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Zinc in PDB 7p3q: Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer

Zinc Binding Sites:

The binding sites of Zinc atom in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer (pdb code 7p3q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer, PDB code: 7p3q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7p3q

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Zinc binding site 1 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:81.6
occ:1.00
 SG A:CYS6 2.3 66.5 1.0
SG A:CYS31 2.3 64.6 1.0
SG A:CYS34 2.3 65.5 1.0
SG A:CYS3 2.3 65.2 1.0
CB A:CYS3 2.9 65.2 1.0
CB A:CYS31 3.2 64.6 1.0
CB A:CYS6 3.5 66.5 1.0
CB A:CYS34 3.8 65.5 1.0
N A:CYS34 3.9 65.5 1.0
N A:CYS6 4.0 66.5 1.0
CA A:CYS6 4.3 66.5 1.0
CA A:CYS3 4.4 65.2 1.0
CB A:ASP33 4.4 68.4 1.0
CA A:CYS34 4.4 65.5 1.0
CA A:CYS31 4.6 64.6 1.0
CB A:HIS8 4.6 67.6 1.0
C A:CYS6 4.7 66.5 1.0
N A:ARG7 4.8 64.1 1.0
CB A:PHE5 4.8 57.0 1.0
C A:PHE5 4.9 57.0 1.0
N A:HIS8 4.9 67.6 1.0
C A:ASP33 4.9 68.4 1.0
C A:CYS3 4.9 65.2 1.0
C A:CYS31 5.0 64.6 1.0
O A:CYS31 5.0 64.6 1.0
N A:ASP33 5.0 68.4 1.0

Zinc binding site 2 out of 8 in 7p3q

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Zinc binding site 2 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:81.9
occ:1.00
 SG C:CYS6 2.3 66.5 1.0
SG C:CYS31 2.3 64.6 1.0
SG C:CYS34 2.3 65.5 1.0
SG C:CYS3 2.3 65.2 1.0
CB C:CYS3 2.9 65.2 1.0
CB C:CYS31 3.2 64.6 1.0
CB C:CYS6 3.5 66.5 1.0
CB C:CYS34 3.8 65.5 1.0
N C:CYS34 3.9 65.5 1.0
N C:CYS6 4.0 66.5 1.0
CA C:CYS6 4.3 66.5 1.0
CA C:CYS3 4.4 65.2 1.0
CB C:ASP33 4.4 68.4 1.0
CA C:CYS34 4.4 65.5 1.0
CA C:CYS31 4.6 64.6 1.0
CB C:HIS8 4.6 67.6 1.0
C C:CYS6 4.7 66.5 1.0
N C:ARG7 4.8 64.1 1.0
CB C:PHE5 4.8 57.0 1.0
C C:PHE5 4.9 57.0 1.0
N C:HIS8 4.9 67.6 1.0
C C:ASP33 4.9 68.4 1.0
C C:CYS3 4.9 65.2 1.0
C C:CYS31 5.0 64.6 1.0
O C:CYS31 5.0 64.6 1.0
N C:ASP33 5.0 68.4 1.0

Zinc binding site 3 out of 8 in 7p3q

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Zinc binding site 3 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn203

b:81.5
occ:1.00
 SG E:CYS6 2.3 66.5 1.0
SG E:CYS31 2.3 64.6 1.0
SG E:CYS34 2.3 65.5 1.0
SG E:CYS3 2.3 65.2 1.0
CB E:CYS3 2.9 65.2 1.0
CB E:CYS31 3.2 64.6 1.0
CB E:CYS6 3.5 66.5 1.0
CB E:CYS34 3.8 65.5 1.0
N E:CYS34 3.9 65.5 1.0
N E:CYS6 4.0 66.5 1.0
CA E:CYS6 4.3 66.5 1.0
CA E:CYS3 4.4 65.2 1.0
CB E:ASP33 4.4 68.4 1.0
CA E:CYS34 4.4 65.5 1.0
CA E:CYS31 4.6 64.6 1.0
CB E:HIS8 4.6 67.6 1.0
C E:CYS6 4.7 66.5 1.0
N E:ARG7 4.8 64.1 1.0
CB E:PHE5 4.8 57.0 1.0
C E:PHE5 4.9 57.0 1.0
N E:HIS8 4.9 67.6 1.0
C E:ASP33 4.9 68.4 1.0
C E:CYS3 4.9 65.2 1.0
C E:CYS31 5.0 64.6 1.0
O E:CYS31 5.0 64.6 1.0
N E:ASP33 5.0 68.4 1.0

