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Zinc in PDB 3hox: Complete Rna Polymerase II Elongation Complex V

Enzymatic activity of Complete Rna Polymerase II Elongation Complex V

All present enzymatic activity of Complete Rna Polymerase II Elongation Complex V:
2.7.7.6;

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex V, PDB code: 3hox was solved by J.F.Sydow, F.Brueckner, A.C.M.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.617, 393.716, 282.576, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25

Other elements in 3hox:

The structure of Complete Rna Polymerase II Elongation Complex V also contains other interesting chemical elements:

Bromine (Br) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 3hox

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Zinc binding site 1 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:87.4
occ:1.00
 SG A:CYS110 2.4 96.6 1.0
SG A:CYS167 2.6 0.5 1.0
SG A:CYS148 2.6 92.7 1.0
SG A:CYS107 2.7 0.2 1.0
CB A:CYS110 3.0 94.3 1.0
CB A:CYS148 3.3 96.7 1.0
O A:CYS167 3.3 0.8 1.0
CB A:CYS107 3.5 97.1 1.0
N A:CYS110 3.6 94.5 1.0
O A:MET108 3.6 96.5 1.0
CA A:CYS110 3.9 93.5 1.0
CB A:CYS167 3.9 0.9 1.0
ND2 A:ASN169 4.2 94.8 1.0
C A:CYS167 4.3 0.8 1.0
O A:GLY166 4.3 0.4 1.0
O A:CYS107 4.5 94.6 1.0
CA A:CYS167 4.6 0.8 1.0
CB A:HIS109 4.6 99.4 1.0
C A:CYS107 4.7 95.0 1.0
N A:GLY111 4.7 90.1 1.0
C A:HIS109 4.7 95.8 1.0
C A:CYS110 4.7 91.7 1.0
CA A:CYS107 4.7 95.1 1.0
ND1 A:HIS109 4.8 0.2 1.0
CA A:CYS148 4.8 98.9 1.0
C A:MET108 4.8 95.9 1.0
C A:GLY166 4.9 1.0 1.0
N A:CYS167 5.0 0.6 1.0

Zinc binding site 2 out of 8 in 3hox

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Zinc binding site 2 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:42.8
occ:1.00
 NE2 A:HIS80 2.3 47.5 1.0
CD2 A:HIS80 2.4 46.5 1.0
SG A:CYS70 2.5 61.4 1.0
SG A:CYS77 2.5 56.0 1.0
SG A:CYS67 2.7 76.0 1.0
CB A:CYS70 3.4 73.2 1.0
CB A:CYS77 3.5 53.2 1.0
CE1 A:HIS80 3.6 47.7 1.0
O A:CYS67 3.6 81.2 1.0
CG A:HIS80 3.7 47.3 1.0
CB A:CYS67 3.8 77.6 1.0
OE1 A:GLN68 3.9 71.8 1.0
CD A:GLN68 4.2 73.4 1.0
ND1 A:HIS80 4.3 48.3 1.0
O A:PRO78 4.4 50.1 1.0
CA A:CYS77 4.5 52.4 1.0
C A:CYS67 4.5 81.1 1.0
NE2 A:GLN68 4.6 71.5 1.0
CA A:CYS67 4.7 80.3 1.0
CG A:GLN68 4.8 76.4 1.0
CA A:CYS70 4.8 79.5 1.0
O A:GLN71 4.9 85.1 1.0
C A:CYS77 4.9 49.9 1.0
CB A:HIS80 4.9 51.2 1.0

