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Zinc in PDB 3qt1: Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit

Enzymatic activity of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit

All present enzymatic activity of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit, PDB code: 3qt1 was solved by W.Ruan, E.Lehmann, M.Thomm, D.Kostrewa, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 4.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.380, 393.380, 281.430, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28.1

Other elements in 3qt1:

The structure of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit (pdb code 3qt1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit, PDB code: 3qt1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3qt1

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Zinc binding site 1 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:1.0
occ:1.00
 CB A:CYS110 2.3 0.9 1.0
SG A:CYS110 2.4 1.0 1.0
SG A:CYS107 2.4 0.3 1.0
SG A:CYS167 2.4 0.7 1.0
SG A:CYS148 2.4 0.6 1.0
CB A:CYS107 3.7 0.3 1.0
CA A:CYS110 3.8 0.1 1.0
CB A:CYS148 3.8 0.0 1.0
CB A:CYS167 4.0 0.0 1.0
O A:CYS167 4.0 0.3 1.0
N A:CYS110 4.4 0.7 1.0
C A:CYS110 4.4 0.5 1.0
ND1 A:HIS109 4.4 0.9 1.0
C A:CYS167 4.4 0.6 1.0
CA A:CYS167 4.6 0.4 1.0
N A:GLY111 4.6 0.8 1.0
CE1 A:HIS109 4.7 0.7 1.0
N A:CYS167 4.9 0.3 1.0
O A:MET108 4.9 0.5 1.0

Zinc binding site 2 out of 7 in 3qt1

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Zinc binding site 2 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:97.5
occ:1.00
 NE2 A:HIS80 2.1 0.8 1.0
SG A:CYS77 2.4 0.1 1.0
SG A:CYS67 2.4 0.6 1.0
SG A:CYS70 2.4 91.0 1.0
CD2 A:HIS80 2.8 0.2 1.0
CE1 A:HIS80 3.2 0.1 1.0
OE1 A:GLN68 3.6 92.8 1.0
CB A:CYS77 3.8 0.1 1.0
O A:PRO78 3.9 0.8 1.0
CB A:CYS70 4.0 98.4 1.0
CB A:CYS67 4.0 0.2 1.0
CG A:HIS80 4.0 0.5 1.0
ND1 A:HIS80 4.2 0.7 1.0
CD A:PRO78 4.4 99.7 1.0
CA A:CYS77 4.5 0.1 1.0
CD A:GLN68 4.8 0.8 1.0
O A:GLN71 4.9 0.2 1.0
N A:PRO78 4.9 99.9 1.0

Zinc binding site 3 out of 7 in 3qt1

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Zinc binding site 3 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:0.3
occ:1.00
 SG B:CYS1185 2.3 83.4 1.0
SG B:CYS1166 2.4 74.7 1.0
SG B:CYS1163 2.4 94.9 1.0
SG B:CYS1182 2.4 0.5 1.0
CB B:CYS1185 2.5 81.0 1.0
CB B:CYS1163 3.0 91.4 1.0
CB B:CYS1166 3.8 82.6 1.0
N B:CYS1166 4.0 84.1 1.0
CA B:CYS1185 4.0 86.2 1.0
CB B:CYS1182 4.1 0.6 1.0
O B:CYS1166 4.3 85.2 1.0
CB B:ILE1165 4.4 85.3 1.0
OG1 B:THR1170 4.4 0.6 1.0
CA B:CYS1166 4.4 84.2 1.0
O B:CYS1182 4.5 0.0 1.0
CA B:CYS1163 4.6 88.2 1.0
C B:CYS1185 4.7 87.6 1.0
O B:CYS1185 4.8 87.5 1.0
C B:ILE1165 4.8 84.3 1.0
CB B:THR1170 4.9 0.1 1.0
C B:CYS1166 4.9 84.1 1.0
N B:CYS1185 4.9 87.4 1.0
CG1 B:ILE1165 5.0 82.8 1.0

Zinc binding site 4 out of 7 in 3qt1

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Zinc binding site 4 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:0.3
occ:1.00
 SG C:CYS88 2.3 61.6 1.0
SG C:CYS95 2.4 81.5 1.0
SG C:CYS92 2.4 69.9 1.0
SG C:CYS86 2.4 0.1 1.0
CB C:CYS86 2.6 0.1 1.0
CB C:CYS95 3.3 84.4 1.0
CB C:CYS92 3.6 71.3 1.0
CB C:CYS88 3.7 61.5 1.0
N C:CYS92 3.9 68.8 1.0
CA C:CYS86 4.0 0.6 1.0
N C:CYS88 4.2 58.2 1.0
C C:CYS86 4.2 0.7 1.0
N C:CYS95 4.3 92.0 1.0
C C:HIS91 4.3 0.9 1.0
CA C:CYS92 4.3 74.2 1.0
CA C:HIS91 4.4 0.9 1.0
N C:PHE87 4.4 94.6 1.0
CA C:CYS95 4.4 88.5 1.0
CA C:CYS88 4.6 61.4 1.0
CB C:LYS94 4.7 0.7 1.0
O C:CYS86 4.8 0.7 1.0
N C:CYS86 4.8 0.3 1.0
C C:LYS94 4.9 0.5 1.0
C C:CYS92 5.0 79.5 1.0

