Zinc in PDB 1tf6: Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region

The structure of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region, PDB code: 1tf6 was solved by R.T.Nolte, R.M.Conlin, S.C.Harrison, R.S.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 3.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	64.180, 64.712, 78.035, 90.07, 92.98, 102.95
R / Rfree (%)	30.8 / 36.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region (pdb code 1tf6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region, PDB code: 1tf6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:27.1 occ:1.00 NE2 A:HIS37 1.8 33.4 1.0 NE2 A:HIS33 2.0 10.8 1.0 SG A:CYS20 2.1 48.8 1.0 SG A:CYS15 2.2 15.9 1.0 CE1 A:HIS33 2.5 13.3 1.0 CE1 A:HIS37 2.5 33.7 1.0 CB A:CYS20 2.7 46.9 1.0 CD2 A:HIS37 3.0 33.5 1.0 CD2 A:HIS33 3.3 15.6 1.0 CB A:CYS15 3.4 14.5 1.0 ND1 A:HIS37 3.7 33.7 1.0 ND1 A:HIS33 3.8 15.7 1.0 CG A:HIS37 4.0 33.2 1.0 CA A:CYS20 4.1 46.8 1.0 CG A:HIS33 4.2 16.9 1.0 CB A:ALA22 4.5 31.3 1.0 CA A:CYS15 4.7 15.3 1.0 C A:CYS20 4.8 44.6 1.0 CB A:PHE17 4.9 15.8 1.0

Zinc binding site 2 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:64.9 occ:1.00 NE2 A:HIS67 2.1 0.0 1.0 NE2 A:HIS63 2.1 57.2 1.0 SG A:CYS50 2.1 85.8 1.0 SG A:CYS45 2.3 70.5 1.0 CD2 A:HIS67 2.5 99.3 1.0 CB A:CYS45 2.6 71.5 1.0 CB A:CYS50 2.8 91.3 1.0 CE1 A:HIS63 2.9 56.9 1.0 CD2 A:HIS63 3.3 55.8 1.0 CE1 A:HIS67 3.4 0.0 1.0 CG A:HIS67 3.8 98.7 1.0 ND1 A:HIS63 4.1 57.3 1.0 CA A:CYS45 4.2 72.0 1.0 ND1 A:HIS67 4.2 99.9 1.0 CA A:CYS50 4.3 94.3 1.0 CG A:GLU47 4.3 91.3 1.0 CG A:HIS63 4.3 57.7 1.0 CB A:LYS52 4.7 82.7 1.0 C A:CYS50 4.7 94.2 1.0 C A:CYS45 4.9 77.1 1.0 N A:CYS45 4.9 66.5 1.0 O A:CYS50 4.9 94.0 1.0 O A:GLU47 5.0 91.5 1.0

Zinc binding site 3 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:84.2 occ:1.00 NE2 A:HIS98 2.0 76.2 1.0 NE2 A:HIS93 2.0 93.8 1.0 SG A:CYS75 2.3 95.5 1.0 SG A:CYS80 2.5 96.6 1.0 CB A:CYS80 2.6 98.0 1.0 CE1 A:HIS98 2.7 76.7 1.0 CE1 A:HIS93 2.9 93.9 1.0 OG A:SER77 2.9 98.0 1.0 CD2 A:HIS98 3.1 77.6 1.0 CD2 A:HIS93 3.1 91.9 1.0 CB A:CYS75 3.7 97.8 1.0 CB A:SER77 3.8 99.1 1.0 ND1 A:HIS98 3.9 77.6 1.0 CA A:CYS80 4.0 99.0 1.0 ND1 A:HIS93 4.1 92.7 1.0 CG A:HIS98 4.1 78.2 1.0 CG A:HIS93 4.2 90.2 1.0 O A:CYS80 4.4 98.5 1.0 C A:CYS80 4.4 98.9 1.0 N A:CYS80 4.5 0.0 1.0 O A:CYS75 4.8 98.9 1.0

