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Zinc in PDB 1y1v: Refined Rna Polymerase II-Tfiis Complex

Enzymatic activity of Refined Rna Polymerase II-Tfiis Complex

All present enzymatic activity of Refined Rna Polymerase II-Tfiis Complex:
2.7.7.6;

Protein crystallography data

The structure of Refined Rna Polymerase II-Tfiis Complex, PDB code: 1y1v was solved by H.Kettenberger, K.-J.Armache, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 218.900, 395.300, 281.000, 90.00, 90.00, 90.00
R / Rfree (%) 28.2 / 29.4

Other elements in 1y1v:

The structure of Refined Rna Polymerase II-Tfiis Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Refined Rna Polymerase II-Tfiis Complex (pdb code 1y1v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Refined Rna Polymerase II-Tfiis Complex, PDB code: 1y1v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 1y1v

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Zinc binding site 1 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:58.5
occ:1.00
 SG A:CYS107 2.5 0.8 1.0
SG A:CYS167 2.6 0.4 1.0
SG A:CYS110 2.7 97.9 1.0
SG A:CYS148 2.7 0.2 1.0
O A:CYS167 3.4 0.2 1.0
CB A:CYS148 3.4 0.7 1.0
O A:GLY166 3.6 0.6 1.0
CB A:CYS110 3.7 0.9 1.0
O A:MET108 3.9 92.0 1.0
CB A:CYS107 4.2 93.4 1.0
N A:CYS110 4.3 0.8 1.0
CB A:CYS167 4.3 0.4 1.0
C A:CYS167 4.4 0.7 1.0
CA A:CYS110 4.5 0.1 1.0
O A:CYS107 4.7 90.4 1.0
N A:GLY111 4.8 97.4 1.0
C A:GLY166 4.8 1.0 1.0
CA A:CYS167 4.9 0.7 1.0
CA A:CYS148 4.9 0.8 1.0
C A:CYS110 4.9 99.8 1.0

Zinc binding site 2 out of 9 in 1y1v

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Zinc binding site 2 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:15.2
occ:1.00
 SG A:CYS67 2.3 0.6 1.0
SG A:CYS77 2.4 40.2 1.0
NE2 A:HIS80 2.4 33.6 1.0
SG A:CYS70 2.7 68.8 1.0
CB A:CYS67 3.0 98.9 1.0
CE1 A:HIS80 3.3 35.2 1.0
O A:CYS67 3.4 99.3 1.0
CD2 A:HIS80 3.4 32.3 1.0
CB A:CYS70 3.4 75.4 1.0
CB A:CYS77 3.7 41.5 1.0
CA A:CYS67 4.1 0.7 1.0
C A:CYS67 4.2 0.9 1.0
O A:GLN71 4.4 83.9 1.0
ND1 A:HIS80 4.4 32.2 1.0
CG A:HIS80 4.5 34.8 1.0
O A:PRO78 4.6 40.2 1.0
OE1 A:GLN68 4.7 0.9 1.0
CA A:CYS77 4.7 42.5 1.0
CA A:CYS70 4.8 81.5 1.0
C A:CYS70 4.9 81.3 1.0
NE2 A:GLN68 4.9 0.6 1.0
CD A:GLN68 5.0 0.2 1.0

Zinc binding site 3 out of 9 in 1y1v

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Zinc binding site 3 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:15.1
occ:1.00
 CB B:CYS1185 2.2 53.4 1.0
SG B:CYS1166 2.3 27.2 1.0
SG B:CYS1163 2.3 26.2 1.0
SG B:CYS1185 2.4 62.5 1.0
SG B:CYS1182 2.6 22.4 1.0
CB B:CYS1163 2.9 23.4 1.0
N B:CYS1166 3.4 33.6 1.0
CA B:CYS1185 3.6 53.6 1.0
CB B:CYS1166 3.7 29.0 1.0
CB B:CYS1182 3.8 37.9 1.0
CG2 B:ILE1165 3.8 29.6 1.0
CB B:ILE1165 4.0 31.7 1.0
O B:CYS1185 4.0 52.8 1.0
C B:CYS1185 4.1 51.7 1.0
CA B:CYS1166 4.1 31.8 1.0
O B:CYS1182 4.2 48.0 1.0
O B:CYS1166 4.2 37.6 1.0
N B:CYS1185 4.2 54.7 1.0
CA B:CYS1163 4.3 24.0 1.0
C B:ILE1165 4.5 34.0 1.0
C B:CYS1166 4.5 34.4 1.0
CA B:ILE1165 4.6 32.2 1.0
N B:ILE1165 4.7 32.6 1.0
OG1 B:THR1170 4.9 33.0 1.0
C B:CYS1163 4.9 23.4 1.0
N B:ASP1186 5.0 51.2 1.0

