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Zinc in PDB 5it5: Thermus Thermophilus Pilb Core Atpase Region

Protein crystallography data

The structure of Thermus Thermophilus Pilb Core Atpase Region, PDB code: 5it5 was solved by J.Mancl, H.Robinson, W.Black, Z.Yang, F.Schubot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.29 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.550, 133.560, 208.420, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 27.4

Other elements in 5it5:

The structure of Thermus Thermophilus Pilb Core Atpase Region also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Pilb Core Atpase Region (pdb code 5it5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Thermus Thermophilus Pilb Core Atpase Region, PDB code: 5it5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5it5

Go back to Zinc Binding Sites List in 5it5
Zinc binding site 1 out of 6 in the Thermus Thermophilus Pilb Core Atpase Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Pilb Core Atpase Region within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn901

b:47.9
occ:1.00
 SG F:CYS785 2.3 38.1 1.0
SG F:CYS817 2.3 35.9 1.0
SG F:CYS820 2.4 28.5 1.0
SG F:CYS782 2.4 31.8 1.0
CB F:CYS782 3.2 31.0 1.0
CB F:CYS820 3.4 30.1 1.0
CB F:CYS817 3.5 29.4 1.0
N F:CYS817 3.5 24.7 1.0
CB F:CYS785 3.7 35.4 1.0
N F:CYS820 3.9 36.0 1.0
CA F:CYS817 4.0 29.2 1.0
C F:GLY816 4.1 33.9 1.0
N F:CYS785 4.1 35.3 1.0
CA F:CYS820 4.3 28.2 1.0
CA F:GLY816 4.3 34.6 1.0
O F:CYS817 4.4 27.5 1.0
N F:GLY816 4.4 33.0 1.0
CB F:ARG819 4.5 36.3 1.0
C F:CYS817 4.5 30.3 1.0
CA F:CYS785 4.5 32.6 1.0
CB F:HIS784 4.6 37.3 1.0
CA F:GLY824 4.6 30.8 1.0
CA F:CYS782 4.7 33.5 1.0
C F:ARG819 4.8 32.5 1.0
N F:ARG819 4.8 34.0 1.0
C F:HIS784 4.8 35.1 1.0
O F:GLY816 4.8 40.1 1.0
N F:GLY824 4.9 38.9 1.0
CA F:ARG819 4.9 35.2 1.0

Zinc binding site 2 out of 6 in 5it5

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Zinc binding site 2 out of 6 in the Thermus Thermophilus Pilb Core Atpase Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Pilb Core Atpase Region within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:0.4
occ:1.00
 SG A:CYS820 1.9 82.9 1.0
CB A:CYS785 2.4 59.1 1.0
CB A:CYS817 2.4 67.5 1.0
SG A:CYS785 2.8 67.5 1.0
SG A:CYS782 3.1 69.6 1.0
N A:CYS817 3.1 63.6 1.0
CB A:CYS820 3.2 46.9 1.0
SG A:CYS817 3.3 82.4 1.0
CB A:CYS782 3.3 49.1 1.0
CA A:CYS817 3.3 62.1 1.0
CA A:CYS785 3.7 53.4 1.0
N A:CYS785 4.0 59.0 1.0
C A:CYS817 4.1 57.1 1.0
C A:GLY816 4.2 58.0 1.0
CA A:CYS820 4.4 50.1 1.0
N A:CYS820 4.4 63.4 1.0
N A:GLY816 4.5 54.0 1.0
CA A:GLY824 4.5 39.4 1.0
C A:HIS784 4.6 63.9 1.0
O A:CYS817 4.6 57.1 1.0
CA A:GLY816 4.6 57.8 1.0
CA A:CYS782 4.7 52.4 1.0
N A:GLY824 4.7 39.3 1.0
N A:GLU818 4.8 59.7 1.0
C A:CYS785 4.9 55.2 1.0
O A:CYS782 4.9 54.4 1.0
C A:CYS782 4.9 54.4 1.0
C A:GLY824 4.9 43.0 1.0

Zinc binding site 3 out of 6 in 5it5

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Zinc binding site 3 out of 6 in the Thermus Thermophilus Pilb Core Atpase Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Pilb Core Atpase Region within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn902

b:63.8
occ:1.00
 SG B:CYS820 2.3 47.9 1.0
CB B:CYS785 2.4 53.3 1.0
SG B:CYS782 2.4 49.5 1.0
CB B:CYS817 2.5 58.2 1.0
SG B:CYS785 2.7 52.5 1.0
CB B:CYS782 3.0 41.6 1.0
SG B:CYS817 3.4 75.7 1.0
CB B:CYS820 3.5 50.4 1.0
N B:CYS817 3.6 58.9 1.0
CA B:CYS817 3.6 53.6 1.0
CA B:CYS785 3.8 53.0 1.0
C B:GLY816 4.2 58.5 1.0
N B:CYS785 4.3 51.9 1.0
C B:CYS817 4.3 62.2 1.0
N B:CYS820 4.3 60.6 1.0
CA B:CYS782 4.4 42.6 1.0
C B:HIS784 4.4 54.3 1.0
O B:CYS817 4.5 59.1 1.0
CA B:CYS820 4.5 56.5 1.0
O B:CYS782 4.6 41.5 1.0
O B:HIS784 4.6 63.9 1.0
CA B:GLY816 4.7 55.4 1.0
N B:GLY816 4.7 49.6 1.0
C B:CYS782 4.7 44.4 1.0
CA B:GLY824 4.8 45.0 1.0
O B:GLY816 4.8 61.7 1.0
O B:THR823 4.8 57.2 1.0
C B:CYS785 4.8 49.0 1.0