Zinc binding site 3 out of 8 in 3hox

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Zinc binding site 3 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:42.3
occ:1.00
 SG B:CYS1166 2.2 36.2 1.0
SG B:CYS1182 2.3 52.4 1.0
SG B:CYS1163 2.4 45.0 1.0
SG B:CYS1185 2.5 60.1 1.0
CB B:CYS1185 2.9 60.0 1.0
CB B:CYS1163 3.1 49.7 1.0
CB B:CYS1182 3.7 58.2 1.0
CB B:CYS1166 3.9 41.8 1.0
N B:CYS1166 4.0 44.2 1.0
O B:CYS1182 4.2 63.3 1.0
O B:CYS1166 4.2 46.0 1.0
CA B:CYS1185 4.3 60.3 1.0
CB B:ILE1165 4.3 51.9 1.0
CA B:CYS1166 4.5 43.1 1.0
N B:CYS1185 4.6 59.8 1.0
CA B:CYS1163 4.6 49.3 1.0
CG2 B:ILE1165 4.7 53.2 1.0
C B:CYS1166 4.9 44.4 1.0
CB B:THR1170 4.9 41.8 1.0
CA B:CYS1182 5.0 58.8 1.0

Zinc binding site 4 out of 8 in 3hox

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Zinc binding site 4 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:40.5
occ:1.00
 SG C:CYS88 2.4 47.2 1.0
SG C:CYS86 2.5 42.6 1.0
SG C:CYS92 2.6 47.7 1.0
SG C:CYS95 2.6 38.4 1.0
CB C:CYS86 3.0 38.1 1.0
CB C:CYS88 3.3 46.1 1.0
CB C:CYS95 3.3 47.0 1.0
N C:CYS92 3.3 49.3 1.0
CB C:CYS92 3.5 49.7 1.0
N C:CYS88 3.8 38.6 1.0
C C:HIS91 3.9 49.4 1.0
CA C:CYS92 3.9 51.2 1.0
CA C:HIS91 4.0 49.1 1.0
CA C:CYS88 4.1 44.6 1.0
N C:CYS95 4.2 52.2 1.0
CA C:CYS86 4.3 37.8 1.0
CA C:CYS95 4.4 49.9 1.0
O C:CYS92 4.5 55.4 1.0
C C:CYS86 4.5 36.5 1.0
C C:CYS92 4.5 54.1 1.0
N C:PHE87 4.6 35.7 1.0
O C:CYS88 4.6 48.1 1.0
O C:HIS91 4.7 50.5 1.0
CB C:LYS94 4.7 57.5 1.0
C C:LYS94 4.8 54.2 1.0
C C:CYS88 4.8 46.8 1.0
N C:HIS91 4.9 50.4 1.0
O C:ASP90 5.0 53.6 1.0

Zinc binding site 5 out of 8 in 3hox

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Zinc binding site 5 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:79.7
occ:1.00
 SG I:CYS32 2.2 75.8 1.0
SG I:CYS10 2.2 77.0 1.0
SG I:CYS7 2.3 71.2 1.0
SG I:CYS29 2.4 73.5 1.0
CB I:CYS29 3.0 75.8 1.0
CB I:CYS32 3.2 72.7 1.0
CB I:CYS7 3.6 78.4 1.0
CB I:CYS10 3.7 79.2 1.0
O I:CYS10 3.8 77.9 1.0
N I:CYS10 3.8 81.4 1.0
N I:CYS32 3.9 74.3 1.0
CA I:CYS10 4.0 79.1 1.0
O I:ARG8 4.0 83.5 1.0
C I:CYS10 4.1 78.0 1.0
CA I:CYS32 4.1 72.7 1.0
CB I:TYR34 4.2 57.9 1.0
CA I:CYS29 4.5 75.6 1.0
OG1 I:THR31 4.6 79.7 1.0
C I:CYS32 4.7 71.8 1.0
CB I:THR31 4.7 78.0 1.0
C I:THR31 4.8 76.7 1.0
CA I:CYS7 4.9 79.9 1.0
N I:TYR34 4.9 63.0 1.0
O I:CYS7 5.0 81.6 1.0
CB I:ASP9 5.0 84.4 1.0
C I:CYS7 5.0 81.1 1.0