Zinc binding site 4 out of 8 in 7p3q

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Zinc binding site 4 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn203

b:81.6
occ:1.00
 SG G:CYS6 2.3 66.5 1.0
SG G:CYS31 2.3 64.6 1.0
SG G:CYS34 2.3 65.5 1.0
SG G:CYS3 2.3 65.2 1.0
CB G:CYS3 2.9 65.2 1.0
CB G:CYS31 3.2 64.6 1.0
CB G:CYS6 3.5 66.5 1.0
CB G:CYS34 3.8 65.5 1.0
N G:CYS34 3.9 65.5 1.0
N G:CYS6 4.0 66.5 1.0
CA G:CYS6 4.3 66.5 1.0
CA G:CYS3 4.4 65.2 1.0
CB G:ASP33 4.4 68.4 1.0
CA G:CYS34 4.4 65.5 1.0
CA G:CYS31 4.6 64.6 1.0
CB G:HIS8 4.6 67.6 1.0
C G:CYS6 4.7 66.5 1.0
N G:ARG7 4.8 64.1 1.0
CB G:PHE5 4.8 57.0 1.0
C G:PHE5 4.9 57.0 1.0
N G:HIS8 4.9 67.6 1.0
C G:ASP33 4.9 68.4 1.0
C G:CYS3 4.9 65.2 1.0
C G:CYS31 5.0 64.6 1.0
O G:CYS31 5.0 64.6 1.0
N G:ASP33 5.0 68.4 1.0

Zinc binding site 5 out of 8 in 7p3q

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Zinc binding site 5 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:133.0
occ:1.00
 SG B:CYS31 2.3 111.2 1.0
SG B:CYS6 2.3 108.8 1.0
SG B:CYS3 2.3 107.3 1.0
SG B:CYS34 2.3 113.8 1.0
CB B:CYS6 2.5 108.8 1.0
CB B:CYS31 2.9 111.2 1.0
CB B:CYS3 3.0 107.3 1.0
N B:CYS6 3.3 108.8 1.0
CA B:CYS6 3.5 108.8 1.0
CB B:CYS34 3.9 113.8 1.0
N B:CYS34 3.9 113.8 1.0
C B:PHE5 4.0 102.6 1.0
CA B:CYS34 4.3 113.8 1.0
O B:ARG36 4.3 106.5 1.0
CA B:CYS31 4.4 111.2 1.0
CB B:PHE5 4.4 102.6 1.0
N B:ARG36 4.4 106.5 1.0
N B:SER35 4.4 112.0 1.0
C B:CYS6 4.4 108.8 1.0
CA B:CYS3 4.5 107.3 1.0
CA B:PHE5 4.5 102.6 1.0
C B:CYS34 4.6 113.8 1.0
N B:PHE5 4.6 102.6 1.0
O B:PHE5 4.6 102.6 1.0
CB B:ARG36 4.7 106.5 1.0
N B:ARG7 4.9 103.5 1.0
C B:CYS31 4.9 111.2 1.0
CB B:ASP33 4.9 112.5 1.0
N B:ASP33 5.0 112.5 1.0
C B:CYS3 5.0 107.3 1.0
CA B:ARG36 5.0 106.5 1.0
CD2 B:PHE5 5.0 102.6 1.0

Zinc binding site 6 out of 8 in 7p3q

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Zinc binding site 6 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:126.7
occ:1.00
 SG D:CYS31 2.3 111.2 1.0
SG D:CYS6 2.3 108.8 1.0
SG D:CYS3 2.3 107.3 1.0
SG D:CYS34 2.3 113.8 1.0
CB D:CYS6 2.5 108.8 1.0
CB D:CYS31 2.9 111.2 1.0
CB D:CYS3 3.0 107.3 1.0
N D:CYS6 3.3 108.8 1.0
CA D:CYS6 3.5 108.8 1.0
CB D:CYS34 3.9 113.8 1.0
N D:CYS34 3.9 113.8 1.0
C D:PHE5 4.0 102.6 1.0
CA D:CYS34 4.3 113.8 1.0
O D:ARG36 4.3 106.5 1.0
CA D:CYS31 4.4 111.2 1.0
CB D:PHE5 4.4 102.6 1.0
N D:ARG36 4.4 106.5 1.0
N D:SER35 4.4 112.0 1.0
C D:CYS6 4.4 108.8 1.0
CA D:CYS3 4.5 107.3 1.0
CA D:PHE5 4.5 102.6 1.0
C D:CYS34 4.6 113.8 1.0
N D:PHE5 4.6 102.6 1.0
O D:PHE5 4.6 102.6 1.0
CB D:ARG36 4.7 106.5 1.0
N D:ARG7 4.9 103.5 1.0
C D:CYS31 4.9 111.2 1.0
CB D:ASP33 4.9 112.5 1.0
N D:ASP33 5.0 112.5 1.0
C D:CYS3 5.0 107.3 1.0
CA D:ARG36 5.0 106.5 1.0
CD2 D:PHE5 5.0 102.6 1.0