Zinc binding site 4 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:24.0 occ:1.00 NE2 A:HIS125 1.9 19.5 1.0 NE2 A:HIS129 2.1 36.1 1.0 SG A:CYS107 2.2 58.6 1.0 SG A:CYS112 2.2 65.2 1.0 CE1 A:HIS129 2.6 35.9 1.0 CD2 A:HIS125 2.8 22.4 1.0 CE1 A:HIS125 2.8 19.5 1.0 CB A:CYS107 3.0 58.7 1.0 CD2 A:HIS129 3.3 38.0 1.0 CB A:CYS112 3.6 63.4 1.0 ND1 A:HIS129 3.8 35.9 1.0 ND1 A:HIS125 3.8 23.7 1.0 CG A:HIS125 3.8 24.4 1.0 CG A:HIS129 4.1 39.0 1.0 CA A:CYS107 4.4 60.7 1.0 O A:CYS107 4.6 58.8 1.0 CB A:PHE109 4.7 48.7 1.0 C A:CYS107 4.8 60.1 1.0 CA A:CYS112 4.9 63.4 1.0 OG A:SER128 4.9 46.2 1.0 CA A:GLN126 5.0 38.3 1.0 CB A:LYS114 5.0 55.6 1.0

Zinc binding site 5 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:32.9 occ:1.00 NE2 A:HIS159 1.9 62.4 1.0 NE2 A:HIS155 2.0 21.5 1.0 SG A:CYS142 2.1 82.2 1.0 CE1 A:HIS159 2.2 62.1 1.0 SG A:CYS137 2.2 54.8 1.0 CE1 A:HIS155 3.0 24.4 1.0 CD2 A:HIS155 3.0 21.9 1.0 CD2 A:HIS159 3.2 62.7 1.0 CB A:CYS142 3.2 85.5 1.0 CB A:CYS137 3.3 60.7 1.0 ND1 A:HIS159 3.4 62.5 1.0 CG A:HIS159 3.9 62.2 1.0 ND1 A:HIS155 4.1 24.3 1.0 CG A:HIS155 4.2 21.8 1.0 CA A:CYS142 4.6 86.9 1.0 CB A:LYS144 4.7 68.4 1.0 CA A:CYS137 4.7 63.5 1.0

Zinc binding site 6 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:0.0 occ:1.00 NE2 A:HIS183 2.0 83.2 1.0 NE2 A:HIS188 2.2 0.0 1.0 CD2 A:HIS183 2.3 83.7 1.0 SG A:CYS164 2.3 85.8 1.0 SG A:CYS170 2.4 96.3 1.0 CD2 A:HIS188 2.8 0.0 1.0 CB A:CYS164 2.8 85.0 1.0 CE1 A:HIS183 3.3 83.7 1.0 CE1 A:HIS188 3.3 99.6 1.0 CG A:HIS183 3.7 84.0 1.0 CB A:CYS170 3.9 97.5 1.0 ND1 A:HIS183 4.1 84.2 1.0 CG A:HIS188 4.1 0.0 1.0 CA A:CYS164 4.2 84.2 1.0 ND1 A:HIS188 4.3 99.8 1.0 CB A:LYS166 4.4 99.5 1.0 O A:HIS183 4.5 83.8 1.0 C A:CYS164 4.7 86.6 1.0 N A:CYS164 4.7 81.0 1.0 CB A:HIS183 4.9 83.5 1.0 C A:HIS183 4.9 83.9 1.0 N A:LYS165 5.0 89.8 1.0

Zinc binding site 7 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:12.8 occ:1.00 NE2 D:HIS37 1.9 33.9 1.0 NE2 D:HIS33 1.9 2.0 1.0 SG D:CYS20 2.1 51.4 1.0 SG D:CYS15 2.2 18.3 1.0 CE1 D:HIS33 2.4 2.0 1.0 CB D:CYS20 2.7 47.7 1.0 CE1 D:HIS37 2.7 33.4 1.0 CD2 D:HIS37 3.0 34.4 1.0 CD2 D:HIS33 3.2 9.9 1.0 CB D:CYS15 3.5 14.0 1.0 ND1 D:HIS33 3.7 8.6 1.0 ND1 D:HIS37 3.9 32.9 1.0 CG D:HIS37 4.0 33.3 1.0 CG D:HIS33 4.1 12.4 1.0 CA D:CYS20 4.1 46.3 1.0 CB D:ALA22 4.5 29.5 1.0 CA D:CYS15 4.8 11.9 1.0 C D:CYS20 4.8 43.6 1.0 CB D:PHE17 5.0 16.7 1.0

