Zinc in PDB 9fvr: Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein

The structure of Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein, PDB code: 9fvr was solved by O.Bimai, B.M.Sjoberg, I.Rozman Grinberg, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.85 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.792, 73.832, 138.046, 90, 90, 90
R / Rfree (%)	22.4 / 27.4

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

Zinc binding site 1 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:122.4 occ:1.00 SG A:CYS6 2.1 136.3 1.0 SG A:CYS34 2.2 122.1 1.0 SG A:CYS3 2.5 137.6 1.0 SG A:CYS31 2.6 117.5 1.0 CB A:CYS34 2.9 117.1 1.0 CB A:CYS6 3.0 133.8 1.0 CB A:CYS31 3.2 115.5 1.0 N A:CYS6 3.4 133.2 1.0 N A:CYS34 3.6 115.4 1.0 CA A:CYS6 3.7 133.5 1.0 CA A:CYS34 3.8 116.2 1.0 CB A:CYS3 3.9 135.0 1.0 C A:CYS6 4.5 133.7 1.0 C A:PHE5 4.6 133.7 1.0 CB A:PHE5 4.6 134.3 1.0 N A:PHE7 4.6 133.5 1.0 C A:CYS34 4.7 116.8 1.0 CA A:CYS31 4.7 115.2 1.0 CB A:ALA8 4.8 134.9 1.0 C A:VAL33 4.8 115.0 1.0 CG2 A:VAL33 4.8 115.5 1.0 CD2 A:PHE5 4.9 135.9 1.0 N A:ASN35 4.9 116.6 1.0 CA A:PHE5 5.0 134.2 1.0

Zinc binding site 2 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:193.3 occ:1.00 O2A B:DTP202 2.8 99.3 1.0 O1G B:DTP202 3.2 100.1 1.0 OE2 A:GLU75 3.9 117.2 1.0 PA B:DTP202 4.0 99.3 1.0 O3A B:DTP202 4.1 99.1 1.0 OE1 A:GLU75 4.6 117.2 1.0 CD A:GLU75 4.7 115.3 1.0 PG B:DTP202 4.7 100.2 1.0 O1G B:ATP201 4.7 114.1 1.0 O1A B:DTP202 4.7 99.2 1.0

Zinc binding site 3 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:220.6 occ:1.00 SG B:CYS3 2.2 158.2 1.0 SG B:CYS34 2.2 153.7 1.0 SG B:CYS6 2.5 153.7 1.0 SG B:CYS31 3.1 158.3 1.0 CB B:CYS31 3.2 154.8 1.0 CB B:CYS6 3.4 152.7 1.0 N B:CYS6 3.5 152.6 1.0 CB B:CYS34 3.6 150.5 1.0 CB B:CYS3 3.6 155.1 1.0 N B:CYS34 3.9 150.6 1.0 CA B:CYS6 4.0 152.7 1.0 CA B:CYS34 4.3 149.9 1.0 CB B:PHE5 4.5 153.0 1.0 CD2 B:PHE5 4.6 154.8 1.0 C B:PHE5 4.6 152.9 1.0 CA B:CYS31 4.6 154.0 1.0 C B:CYS6 4.7 153.0 1.0 N B:PHE7 4.7 152.8 1.0 OE1 B:GLU36 4.8 160.5 1.0 N B:PHE5 4.8 152.8 1.0 CB B:ALA8 4.8 153.2 1.0 CA B:PHE5 4.9 153.0 1.0 CA B:CYS3 4.9 154.3 1.0 CB B:VAL33 4.9 153.2 1.0

Zinc binding site 4 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:140.2 occ:1.00 O2A A:DTP202 2.3 96.6 1.0 OE2 B:GLU75 3.3 118.6 1.0 PA A:DTP202 3.6 96.5 1.0 OE1 B:GLU75 3.8 118.8 1.0 O3A A:DTP202 3.9 95.8 1.0 O C:ASN55 3.9 119.9 1.0 CG1 C:VAL57 3.9 120.2 1.0 O2G A:DTP202 3.9 98.4 1.0 CD B:GLU75 3.9 116.7 1.0 O5' A:DTP202 4.6 97.6 1.0 O1A A:DTP202 4.7 96.4 1.0 ND2 C:ASN55 4.8 122.2 1.0 PG A:DTP202 4.9 98.2 1.0 O1G A:DTP202 5.0 98.4 1.0