Zinc binding site 4 out of 6 in 5it5

Go back to Zinc Binding Sites List in 5it5
Zinc binding site 4 out of 6 in the Thermus Thermophilus Pilb Core Atpase Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus Pilb Core Atpase Region within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn902

b:0.2
occ:1.00
 SG E:CYS820 2.0 59.6 1.0
SG E:CYS785 2.1 63.5 1.0
SG E:CYS782 2.4 65.8 1.0
SG E:CYS817 2.9 77.6 1.0
CB E:CYS782 3.1 51.4 1.0
CB E:CYS785 3.1 62.7 1.0
N E:CYS817 3.5 67.8 1.0
N E:CYS785 3.6 68.3 1.0
CB E:CYS820 3.8 62.2 1.0
CA E:CYS785 3.9 62.2 1.0
CB E:CYS817 4.0 65.4 1.0
C E:GLY816 4.1 66.9 1.0
CA E:GLY816 4.2 68.3 1.0
CA E:CYS817 4.3 68.7 1.0
N E:CYS820 4.3 73.1 1.0
CA E:CYS782 4.5 46.8 1.0
CB E:HIS784 4.6 69.7 1.0
N E:GLY816 4.6 69.0 1.0
CA E:CYS820 4.6 66.3 1.0
C E:HIS784 4.7 67.7 1.0
C E:CYS817 4.7 71.0 1.0
O E:CYS817 4.8 66.7 1.0
C E:CYS785 4.8 60.4 1.0
O E:GLY816 4.9 69.5 1.0
C E:CYS782 4.9 54.8 1.0
N E:HIS784 5.0 55.2 1.0
CB E:ARG819 5.0 69.5 1.0
CA E:GLY824 5.0 54.9 1.0
CA E:HIS784 5.0 60.9 1.0

Zinc binding site 5 out of 6 in 5it5

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Zinc binding site 5 out of 6 in the Thermus Thermophilus Pilb Core Atpase Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thermus Thermophilus Pilb Core Atpase Region within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn902

b:92.4
occ:1.00
 SG C:CYS785 2.0 60.3 1.0
SG C:CYS817 2.1 41.4 1.0
SG C:CYS820 2.2 40.3 1.0
SG C:CYS782 2.4 42.4 1.0
CB C:CYS785 3.0 41.4 1.0
CB C:CYS782 3.2 32.9 1.0
CB C:CYS817 3.3 38.7 1.0
CB C:CYS820 3.4 34.9 1.0
N C:CYS817 3.5 33.3 1.0
N C:CYS785 3.8 38.4 1.0
CA C:CYS817 3.9 32.8 1.0
CA C:CYS785 4.0 37.5 1.0
N C:CYS820 4.1 39.0 1.0
C C:GLY816 4.1 38.5 1.0
CA C:GLY816 4.2 37.8 1.0
N C:GLY816 4.3 35.0 1.0
CA C:CYS820 4.4 34.1 1.0
C C:CYS817 4.5 35.4 1.0
O C:CYS817 4.6 35.4 1.0
CA C:GLY824 4.6 29.3 1.0
CA C:CYS782 4.6 31.3 1.0
C C:ARG819 4.7 38.9 1.0
CB C:HIS784 4.8 42.0 1.0
N C:GLY824 4.8 39.3 1.0
C C:HIS784 4.8 39.0 1.0
C C:CYS785 4.9 33.0 1.0
O C:GLY816 4.9 40.3 1.0
C C:CYS782 5.0 30.8 1.0
N C:ARG819 5.0 36.6 1.0

Zinc binding site 6 out of 6 in 5it5

Go back to Zinc Binding Sites List in 5it5
Zinc binding site 6 out of 6 in the Thermus Thermophilus Pilb Core Atpase Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Thermus Thermophilus Pilb Core Atpase Region within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn902

b:59.0
occ:1.00
 SG D:CYS785 2.0 52.5 1.0
SG D:CYS782 2.3 49.3 1.0
SG D:CYS817 2.6 55.0 1.0
SG D:CYS820 2.7 63.5 1.0
CB D:CYS820 3.0 38.1 1.0
CB D:CYS782 3.0 40.6 1.0
CB D:CYS817 3.4 42.7 1.0
CB D:CYS785 3.4 49.0 1.0
N D:CYS817 3.6 42.5 1.0
N D:CYS820 3.7 44.5 1.0
N D:CYS785 3.8 50.5 1.0
CA D:CYS817 4.0 42.8 1.0
CA D:CYS820 4.0 38.0 1.0
CA D:CYS785 4.1 48.3 1.0
C D:HIS784 4.3 55.2 1.0
CB D:HIS784 4.4 55.1 1.0
O D:CYS817 4.4 43.6 1.0
CA D:CYS782 4.4 41.9 1.0
C D:GLY816 4.5 44.0 1.0
C D:CYS817 4.5 42.7 1.0
N D:HIS784 4.5 55.0 1.0
CA D:HIS784 4.6 53.5 1.0
C D:ARG819 4.7 42.9 1.0
C D:CYS782 4.8 46.7 1.0
CA D:GLY816 4.8 45.4 1.0
O D:HIS784 4.9 63.3 1.0
CB D:ARG819 4.9 47.7 1.0
CA D:GLY824 4.9 34.2 1.0
N D:ARG819 5.0 46.7 1.0

Reference:

J.M.Mancl, W.P.Black, H.Robinson, Z.Yang, F.D.Schubot. Crystal Structure of A Type IV Pilus Assembly Atpase: Insights Into the Molecular Mechanism of Pilb From Thermus Thermophilus. Structure V. 24 1886 2016.
ISSN: ISSN 0969-2126
PubMed: 27667690
DOI: 10.1016/J.STR.2016.08.010
Page generated: Sun Oct 27 18:21:18 2024

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