Zinc binding site 4 out of 9 in 1y1v

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Zinc binding site 4 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:20.5
occ:1.00
 SG C:CYS88 2.2 48.1 1.0
CB C:CYS86 2.4 49.7 1.0
SG C:CYS92 2.5 43.7 1.0
SG C:CYS86 2.7 52.5 1.0
O C:CYS86 2.7 43.5 1.0
CB C:CYS92 2.8 51.9 1.0
CB C:CYS88 2.8 42.7 1.0
N C:CYS92 2.9 54.4 1.0
SG C:CYS95 3.1 28.6 1.0
C C:CYS86 3.3 44.0 1.0
CA C:CYS86 3.4 49.0 1.0
CA C:CYS92 3.4 55.4 1.0
C C:HIS91 3.5 54.6 1.0
N C:CYS88 3.7 36.4 1.0
CA C:CYS88 3.8 39.9 1.0
CA C:HIS91 3.8 55.5 1.0
O C:CYS88 3.9 45.1 1.0
N C:HIS91 4.1 57.6 1.0
CB C:CYS95 4.2 36.1 1.0
C C:CYS88 4.2 42.0 1.0
O C:HIS91 4.3 52.5 1.0
N C:CYS86 4.4 55.7 1.0
C C:CYS92 4.5 58.2 1.0
N C:PHE87 4.5 38.7 1.0
O C:CYS92 4.7 59.5 1.0
C C:PHE87 4.8 33.7 1.0

Zinc binding site 5 out of 9 in 1y1v

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Zinc binding site 5 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:63.8
occ:1.00
 SG I:CYS32 2.1 51.7 1.0
SG I:CYS7 2.2 81.9 1.0
SG I:CYS29 2.7 77.5 1.0
SG I:CYS10 2.9 78.3 1.0
CB I:CYS7 3.0 86.9 1.0
CB I:CYS29 3.1 77.8 1.0
CB I:CYS10 3.8 91.3 1.0
CB I:CYS32 3.8 68.9 1.0
O I:ARG8 3.9 92.9 1.0
C I:CYS10 4.0 93.0 1.0
O I:CYS10 4.2 93.8 1.0
CA I:CYS10 4.2 94.2 1.0
CB I:TYR34 4.3 47.8 1.0
N I:CYS10 4.3 98.6 1.0
CA I:CYS7 4.4 90.2 1.0
N I:ASN11 4.5 89.7 1.0
CA I:CYS29 4.5 77.0 1.0
OD2 I:ASP9 4.6 0.9 1.0
N I:CYS32 4.6 80.7 1.0
N I:ARG8 4.7 89.9 1.0
CA I:CYS32 4.8 73.5 1.0
N I:CYS7 4.9 92.8 1.0
N I:ASN12 4.9 88.9 1.0
C I:CYS7 4.9 90.7 1.0
CG I:TYR34 5.0 43.3 1.0

Zinc binding site 6 out of 9 in 1y1v

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Zinc binding site 6 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:97.5
occ:1.00
 SG I:CYS103 2.6 0.8 1.0
SG I:CYS106 2.6 0.9 1.0
CB I:CYS78 2.7 0.2 1.0
SG I:CYS78 2.9 0.2 1.0
SG I:CYS75 2.9 0.3 1.0
CB I:CYS103 3.0 0.1 1.0
CB I:CYS106 3.2 0.1 1.0
CB I:CYS75 3.3 0.7 1.0
CA I:CYS78 3.8 0.6 1.0
N I:CYS78 3.8 0.4 1.0
O I:SER105 4.4 0.5 1.0
C I:CYS78 4.5 0.5 1.0
CA I:CYS103 4.5 0.6 1.0
N I:HIS79 4.6 0.1 1.0
CA I:CYS106 4.6 0.5 1.0
CB I:HIS108 4.6 1.0 1.0
C I:SER105 4.7 0.5 1.0
N I:CYS106 4.8 0.2 1.0
CA I:CYS75 4.8 0.5 1.0

Zinc binding site 7 out of 9 in 1y1v

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Zinc binding site 7 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

