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Zinc in PDB 9fxk: Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State

Protein crystallography data

The structure of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State, PDB code: 9fxk was solved by O.Bimai, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.37 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.797, 129.791, 143.877, 90, 90, 90
R / Rfree (%) 22.4 / 25.7

Other elements in 9fxk:

The structure of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State (pdb code 9fxk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State, PDB code: 9fxk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9fxk

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Zinc binding site 1 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:63.4
occ:1.00
 SG A:CYS34 2.2 66.0 1.0
SG A:CYS6 2.2 61.7 1.0
SG A:CYS3 2.3 57.5 1.0
SG A:CYS31 2.4 66.7 1.0
CB A:CYS34 3.1 65.5 1.0
CB A:CYS31 3.1 64.2 1.0
CB A:CYS3 3.2 55.1 1.0
CB A:CYS6 3.3 59.2 1.0
N A:CYS6 3.6 57.4 1.0
N A:CYS34 3.7 66.2 1.0
CA A:CYS6 3.9 58.8 1.0
CA A:CYS34 4.0 65.7 1.0
CG2 A:VAL33 4.5 69.7 1.0
CB A:PHE5 4.6 54.2 1.0
C A:CYS6 4.6 60.5 1.0
CB A:ALA8 4.6 64.7 1.0
CA A:CYS31 4.6 64.1 1.0
CA A:CYS3 4.6 54.8 1.0
C A:PHE5 4.7 56.5 1.0
N A:PHE7 4.7 61.3 1.0
C A:CYS34 4.7 65.9 1.0
N A:ALA8 4.9 64.0 1.0
C A:VAL33 5.0 67.3 1.0
N A:ASN35 5.0 65.6 1.0
CA A:PHE5 5.0 55.0 1.0

Zinc binding site 2 out of 8 in 9fxk

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Zinc binding site 2 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:95.7
occ:1.00
 SG B:CYS3 2.2 82.5 1.0
SG B:CYS6 2.3 97.0 1.0
SG B:CYS34 2.3 94.9 1.0
SG B:CYS31 2.4 85.3 1.0
CB B:CYS31 3.0 82.9 1.0
CB B:CYS3 3.1 78.5 1.0
CB B:CYS6 3.3 90.7 1.0
CB B:CYS34 3.3 89.7 1.0
N B:CYS6 3.5 87.2 1.0
N B:CYS34 3.9 88.5 1.0
CA B:CYS6 3.9 89.2 1.0
CA B:CYS34 4.1 88.5 1.0
CA B:CYS31 4.5 82.5 1.0
CA B:CYS3 4.5 77.3 1.0
CB B:PHE5 4.6 83.4 1.0
C B:CYS6 4.6 90.6 1.0
C B:PHE5 4.6 85.9 1.0
CB B:ALA8 4.7 90.2 1.0
N B:PHE7 4.7 91.2 1.0
C B:CYS34 4.8 88.0 1.0
N B:ALA8 4.9 90.8 1.0
CA B:PHE5 4.9 83.8 1.0
N B:PHE5 4.9 82.4 1.0

Zinc binding site 3 out of 8 in 9fxk

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Zinc binding site 3 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:66.2
occ:1.00
 SG C:CYS6 2.2 63.9 1.0
SG C:CYS3 2.2 67.4 1.0
SG C:CYS34 2.3 66.3 1.0
SG C:CYS31 2.4 59.3 1.0
CB C:CYS31 3.0 54.9 1.0
CB C:CYS3 3.1 63.5 1.0
CB C:CYS6 3.3 64.1 1.0
CB C:CYS34 3.4 61.3 1.0
N C:CYS6 3.5 64.4 1.0
CA C:CYS6 3.9 64.5 1.0
N C:CYS34 3.9 60.4 1.0
CA C:CYS34 4.2 60.9 1.0
C C:CYS6 4.5 65.8 1.0
CA C:CYS31 4.5 54.2 1.0
CA C:CYS3 4.5 62.7 1.0
CB C:ALA8 4.6 65.4 1.0
CB C:PHE5 4.6 65.9 1.0
N C:PHE7 4.6 66.8 1.0
C C:PHE5 4.6 65.3 1.0
N C:ALA8 4.8 66.6 1.0
CA C:PHE5 4.9 65.5 1.0
C C:CYS34 4.9 61.6 1.0
N C:PHE5 5.0 64.9 1.0

