Zinc in PDB 8dze: Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) (pdb code 8dze). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1), PDB code: 8dze:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8dze

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Zinc binding site 1 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:95.8
occ:1.00
 SG A:CYS406 2.3 74.1 1.0
SG A:CYS403 2.3 67.9 1.0
SG A:CYS445 2.3 91.7 1.0
SG A:CYS446 2.3 87.2 1.0
CB A:CYS403 3.1 67.9 1.0
CB A:CYS445 3.5 91.7 1.0
CB A:CYS446 3.5 87.2 1.0
CB A:CYS406 3.8 74.1 1.0
C A:CYS445 3.8 91.7 1.0
O A:CYS445 3.8 91.7 1.0
N A:CYS406 4.0 74.1 1.0
N A:CYS446 4.2 87.2 1.0
CA A:CYS445 4.3 91.7 1.0
CB A:GLN405 4.4 73.8 1.0
CA A:CYS446 4.4 87.2 1.0
CA A:CYS406 4.5 74.1 1.0
CA A:CYS403 4.5 67.9 1.0
CA A:GLY449 4.5 70.5 1.0
C A:GLN405 4.8 73.8 1.0
N A:GLN405 4.9 73.8 1.0
N A:GLY449 4.9 70.5 1.0
CA A:GLN405 4.9 73.8 1.0
N A:CYS445 4.9 91.7 1.0
C A:CYS403 4.9 67.9 1.0

Zinc binding site 2 out of 6 in 8dze

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:96.6
occ:1.00
 SG B:CYS406 2.3 77.9 1.0
SG B:CYS403 2.3 71.3 1.0
SG B:CYS445 2.3 92.9 1.0
SG B:CYS446 2.3 87.0 1.0
CB B:CYS403 3.1 71.3 1.0
CB B:CYS445 3.5 92.9 1.0
CB B:CYS446 3.5 87.0 1.0
CB B:CYS406 3.8 77.9 1.0
O B:CYS445 3.8 92.9 1.0
C B:CYS445 3.8 92.9 1.0
N B:CYS406 4.0 77.9 1.0
N B:CYS446 4.2 87.0 1.0
CA B:CYS445 4.3 92.9 1.0
CB B:GLN405 4.4 77.3 1.0
CA B:CYS446 4.4 87.0 1.0
CA B:CYS406 4.5 77.9 1.0
CA B:CYS403 4.5 71.3 1.0
CA B:GLY449 4.5 71.0 1.0
C B:GLN405 4.8 77.3 1.0
N B:GLY449 4.9 71.0 1.0
N B:GLN405 4.9 77.3 1.0
CA B:GLN405 4.9 77.3 1.0
N B:CYS445 4.9 92.9 1.0
C B:CYS403 4.9 71.3 1.0

Zinc binding site 3 out of 6 in 8dze

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:104.0
occ:1.00
 SG C:CYS406 2.3 77.9 1.0
SG C:CYS403 2.3 71.6 1.0
SG C:CYS445 2.3 90.0 1.0
SG C:CYS446 2.3 86.5 1.0
CB C:CYS403 3.1 71.6 1.0
CB C:CYS445 3.5 90.0 1.0
CB C:CYS446 3.5 86.5 1.0
CB C:CYS406 3.8 77.9 1.0
C C:CYS445 3.8 90.0 1.0
O C:CYS445 3.8 90.0 1.0
N C:CYS406 4.0 77.9 1.0
N C:CYS446 4.2 86.5 1.0
CA C:CYS445 4.3 90.0 1.0
CB C:GLN405 4.4 79.2 1.0
CA C:CYS446 4.4 86.5 1.0
CA C:CYS406 4.5 77.9 1.0
CA C:CYS403 4.5 71.6 1.0
CA C:GLY449 4.5 71.2 1.0
C C:GLN405 4.8 79.2 1.0
N C:GLN405 4.9 79.2 1.0
N C:GLY449 4.9 71.2 1.0
CA C:GLN405 4.9 79.2 1.0
N C:CYS445 4.9 90.0 1.0
C C:CYS403 4.9 71.6 1.0