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

b:16.4
occ:1.00
 SG J:CYS10 2.3 47.6 1.0
SG J:CYS7 2.4 49.5 1.0
SG J:CYS46 2.6 47.6 1.0
SG J:CYS45 2.7 28.7 1.0
N J:CYS46 3.0 31.1 1.0
CB J:CYS46 3.1 37.4 1.0
CB J:CYS7 3.1 40.7 1.0
OG J:SER9 3.2 52.6 1.0
CA J:CYS46 3.2 34.3 1.0
CB J:CYS10 3.5 47.1 1.0
N J:CYS10 3.5 46.1 1.0
CB J:CYS45 3.6 33.4 1.0
C J:CYS45 3.6 32.0 1.0
CA J:CYS10 3.9 47.2 1.0
O J:CYS7 4.1 36.6 1.0
CA J:CYS45 4.2 33.4 1.0
O J:CYS45 4.2 31.5 1.0
N J:GLY11 4.3 44.0 1.0
CB J:SER9 4.4 46.4 1.0
CA J:CYS7 4.5 38.8 1.0
C J:CYS10 4.5 45.2 1.0
NE J:ARG43 4.5 61.5 1.0
C J:CYS7 4.6 39.1 1.0
C J:SER9 4.6 44.8 1.0
C J:CYS46 4.7 34.7 1.0
CG J:ARG43 4.7 60.4 1.0
CA J:SER9 4.9 44.1 1.0

Zinc binding site 8 out of 9 in 1y1v

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Zinc binding site 8 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:68.3
occ:1.00
 SG L:CYS34 2.4 92.8 1.0
O L:CYS51 2.5 0.1 1.0
SG L:CYS51 2.5 0.4 1.0
SG L:CYS31 2.5 0.4 1.0
CB L:CYS51 2.7 0.7 1.0
CB L:CYS48 2.7 0.6 1.0
SG L:CYS48 2.9 0.2 1.0
C L:CYS51 3.3 0.1 1.0
CA L:CYS51 3.4 0.7 1.0
CB L:CYS31 3.7 0.4 1.0
N L:CYS51 3.9 0.6 1.0
CB L:CYS34 4.1 0.4 1.0
CA L:CYS48 4.1 0.2 1.0
CA L:CYS31 4.5 0.5 1.0
C L:CYS48 4.5 0.2 1.0
N L:GLY52 4.6 0.9 1.0
O L:CYS34 4.8 0.3 1.0
C L:ASP50 4.8 0.7 1.0
N L:LYS49 4.9 0.4 1.0
N L:CYS48 4.9 0.4 1.0
O L:CYS48 4.9 0.9 1.0

Zinc binding site 9 out of 9 in 1y1v

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Zinc binding site 9 out of 9 in the Refined Rna Polymerase II-Tfiis Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Refined Rna Polymerase II-Tfiis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn310

b:94.0
occ:1.00
 SG S:CYS274 2.2 93.9 1.0
CB S:CYS299 2.6 1.0 1.0
SG S:CYS271 2.9 0.4 1.0
CB S:CYS271 3.1 0.6 1.0
SG S:CYS302 3.2 85.5 1.0
N S:CYS302 3.3 97.6 1.0
SG S:CYS299 3.4 0.6 1.0
CA S:CYS299 3.5 98.3 1.0
CB S:CYS274 3.8 0.8 1.0
C S:CYS299 3.9 100.0 1.0
CB S:CYS302 3.9 94.0 1.0
CA S:CYS302 4.0 96.5 1.0
N S:ALA301 4.1 0.2 1.0
O S:CYS299 4.2 0.9 1.0
C S:ALA301 4.3 99.3 1.0
CB S:ALA301 4.3 0.6 1.0
O S:GLU276 4.3 0.7 1.0
O S:LYS278 4.3 83.5 1.0
CA S:ALA301 4.4 0.6 1.0
CG2 S:VAL279 4.6 79.4 1.0
CA S:CYS271 4.6 0.3 1.0
N S:GLY303 4.6 96.0 1.0
N S:GLU300 4.6 0.0 1.0
ND2 S:ASN304 4.7 0.5 1.0
C S:CYS302 4.8 97.2 1.0
CA S:CYS274 4.8 0.4 1.0
O S:CYS274 4.8 0.3 1.0
N S:CYS299 4.9 90.9 1.0
C S:CYS274 4.9 0.9 1.0
N S:GLU276 4.9 0.3 1.0

Reference:

H.Kettenberger, K.J.Armache, P.Cramer. Complete Rna Polymerase II Elongation Complex Structure and Its Interactions with Ntp and Tfiis. Mol.Cell V. 16 955 2004.
ISSN: ISSN 1097-2765
PubMed: 15610738
DOI: 10.1016/J.MOLCEL.2004.11.040
Page generated: Wed Dec 16 03:13:32 2020

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