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Zinc in PDB 5ip9: Structure of Rna Polymerase II-Tfiif Complex

Enzymatic activity of Structure of Rna Polymerase II-Tfiif Complex

All present enzymatic activity of Structure of Rna Polymerase II-Tfiif Complex:
2.7.7.6;

Protein crystallography data

The structure of Structure of Rna Polymerase II-Tfiif Complex, PDB code: 5ip9 was solved by C.Plaschka, M.Hantsche, C.Dienemann, C.Burzinski, J.Plitzko, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.93 / 3.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.820, 392.730, 283.420, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.4

Other elements in 5ip9:

The structure of Structure of Rna Polymerase II-Tfiif Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Rna Polymerase II-Tfiif Complex (pdb code 5ip9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Rna Polymerase II-Tfiif Complex, PDB code: 5ip9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ip9

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Zinc binding site 1 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.2
occ:1.00
 SG A:CYS107 2.3 1.0 1.0
SG A:CYS110 2.3 0.1 1.0
SG A:CYS148 2.4 0.3 1.0
SG A:CYS167 2.4 0.0 1.0
CB A:CYS107 3.2 0.3 1.0
CB A:CYS148 3.4 0.5 1.0
CB A:CYS110 3.5 0.1 1.0
N A:CYS167 3.8 0.7 1.0
N A:CYS110 3.8 1.0 1.0
CB A:CYS167 3.9 0.8 1.0
O A:CYS167 4.1 0.6 1.0
CA A:CYS110 4.2 0.6 1.0
CA A:CYS167 4.2 0.1 1.0
C A:CYS167 4.3 0.3 1.0
C A:GLY166 4.6 0.4 1.0
CA A:CYS107 4.6 0.0 1.0
C A:HIS109 4.6 0.2 1.0
CB A:HIS109 4.6 0.6 1.0
CA A:GLY166 4.7 0.7 1.0
CA A:CYS148 4.8 0.1 1.0
CB A:LYS112 4.8 0.7 1.0
NE2 A:GLN171 4.9 0.7 1.0
C A:CYS110 4.9 0.5 1.0

Zinc binding site 2 out of 8 in 5ip9

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Zinc binding site 2 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:97.4
occ:1.00
 NE2 A:HIS80 2.0 92.1 1.0
SG A:CYS67 2.2 0.1 1.0
SG A:CYS77 2.2 87.4 1.0
SG A:CYS70 2.5 88.8 1.0
CD2 A:HIS80 2.6 91.6 1.0
CE1 A:HIS80 3.2 89.7 1.0
CB A:CYS77 3.6 85.5 1.0
CB A:CYS67 3.7 0.4 1.0
CB A:CYS70 3.8 89.3 1.0
CG A:HIS80 3.8 88.0 1.0
N A:CYS70 3.9 95.5 1.0
ND1 A:HIS80 4.1 88.5 1.0
CB A:THR69 4.4 97.4 1.0
CA A:CYS70 4.4 95.6 1.0
CA A:CYS77 4.6 83.2 1.0
C A:THR69 4.8 0.7 1.0
CA A:CYS67 4.9 0.8 1.0
O A:CYS67 4.9 0.1 1.0
O A:LEU58 4.9 88.0 1.0
CA A:THR69 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 5ip9

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Zinc binding site 3 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.2
occ:1.00
 SG B:CYS1163 2.2 97.2 1.0
SG B:CYS1166 2.2 94.3 1.0
SG B:CYS1185 2.3 0.8 1.0
SG B:CYS1182 2.3 94.2 1.0
CB B:CYS1166 2.9 91.5 1.0
CB B:CYS1185 3.2 0.9 1.0
CB B:CYS1163 3.2 90.9 1.0
N B:CYS1166 3.5 91.4 1.0
CB B:CYS1182 3.7 91.7 1.0
CA B:CYS1166 3.7 90.2 1.0
CB B:ILE1165 4.5 96.6 1.0
CA B:CYS1185 4.6 0.9 1.0
C B:CYS1166 4.6 90.4 1.0
CA B:CYS1163 4.6 88.6 1.0
O B:GLY1184 4.6 0.2 1.0
C B:ILE1165 4.6 95.6 1.0
CG2 B:ILE1165 4.9 99.5 1.0
N B:GLY1167 4.9 85.8 1.0
ND2 B:ASN1187 4.9 0.4 1.0
O B:CYS1182 4.9 0.7 1.0
CA B:CYS1182 5.0 94.3 1.0
CA B:ILE1165 5.0 92.0 1.0
CD1 A:ILE30 5.0 0.1 1.0