Zinc binding site 5 out of 7 in 3qt1

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Zinc binding site 5 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:0.8
occ:1.00
 SG I:CYS32 2.3 0.7 1.0
SG I:CYS10 2.3 0.4 1.0
SG I:CYS7 2.4 0.8 1.0
SG I:CYS29 2.4 0.9 1.0
CB I:CYS29 3.5 0.0 1.0
CB I:CYS32 3.9 0.8 1.0
CB I:CYS7 3.9 0.6 1.0
CB I:CYS10 3.9 0.1 1.0
N I:CYS32 3.9 0.0 1.0
N I:CYS10 4.0 0.3 1.0
O I:ARG8 4.2 0.6 1.0
CA I:CYS10 4.3 0.5 1.0
CB I:THR31 4.4 0.2 1.0
CA I:CYS32 4.4 0.0 1.0
CB I:ASP9 4.6 0.5 1.0
C I:CYS10 4.6 0.8 1.0
N I:ASN12 4.8 0.7 1.0
C I:THR31 4.8 0.3 1.0
CB I:TYR34 4.8 0.5 1.0
CB I:ASN12 4.9 0.5 1.0
N I:ASN11 4.9 0.9 1.0
CA I:CYS29 4.9 0.4 1.0

Zinc binding site 6 out of 7 in 3qt1

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Zinc binding site 6 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:0.1
occ:1.00
 SG J:CYS10 2.3 0.6 1.0
SG J:CYS7 2.3 0.1 1.0
SG J:CYS45 2.4 0.7 1.0
SG J:CYS46 2.4 0.5 1.0
N J:CYS46 3.3 0.5 1.0
CA J:CYS46 3.4 0.5 1.0
CB J:CYS46 3.5 0.7 1.0
CB J:CYS7 3.5 0.0 1.0
C J:CYS45 3.5 0.7 1.0
O J:CYS45 3.8 1.0 1.0
CB J:CYS45 3.8 1.0 1.0
CB J:CYS10 3.8 0.7 1.0
N J:CYS10 3.8 0.7 1.0
NE J:ARG43 4.2 0.5 1.0
CA J:CYS45 4.3 0.6 1.0
CA J:CYS10 4.3 0.6 1.0
CG J:ARG43 4.5 0.1 1.0
CB J:SER9 4.6 0.8 1.0
N J:GLY11 4.7 0.2 1.0
NH2 J:ARG43 4.7 0.1 1.0
CA J:CYS7 4.8 0.6 1.0
O J:CYS7 4.9 0.8 1.0
C J:SER9 4.9 0.2 1.0
CZ J:ARG43 4.9 1.0 1.0
C J:CYS10 4.9 0.9 1.0
C J:CYS46 4.9 0.1 1.0
C J:CYS7 5.0 0.9 1.0
CD J:ARG43 5.0 0.6 1.0

Zinc binding site 7 out of 7 in 3qt1

Go back to Zinc Binding Sites List in 3qt1
Zinc binding site 7 out of 7 in the Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Variant Containing A Chimeric RPB9-C11 Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:0.3
occ:1.00
 SG L:CYS51 2.3 0.2 1.0
SG L:CYS48 2.4 0.6 1.0
SG L:CYS34 2.4 0.1 1.0
SG L:CYS31 2.4 0.5 1.0
CB L:CYS51 2.5 0.3 1.0
N L:CYS51 3.3 0.3 1.0
CB L:CYS48 3.4 1.0 1.0
CB L:CYS31 3.4 0.5 1.0
CA L:CYS51 3.5 0.8 1.0
CB L:CYS34 4.2 0.1 1.0
CB L:ASP50 4.4 0.1 1.0
C L:ASP50 4.5 0.5 1.0
C L:CYS51 4.5 0.7 1.0
O L:CYS51 4.6 0.9 1.0
CA L:CYS31 4.7 0.9 1.0
CA L:CYS48 4.7 1.0 1.0
CA L:ASP50 4.8 1.0 1.0
N L:ASP50 4.9 0.0 1.0

Reference:

W.Ruan, E.Lehmann, M.Thomm, D.Kostrewa, P.Cramer. Evolution of Two Modes of Intrinsic Rna Polymerase Transcript Cleavage. J.Biol.Chem. V. 286 18701 2011.
ISSN: ISSN 0021-9258
PubMed: 21454497
DOI: 10.1074/JBC.M111.222273
Page generated: Sat Oct 26 12:17:53 2024

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