Zinc binding site 8 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:92.0 occ:1.00 NE2 D:HIS67 2.1 0.0 1.0 SG D:CYS50 2.1 89.1 1.0 NE2 D:HIS63 2.2 55.5 1.0 SG D:CYS45 2.3 71.1 1.0 CD2 D:HIS67 2.5 99.9 1.0 CB D:CYS45 2.7 71.2 1.0 CB D:CYS50 2.8 92.8 1.0 CE1 D:HIS63 3.0 54.4 1.0 CD2 D:HIS63 3.3 54.4 1.0 CE1 D:HIS67 3.4 100.0 1.0 CG D:HIS67 3.8 99.0 1.0 CA D:CYS45 4.2 72.2 1.0 ND1 D:HIS63 4.2 54.3 1.0 CG D:GLU47 4.2 92.3 1.0 ND1 D:HIS67 4.2 99.6 1.0 CA D:CYS50 4.3 95.4 1.0 CG D:HIS63 4.4 55.3 1.0 CB D:LYS52 4.8 83.5 1.0 C D:CYS50 4.8 94.9 1.0 C D:CYS45 4.9 77.9 1.0 O D:GLU47 4.9 91.3 1.0 O D:CYS50 5.0 95.5 1.0 N D:LYS46 5.0 82.2 1.0

Zinc binding site 9 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn203 b:0.0 occ:1.00 NE2 D:HIS98 2.1 77.6 1.0 NE2 D:HIS93 2.1 95.8 1.0 SG D:CYS75 2.3 95.6 1.0 SG D:CYS80 2.5 94.9 1.0 CB D:CYS80 2.5 97.0 1.0 CE1 D:HIS98 2.8 78.4 1.0 OG D:SER77 2.9 98.8 1.0 CE1 D:HIS93 3.0 94.6 1.0 CD2 D:HIS93 3.3 93.9 1.0 CD2 D:HIS98 3.3 78.1 1.0 CB D:CYS75 3.7 97.6 1.0 CB D:SER77 3.7 99.3 1.0 CA D:CYS80 3.8 98.5 1.0 ND1 D:HIS98 4.1 78.6 1.0 O D:CYS80 4.1 98.9 1.0 C D:CYS80 4.2 98.9 1.0 ND1 D:HIS93 4.2 93.3 1.0 N D:CYS80 4.2 99.8 1.0 CG D:HIS98 4.3 78.5 1.0 CG D:HIS93 4.4 91.6 1.0 O D:CYS75 4.7 99.1 1.0

Zinc binding site 10 out of 12 in the Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Co-Crystal Structure of Xenopus Tfiiia Zinc Finger Domain Bound to the 5S Ribosomal Rna Gene Internal Control Region within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn204 b:40.2 occ:1.00 NE2 D:HIS129 1.9 40.2 1.0 NE2 D:HIS125 1.9 18.0 1.0 SG D:CYS107 2.2 55.9 1.0 CE1 D:HIS129 2.4 40.1 1.0 CE1 D:HIS125 2.5 19.5 1.0 SG D:CYS112 2.5 68.5 1.0 CD2 D:HIS125 2.7 22.7 1.0 CB D:CYS107 3.0 58.3 1.0 CD2 D:HIS129 3.1 42.0 1.0 ND1 D:HIS125 3.4 23.1 1.0 CG D:HIS125 3.5 24.6 1.0 ND1 D:HIS129 3.6 40.8 1.0 CB D:CYS112 3.8 64.2 1.0 CG D:HIS129 4.0 41.9 1.0 CA D:CYS107 4.5 60.8 1.0 OG D:SER128 4.5 50.2 1.0 CA D:GLN126 4.6 36.4 1.0 N D:GLN126 4.7 34.9 1.0 O D:CYS107 4.7 58.6 1.0 CB D:PHE109 4.8 48.9 1.0 CB D:HIS125 4.9 27.6 1.0 C D:HIS125 4.9 32.6 1.0 C D:CYS107 5.0 59.5 1.0

R.T.Nolte, R.M.Conlin, S.C.Harrison, R.S.Brown. Differing Roles For Zinc Fingers in Dna Recognition: Structure of A Six-Finger Transcription Factor Iiia Complex. Proc.Natl.Acad.Sci.Usa V. 95 2938 1998.
ISSN: ISSN 0027-8424
PubMed: 9501194
DOI: 10.1073/PNAS.95.6.2938