Atomistry » Zinc » PDB 1xuj-1y7w » 1y1v
Atomistry »
  Zinc »
    PDB 1xuj-1y7w »
      1y1v »

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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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

Go back to Zinc Binding Sites List in 1y1v
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 Oct 16 20:42:28 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy