
CA D:CYS458 4.5 41.8 1.0
CA D:GLY492 4.6 52.6 1.0
C D:GLU460 4.6 54.8 1.0
CA D:GLY500 4.8 38.5 1.0
C D:LYS495 4.8 59.7 1.0
N D:GLY492 4.8 54.1 1.0
N D:GLU460 4.8 55.5 1.0
CA D:GLU460 4.9 58.0 1.0
C D:CYS458 4.9 39.8 1.0
N D:LYS495 4.9 55.9 1.0
O D:CYS458 5.0 39.6 1.0
CB D:LYS495 5.0 59.3 1.0
N D:GLY500 5.0 46.8 1.0

Zinc binding site 5 out of 6 in 5tsh

Go back to Zinc Binding Sites List in 5tsh
Zinc binding site 5 out of 6 in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pilb From Geobacter Metallireducens Bound to Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:57.5
occ:1.00
SG E:CYS461 2.3 50.2 1.0
SG E:CYS493 2.4 63.6 1.0
SG E:CYS458 2.4 52.6 1.0
SG E:CYS496 2.4 52.6 1.0
CB E:CYS458 3.2 47.2 1.0
CB E:CYS496 3.2 49.5 1.0
CB E:CYS461 3.4 52.0 1.0
CB E:CYS493 3.5 59.5 1.0
N E:CYS493 3.5 54.3 1.0
N E:CYS461 3.9 59.0 1.0
N E:CYS496 4.0 61.3 1.0
CA E:CYS493 4.0 59.9 1.0
C E:GLY492 4.1 53.2 1.0
CA E:CYS496 4.2 57.2 1.0
CA E:CYS461 4.3 56.7 1.0
CA E:GLY492 4.4 51.0 1.0
C E:CYS493 4.5 64.4 1.0
O E:CYS493 4.6 67.2 1.0
CB E:GLU460 4.6 52.1 1.0
C E:LYS495 4.6 63.4 1.0
N E:GLY492 4.7 51.2 1.0
CA E:CYS458 4.7 50.9 1.0
CB E:LYS495 4.8 61.9 1.0
C E:GLU460 4.8 58.9 1.0
CA E:GLY500 4.8 46.8 1.0
N E:LYS495 4.8 62.9 1.0
O E:GLY492 4.9 56.6 1.0
N E:GLY500 5.0 46.9 1.0
N E:GLU460 5.0 51.5 1.0
CA E:LYS495 5.0 62.9 1.0

Zinc binding site 6 out of 6 in 5tsh

Go back to Zinc Binding Sites List in 5tsh
Zinc binding site 6 out of 6 in the Pilb From Geobacter Metallireducens Bound to Amp-Pnp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pilb From Geobacter Metallireducens Bound to Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn601

b:40.1
occ:1.00
SG F:CYS461 2.2 39.9 1.0
SG F:CYS496 2.3 48.7 1.0
SG F:CYS493 2.3 51.8 1.0
SG F:CYS458 2.3 52.0 1.0
CB F:CYS458 3.1 38.5 1.0
CB F:CYS496 3.2 38.6 1.0
N F:CYS493 3.4 45.5 1.0
CB F:CYS461 3.5 41.2 1.0
CB F:CYS493 3.5 42.9 1.0
N F:CYS461 3.9 44.3 1.0
CA F:CYS493 3.9 46.7 1.0
N F:CYS496 4.0 43.7 1.0
C F:GLY492 4.1 41.9 1.0
CA F:CYS496 4.2 40.0 1.0
O F:CYS493 4.3 45.0 1.0
CA F:CYS461 4.3 42.7 1.0
C F:CYS493 4.3 46.4 1.0
CA F:GLY492 4.4 39.5 1.0
CA F:CYS458 4.6 45.6 1.0
N F:GLY492 4.7 46.6 1.0
CB F:GLU460 4.7 60.9 1.0
C F:LYS495 4.8 51.1 1.0
CB F:LYS495 4.9 49.3 1.0
CA F:GLY500 4.9 36.7 1.0
C F:GLU460 4.9 54.4 1.0
N F:LYS495 4.9 57.8 1.0
N F:GLU460 5.0 53.3 1.0
C F:CYS458 5.0 46.2 1.0
O F:GLY492 5.0 42.0 1.0

Reference:

M.Mccallum, S.Tammam, A.Khan, L.L.Burrows, P.L.Howell. The Molecular Mechanism of the Type Iva Pilus Motors. Nat Commun V. 8 15091 2017.
ISSN: ESSN 2041-1723
PubMed: 28474682
DOI: 10.1038/NCOMMS15091
Page generated: Wed Dec 16 10:56:36 2020

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