Zinc binding site 7 out of 8 in 7p3q

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Zinc binding site 7 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn203

b:126.2
occ:1.00
 SG F:CYS31 2.3 111.2 1.0
SG F:CYS6 2.3 108.8 1.0
SG F:CYS3 2.3 107.3 1.0
SG F:CYS34 2.3 113.8 1.0
CB F:CYS6 2.5 108.8 1.0
CB F:CYS31 2.9 111.2 1.0
CB F:CYS3 3.0 107.3 1.0
N F:CYS6 3.3 108.8 1.0
CA F:CYS6 3.5 108.8 1.0
CB F:CYS34 3.9 113.8 1.0
N F:CYS34 3.9 113.8 1.0
C F:PHE5 4.0 102.6 1.0
CA F:CYS34 4.3 113.8 1.0
O F:ARG36 4.3 106.5 1.0
CA F:CYS31 4.4 111.2 1.0
CB F:PHE5 4.4 102.6 1.0
N F:ARG36 4.4 106.5 1.0
N F:SER35 4.4 112.0 1.0
C F:CYS6 4.4 108.8 1.0
CA F:CYS3 4.5 107.3 1.0
CA F:PHE5 4.5 102.6 1.0
C F:CYS34 4.6 113.8 1.0
N F:PHE5 4.6 102.6 1.0
O F:PHE5 4.6 102.6 1.0
CB F:ARG36 4.7 106.5 1.0
N F:ARG7 4.9 103.5 1.0
C F:CYS31 4.9 111.2 1.0
CB F:ASP33 4.9 112.5 1.0
N F:ASP33 5.0 112.5 1.0
C F:CYS3 5.0 107.3 1.0
CA F:ARG36 5.0 106.5 1.0
CD2 F:PHE5 5.0 102.6 1.0

Zinc binding site 8 out of 8 in 7p3q

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Zinc binding site 8 out of 8 in the Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Streptomyces Coelicolor Datp/Atp-Loaded Nrdr Octamer within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn203

b:129.6
occ:1.00
 SG H:CYS31 2.3 111.2 1.0
SG H:CYS6 2.3 108.8 1.0
SG H:CYS3 2.3 107.3 1.0
SG H:CYS34 2.3 113.8 1.0
CB H:CYS6 2.5 108.8 1.0
CB H:CYS31 2.9 111.2 1.0
CB H:CYS3 3.0 107.3 1.0
N H:CYS6 3.3 108.8 1.0
CA H:CYS6 3.5 108.8 1.0
CB H:CYS34 3.9 113.8 1.0
N H:CYS34 3.9 113.8 1.0
C H:PHE5 4.0 102.6 1.0
CA H:CYS34 4.3 113.8 1.0
O H:ARG36 4.3 106.5 1.0
CA H:CYS31 4.4 111.2 1.0
CB H:PHE5 4.4 102.6 1.0
N H:ARG36 4.4 106.5 1.0
N H:SER35 4.4 112.0 1.0
C H:CYS6 4.4 108.8 1.0
CA H:CYS3 4.5 107.3 1.0
CA H:PHE5 4.5 102.6 1.0
C H:CYS34 4.6 113.8 1.0
N H:PHE5 4.6 102.6 1.0
O H:PHE5 4.6 102.6 1.0
CB H:ARG36 4.7 106.5 1.0
N H:ARG7 4.9 103.5 1.0
C H:CYS31 4.9 111.2 1.0
CB H:ASP33 4.9 112.5 1.0
N H:ASP33 5.0 112.5 1.0
C H:CYS3 5.0 107.3 1.0
CA H:ARG36 5.0 106.5 1.0
CD2 H:PHE5 5.0 102.6 1.0

Reference:

I.Rozman Grinberg, M.Martinez-Carranza, O.Bimai, G.Nouairia, S.Shahid, D.Lundin, D.T.Logan, B.M.Sjoberg, P.Stenmark. A Nucleotide-Sensing Oligomerization Mechanism That Controls Nrdr-Dependent Transcription of Ribonucleotide Reductases. Nat Commun V. 13 2700 2022.
ISSN: ESSN 2041-1723
PubMed: 35577776
DOI: 10.1038/S41467-022-30328-1
Page generated: Wed Oct 30 08:59:53 2024

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