Zinc binding site 4 out of 8 in 5ip9

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Zinc binding site 4 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:94.9
occ:1.00
 SG C:CYS86 2.2 83.4 1.0
SG C:CYS88 2.3 89.9 1.0
SG C:CYS95 2.3 90.0 1.0
SG C:CYS92 2.3 0.4 1.0
CB C:CYS92 3.1 98.8 1.0
N C:CYS92 3.2 93.8 1.0
CB C:CYS86 3.2 76.5 1.0
CB C:CYS95 3.3 87.5 1.0
CB C:CYS88 3.4 88.9 1.0
CA C:CYS92 3.7 96.5 1.0
C C:HIS91 3.9 96.6 1.0
N C:CYS95 4.0 92.5 1.0
C C:CYS92 4.2 99.5 1.0
N C:CYS88 4.2 86.4 1.0
CA C:HIS91 4.2 92.0 1.0
O C:CYS92 4.3 97.1 1.0
CA C:CYS95 4.3 89.9 1.0
CA C:CYS88 4.4 88.3 1.0
CA C:CYS86 4.6 76.5 1.0
CB C:LYS94 4.8 95.6 1.0
O C:HIS91 4.8 96.2 1.0
C C:LYS94 4.9 97.7 1.0
C C:CYS86 4.9 82.4 1.0
N C:LYS94 4.9 95.3 1.0
O C:ASP90 4.9 0.8 1.0
N C:PHE87 4.9 83.0 1.0

Zinc binding site 5 out of 8 in 5ip9

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Zinc binding site 5 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.8
occ:1.00
 SG I:CYS32 2.3 0.9 1.0
SG I:CYS10 2.3 0.1 1.0
SG I:CYS7 2.3 0.5 1.0
SG I:CYS29 2.4 0.4 1.0
CB I:CYS10 2.5 0.2 1.0
CB I:CYS32 3.3 0.6 1.0
CB I:CYS29 3.4 0.3 1.0
CB I:CYS7 3.6 0.4 1.0
N I:CYS32 3.8 0.9 1.0
CA I:CYS10 4.0 0.9 1.0
CA I:CYS32 4.0 0.2 1.0
O I:ARG8 4.1 0.8 1.0
N I:CYS10 4.5 0.7 1.0
CB I:TYR34 4.5 0.2 1.0
CB I:THR31 4.6 0.5 1.0
C I:THR31 4.6 0.6 1.0
C I:CYS32 4.7 0.3 1.0
OD1 I:ASP9 4.7 0.0 1.0
CA I:CYS29 4.8 0.1 1.0
O I:CYS7 4.8 0.8 1.0
C I:ASP9 4.9 0.9 1.0
CA I:CYS7 4.9 0.7 1.0
O I:ASP9 4.9 0.4 1.0
C I:CYS7 4.9 0.9 1.0
C I:CYS10 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 5ip9