Zinc binding site 4 out of 8 in 9fxk

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Zinc binding site 4 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:74.5
occ:1.00
 SG D:CYS34 2.3 79.4 1.0
SG D:CYS6 2.3 66.2 1.0
SG D:CYS3 2.3 66.0 1.0
SG D:CYS31 2.3 75.3 1.0
CB D:CYS31 2.9 72.6 1.0
CB D:CYS3 3.1 61.4 1.0
CB D:CYS34 3.3 77.7 1.0
CB D:CYS6 3.3 65.2 1.0
N D:CYS6 3.6 64.6 1.0
N D:CYS34 3.8 76.9 1.0
CA D:CYS6 4.0 65.0 1.0
CA D:CYS34 4.1 77.5 1.0
CA D:CYS31 4.4 72.2 1.0
CB D:ALA8 4.5 67.6 1.0
CG2 D:VAL33 4.6 78.1 1.0
C D:CYS6 4.6 66.2 1.0
CA D:CYS3 4.6 60.4 1.0
N D:PHE7 4.7 66.4 1.0
CB D:PHE5 4.7 64.1 1.0
C D:PHE5 4.7 65.0 1.0
C D:CYS34 4.8 78.4 1.0
N D:ALA8 4.8 67.7 1.0
N D:ASN35 5.0 78.8 1.0

Zinc binding site 5 out of 8 in 9fxk

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Zinc binding site 5 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:67.0
occ:1.00
 SG E:CYS6 2.2 78.0 1.0
SG E:CYS34 2.2 65.0 1.0
SG E:CYS31 2.3 66.8 1.0
SG E:CYS3 2.3 62.7 1.0
CB E:CYS31 3.0 62.5 1.0
CB E:CYS34 3.1 61.4 1.0
CB E:CYS3 3.3 63.2 1.0
CB E:CYS6 3.3 76.0 1.0
N E:CYS34 3.6 61.9 1.0
N E:CYS6 3.8 74.9 1.0
CA E:CYS34 3.9 61.3 1.0
CA E:CYS6 4.1 76.0 1.0
CA E:CYS31 4.5 61.3 1.0
CB E:ALA8 4.5 79.8 1.0
C E:CYS34 4.6 61.3 1.0
CB E:PHE5 4.7 72.8 1.0
CA E:CYS3 4.7 64.0 1.0
C E:CYS6 4.7 77.7 1.0
C E:VAL33 4.8 63.1 1.0
N E:ASN35 4.8 61.1 1.0
C E:PHE5 4.8 74.2 1.0
N E:PHE7 4.9 78.6 1.0
N E:ALA8 4.9 80.4 1.0
CB E:GLU36 5.0 60.7 1.0

Zinc binding site 6 out of 8 in 9fxk

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Zinc binding site 6 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:105.0
occ:1.00
 SG F:CYS34 2.2 105.2 1.0
SG F:CYS6 2.2 99.9 1.0
SG F:CYS3 2.3 96.4 1.0
SG F:CYS31 2.5 98.7 1.0
CB F:CYS31 3.1 95.0 1.0
CB F:CYS3 3.2 90.5 1.0
CB F:CYS34 3.2 102.8 1.0
CB F:CYS6 3.2 97.7 1.0
N F:CYS6 3.5 95.9 1.0
CA F:CYS6 3.9 97.3 1.0
N F:CYS34 3.9 102.1 1.0
CA F:CYS34 4.1 102.1 1.0
CB F:PHE5 4.5 93.7 1.0
C F:CYS6 4.5 99.0 1.0
C F:PHE5 4.6 95.3 1.0
CG2 F:VAL33 4.6 103.4 1.0
CA F:CYS31 4.6 94.4 1.0
CA F:CYS3 4.6 89.0 1.0
N F:PHE7 4.7 100.0 1.0
CB F:ALA8 4.7 102.0 1.0
C F:CYS34 4.8 101.7 1.0
CA F:PHE5 4.9 93.9 1.0
N F:ALA8 4.9 101.7 1.0
N F:PHE5 4.9 92.6 1.0