Zinc binding site 5 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:180.6 occ:1.00 SG C:CYS34 2.2 160.7 1.0 SG C:CYS31 2.2 160.1 1.0 SG C:CYS3 2.4 155.0 1.0 SG C:CYS6 2.5 155.9 1.0 CB C:CYS31 2.7 156.2 1.0 CB C:CYS34 3.2 157.3 1.0 N C:CYS34 3.6 156.4 1.0 CB C:CYS6 3.6 152.4 1.0 CB C:CYS3 3.7 151.0 1.0 CA C:CYS34 3.9 156.6 1.0 N C:CYS6 3.9 150.9 1.0 CA C:CYS31 4.2 155.3 1.0 CA C:CYS6 4.3 151.6 1.0 C C:CYS34 4.6 156.6 1.0 CB C:ALA8 4.6 153.2 1.0 N C:ASN35 4.7 156.3 1.0 C C:VAL33 4.8 156.6 1.0 CD2 C:PHE5 4.8 149.4 1.0 C C:CYS31 4.8 155.8 1.0 CB C:PHE5 4.8 149.1 1.0 N C:VAL33 4.9 156.4 1.0 C C:CYS6 4.9 152.0 1.0 N C:PHE7 5.0 152.3 1.0

Zinc binding site 6 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn204 b:165.0 occ:1.00 O2A D:DTP202 3.1 92.4 1.0 OE2 C:GLU75 3.6 119.1 1.0 OE1 C:GLU75 3.7 117.0 1.0 O2G D:DTP202 3.8 94.4 1.0 CD C:GLU75 4.0 115.8 1.0 NH2 D:ARG72 4.2 106.0 1.0 PA D:DTP202 4.3 92.4 1.0 O3A D:DTP202 4.5 93.0 1.0 O1A D:DTP202 4.9 92.4 1.0

Zinc binding site 7 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:196.9 occ:1.00 SG D:CYS34 2.2 159.8 1.0 SG D:CYS3 2.2 153.4 1.0 SG D:CYS6 2.3 154.3 1.0 CB D:CYS6 2.9 152.1 1.0 N D:CYS6 2.9 150.9 1.0 CB D:CYS34 3.1 155.1 1.0 SG D:CYS31 3.2 154.1 1.0 CA D:CYS6 3.4 151.6 1.0 CB D:CYS31 3.6 152.4 1.0 CB D:CYS3 3.8 149.4 1.0 CB D:PHE5 4.0 150.7 1.0 C D:PHE5 4.0 150.8 1.0 N D:CYS34 4.1 153.9 1.0 CA D:CYS34 4.2 153.9 1.0 C D:CYS6 4.2 152.1 1.0 CA D:PHE5 4.3 150.4 1.0 N D:PHE7 4.3 152.1 1.0 CD2 D:PHE5 4.4 152.6 1.0 N D:PHE5 4.4 149.6 1.0 CG D:PHE5 4.7 151.7 1.0 C D:CYS34 5.0 153.5 1.0

Zinc binding site 8 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


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, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn204 b:148.0 occ:1.00 O2A C:DTP202 2.7 90.8 1.0 O3G C:DTP202 3.4 93.6 1.0 OE1 D:GLU75 3.7 107.6 1.0 PA C:DTP202 3.8 90.7 1.0 O3A C:DTP202 3.9 90.6 1.0 O1A C:DTP202 4.5 90.6 1.0 PG C:DTP202 4.7 93.4 1.0 O1G C:ATP201 4.7 109.1 1.0 CD D:GLU75 4.7 106.3 1.0 O2G C:DTP202 4.9 93.8 1.0

Zinc binding site 9 out of 9 in the Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Transcription Repressor Nrdr From E. Coli, Atp/Datp-Bound State, Semet Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn205 b:151.7 occ:1.00 OE2 D:GLU135 3.4 132.0 1.0 OE1 D:GLU135 3.5 131.3 1.0 O D:SER133 3.5 106.1 1.0 CD D:GLU135 3.6 129.1 1.0 O D:ARG132 3.7 103.7 1.0 OD2 D:ASP139 3.9 121.0 1.0 C D:SER133 4.5 106.3 1.0 CG D:GLU135 4.6 119.8 1.0 N D:GLU135 4.7 109.6 1.0 CA D:PHE134 4.9 108.0 1.0 C D:ARG132 4.9 103.7 1.0 CG D:ASP139 5.0 119.5 1.0 CB D:GLU135 5.0 113.5 1.0

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