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Zinc binding site 6 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.7
occ:1.00
 SG I:CYS106 2.3 0.7 1.0
SG I:CYS78 2.3 0.5 1.0
SG I:CYS75 2.4 0.8 1.0
SG I:CYS103 2.5 0.6 1.0
CB I:CYS106 3.0 0.5 1.0
CB I:CYS75 3.2 0.0 1.0
CB I:CYS103 3.2 0.5 1.0
CB I:CYS78 3.6 0.6 1.0
N I:CYS78 3.6 0.9 1.0
N I:CYS106 3.7 0.2 1.0
CA I:CYS106 3.9 0.5 1.0
CA I:CYS78 4.1 0.5 1.0
CB I:LYS77 4.4 0.3 1.0
C I:CYS106 4.6 1.0 1.0
CA I:CYS75 4.6 0.5 1.0
C I:LYS77 4.7 0.1 1.0
CA I:CYS103 4.7 0.3 1.0
N I:SER107 4.7 0.7 1.0
C I:CYS78 4.7 0.3 1.0
CB I:SER105 4.7 0.8 1.0
CB I:SER80 4.8 0.1 1.0
N I:HIS79 4.8 0.4 1.0
CA I:LYS77 4.9 0.7 1.0
C I:SER105 4.9 0.1 1.0
N I:LYS77 4.9 0.6 1.0
N I:SER80 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 5ip9

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Zinc binding site 7 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.8
occ:1.00
 SG J:CYS46 2.2 0.1 1.0
SG J:CYS10 2.3 97.8 1.0
SG J:CYS45 2.3 0.2 1.0
SG J:CYS7 2.4 0.0 1.0
CB J:CYS7 3.1 98.5 1.0
N J:CYS46 3.3 0.2 1.0
CB J:CYS46 3.5 0.7 1.0
CB J:CYS45 3.5 94.5 1.0
CB J:CYS10 3.6 93.6 1.0
CA J:CYS46 3.6 0.9 1.0
C J:CYS45 3.7 0.7 1.0
N J:CYS10 3.8 88.1 1.0
CA J:CYS10 4.2 90.7 1.0
CA J:CYS45 4.2 95.7 1.0
O J:CYS45 4.4 0.1 1.0
CB J:LYS12 4.5 0.9 1.0
CA J:CYS7 4.6 95.7 1.0
CB J:SER9 4.6 89.2 1.0
N J:GLY11 4.7 92.9 1.0
C J:CYS10 4.8 96.6 1.0
NH2 J:ARG43 4.8 0.4 1.0
CZ J:ARG43 4.8 0.5 1.0
N J:LYS12 4.8 0.6 1.0
CG J:ARG43 4.9 0.9 1.0
C J:CYS7 4.9 95.2 1.0
C J:SER9 4.9 89.3 1.0
N J:CYS45 4.9 99.0 1.0

Zinc binding site 8 out of 8 in 5ip9

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Zinc binding site 8 out of 8 in the Structure of Rna Polymerase II-Tfiif Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Rna Polymerase II-Tfiif Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.7
occ:1.00
 SG L:CYS48 2.3 0.4 1.0
SG L:CYS34 2.3 0.6 1.0
SG L:CYS51 2.4 0.8 1.0
SG L:CYS31 2.5 0.7 1.0
CB L:CYS34 3.1 0.1 1.0
CB L:CYS31 3.4 0.4 1.0
CB L:CYS48 3.4 0.2 1.0
CB L:CYS51 3.8 0.9 1.0
N L:CYS34 3.9 0.9 1.0
CA L:CYS34 4.0 1.0 1.0
O L:CYS51 4.0 0.2 1.0
N L:CYS51 4.2 0.6 1.0
O L:LYS49 4.4 0.5 1.0
CA L:CYS51 4.4 1.0 1.0
N L:SER35 4.6 0.3 1.0
C L:CYS34 4.7 0.8 1.0
C L:CYS51 4.7 0.1 1.0
CB L:HIS53 4.8 0.0 1.0
CA L:CYS48 4.8 0.7 1.0
CA L:CYS31 4.9 0.6 1.0

Reference:

C.Plaschka, M.Hantsche, C.Dienemann, C.Burzinski, J.Plitzko, P.Cramer. Transcription Initiation Complex Structures Elucidate Dna Opening. Nature V. 533 353 2016.
ISSN: ESSN 1476-4687
PubMed: 27193681
DOI: 10.1038/NATURE17990
Page generated: Sun Oct 27 18:18:35 2024

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