Zinc binding site 4 out of 6 in 8dze

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn601

b:95.4
occ:1.00
 SG D:CYS406 2.3 74.1 1.0
SG D:CYS403 2.3 67.8 1.0
SG D:CYS445 2.3 91.7 1.0
SG D:CYS446 2.3 87.4 1.0
CB D:CYS403 3.1 67.8 1.0
CB D:CYS445 3.5 91.7 1.0
CB D:CYS446 3.5 87.4 1.0
CB D:CYS406 3.8 74.1 1.0
C D:CYS445 3.8 91.7 1.0
O D:CYS445 3.8 91.7 1.0
N D:CYS406 4.0 74.1 1.0
N D:CYS446 4.2 87.4 1.0
CA D:CYS445 4.3 91.7 1.0
CB D:GLN405 4.4 73.8 1.0
CA D:CYS446 4.4 87.4 1.0
CA D:CYS406 4.5 74.1 1.0
CA D:CYS403 4.5 67.8 1.0
CA D:GLY449 4.5 70.5 1.0
C D:GLN405 4.8 73.8 1.0
N D:GLN405 4.9 73.8 1.0
N D:GLY449 4.9 70.5 1.0
CA D:GLN405 4.9 73.8 1.0
N D:CYS445 4.9 91.7 1.0
C D:CYS403 4.9 67.8 1.0

Zinc binding site 5 out of 6 in 8dze

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn601

b:96.5
occ:1.00
 SG E:CYS406 2.3 77.0 1.0
SG E:CYS403 2.3 70.7 1.0
SG E:CYS445 2.3 92.5 1.0
SG E:CYS446 2.3 86.1 1.0
CB E:CYS403 3.1 70.7 1.0
CB E:CYS445 3.5 92.5 1.0
CB E:CYS446 3.5 86.1 1.0
CB E:CYS406 3.8 77.0 1.0
O E:CYS445 3.8 92.5 1.0
C E:CYS445 3.8 92.5 1.0
N E:CYS406 4.0 77.0 1.0
N E:CYS446 4.2 86.1 1.0
CA E:CYS445 4.3 92.5 1.0
CB E:GLN405 4.4 76.6 1.0
CA E:CYS446 4.4 86.1 1.0
CA E:CYS406 4.5 77.0 1.0
CA E:CYS403 4.5 70.7 1.0
CA E:GLY449 4.5 70.8 1.0
C E:GLN405 4.8 76.6 1.0
N E:GLY449 4.9 70.8 1.0
N E:GLN405 4.9 76.6 1.0
CA E:GLN405 4.9 76.6 1.0
N E:CYS445 4.9 92.5 1.0
C E:CYS403 4.9 70.7 1.0

Zinc binding site 6 out of 6 in 8dze

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Zinc binding site 6 out of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E. Coli in the Presence of Amp-Pnp (Class-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn601

b:102.7
occ:1.00
 SG F:CYS406 2.3 78.0 1.0
SG F:CYS403 2.3 71.4 1.0
SG F:CYS445 2.3 90.3 1.0
SG F:CYS446 2.3 86.5 1.0
CB F:CYS403 3.1 71.4 1.0
CB F:CYS445 3.5 90.3 1.0
CB F:CYS446 3.5 86.5 1.0
CB F:CYS406 3.8 78.0 1.0
C F:CYS445 3.8 90.3 1.0
O F:CYS445 3.8 90.3 1.0
N F:CYS406 4.0 78.0 1.0
N F:CYS446 4.2 86.5 1.0
CA F:CYS445 4.3 90.3 1.0
CB F:GLN405 4.4 78.9 1.0
CA F:CYS446 4.4 86.5 1.0
CA F:CYS406 4.5 78.0 1.0
CA F:CYS403 4.5 71.4 1.0
CA F:GLY449 4.5 70.8 1.0
C F:GLN405 4.8 78.9 1.0
N F:GLN405 4.9 78.9 1.0
N F:GLY449 4.9 70.8 1.0
CA F:GLN405 4.9 78.9 1.0
N F:CYS445 4.9 90.3 1.0
C F:CYS403 4.9 71.4 1.0

Reference:

A.R.Nayak, P.K.Singh, J.Zhao, M.Samso, M.S.Donnenberg. Cryo-Em Structure of the Type IV Pilus Extension Atpase From Enteropathogenic Escherichia Coli. Mbio V. 13 2022.
ISSN: ESSN 2150-7511
PubMed: 36326250
DOI: 10.1128/MBIO.02270-22
Page generated: Wed Oct 30 19:21:14 2024

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