Zinc binding site 7 out of 8 in 9fxk

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Zinc binding site 7 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn203

b:70.8
occ:1.00
 SG G:CYS6 2.2 74.5 1.0
SG G:CYS31 2.3 66.6 1.0
SG G:CYS3 2.4 75.2 1.0
SG G:CYS34 2.4 70.2 1.0
CB G:CYS31 3.0 66.3 1.0
CB G:CYS3 3.2 72.0 1.0
CB G:CYS6 3.3 71.8 1.0
CB G:CYS34 3.3 67.1 1.0
N G:CYS6 3.6 71.0 1.0
N G:CYS34 3.8 66.5 1.0
CA G:CYS6 3.9 71.8 1.0
CA G:CYS34 4.1 66.3 1.0
CB G:ALA8 4.4 75.2 1.0
C G:CYS6 4.5 73.7 1.0
CA G:CYS31 4.5 66.6 1.0
CB G:PHE5 4.6 68.7 1.0
CA G:CYS3 4.7 71.3 1.0
C G:PHE5 4.7 70.7 1.0
O G:CYS6 4.8 74.1 1.0
C G:CYS34 4.8 66.1 1.0
C G:VAL33 4.9 67.5 1.0
N G:ALA8 4.9 75.4 1.0
CB G:VAL33 4.9 69.2 1.0

Zinc binding site 8 out of 8 in 9fxk

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Zinc binding site 8 out of 8 in the Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Transcription Repressor Nrdr From E. Coli, Amppnp/Atp-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:71.7
occ:1.00
 SG H:CYS34 2.2 78.2 1.0
SG H:CYS6 2.3 80.4 1.0
SG H:CYS3 2.4 66.6 1.0
SG H:CYS31 2.4 68.2 1.0
CB H:CYS31 3.1 64.8 1.0
CB H:CYS34 3.1 71.7 1.0
CB H:CYS3 3.2 61.7 1.0
CB H:CYS6 3.3 75.9 1.0
N H:CYS6 3.7 73.0 1.0
N H:CYS34 3.7 70.1 1.0
CA H:CYS6 3.9 74.9 1.0
CA H:CYS34 3.9 70.2 1.0
C H:CYS6 4.2 77.2 1.0
O H:CYS6 4.4 77.8 1.0
CB H:ALA8 4.5 80.0 1.0
CG2 H:VAL33 4.5 71.1 1.0
CA H:CYS31 4.5 64.3 1.0
CA H:CYS3 4.7 60.6 1.0
C H:CYS34 4.7 69.5 1.0
N H:ALA8 4.8 79.9 1.0
C H:PHE5 4.9 72.1 1.0
N H:PHE7 4.9 78.4 1.0
N H:ASN35 4.9 68.3 1.0
C H:VAL33 4.9 70.6 1.0

Reference:

I.Rozman Grinberg, O.Bimai, S.Shahid, L.Philipp, M.Martinez-Carranza, I.Banerjee, D.Lundin, P.Stenmark, B.M.Sjoberg, D.T.Logan. Bacterial Transcriptional Repressor Nrdr - A Flexible Multifactorial Nucleotide Sensor. Febs J. 2025.
ISSN: ISSN 1742-464X
PubMed: 40029022
DOI: 10.1111/FEBS.70037
Page generated: Fri Aug 22 17:42:53 2025

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