Zinc binding site 6 out of 8 in 3hox

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Zinc binding site 6 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.0
occ:1.00
 SG I:CYS75 2.5 0.9 1.0
SG I:CYS106 2.6 95.5 1.0
CB I:CYS75 2.8 0.5 1.0
SG I:CYS78 3.1 0.2 1.0
SG I:CYS103 3.1 0.8 1.0
CB I:HIS108 3.3 96.6 1.0
CB I:CYS103 3.5 0.9 1.0
N I:CYS78 3.8 0.3 1.0
CB I:CYS106 4.0 97.7 1.0
N I:LYS77 4.0 0.5 1.0
CG I:HIS108 4.1 96.0 1.0
CD I:PRO76 4.1 0.5 1.0
CB I:LYS77 4.1 0.7 1.0
CA I:CYS75 4.2 0.5 1.0
CD2 I:HIS108 4.2 95.5 1.0
N I:PRO76 4.4 0.8 1.0
CA I:HIS108 4.4 97.8 1.0
CB I:CYS78 4.4 0.9 1.0
CA I:LYS77 4.4 0.4 1.0
N I:HIS108 4.4 97.8 1.0
C I:CYS75 4.5 0.1 1.0
C I:LYS77 4.5 0.1 1.0
CA I:CYS78 4.6 0.8 1.0
O I:HIS108 4.6 97.8 1.0
CA I:CYS103 4.9 0.6 1.0
CG I:LYS77 4.9 99.1 1.0
C I:HIS108 5.0 97.9 1.0

Zinc binding site 7 out of 8 in 3hox

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Zinc binding site 7 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:47.5
occ:1.00
 SG J:CYS46 2.2 57.7 1.0
SG J:CYS10 2.3 58.9 1.0
SG J:CYS7 2.4 58.6 1.0
SG J:CYS45 2.4 50.4 1.0
CB J:CYS7 3.0 56.5 1.0
N J:CYS46 3.3 56.9 1.0
CB J:CYS45 3.4 53.8 1.0
N J:CYS10 3.4 57.8 1.0
CB J:CYS10 3.4 57.8 1.0
CB J:CYS46 3.5 56.0 1.0
C J:CYS45 3.5 55.8 1.0
CA J:CYS46 3.6 57.9 1.0
CA J:CYS10 3.9 58.7 1.0
O J:CYS45 4.0 55.4 1.0
CA J:CYS45 4.1 54.2 1.0
CB J:SER9 4.4 54.6 1.0
CA J:CYS7 4.5 54.0 1.0
C J:SER9 4.5 55.1 1.0
N J:GLY11 4.5 59.2 1.0
C J:CYS10 4.5 58.1 1.0
NE J:ARG43 4.6 53.8 1.0
CA J:SER9 4.8 53.2 1.0
C J:CYS7 4.9 53.8 1.0
N J:SER9 4.9 50.7 1.0
N J:LYS12 4.9 62.5 1.0
O J:CYS7 4.9 55.0 1.0
N J:CYS45 4.9 55.5 1.0
CB J:LYS12 5.0 63.7 1.0

Zinc binding site 8 out of 8 in 3hox

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Zinc binding site 8 out of 8 in the Complete Rna Polymerase II Elongation Complex V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complete Rna Polymerase II Elongation Complex V within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.1
occ:1.00
 SG L:CYS48 2.3 97.6 1.0
SG L:CYS34 2.3 81.4 1.0
CB L:CYS48 2.6 99.7 1.0
CB L:CYS51 2.8 0.1 1.0
SG L:CYS31 2.8 96.0 1.0
O L:CYS51 3.1 0.6 1.0
N L:CYS51 3.2 0.1 1.0
SG L:CYS51 3.4 0.7 1.0
CA L:CYS51 3.4 0.9 1.0
CB L:CYS31 3.4 93.0 1.0
C L:CYS51 3.7 0.8 1.0
CB L:CYS34 3.9 88.3 1.0
CA L:CYS48 4.1 0.5 1.0
O L:CYS34 4.3 92.8 1.0
CB L:ASP50 4.4 0.5 1.0
C L:ASP50 4.4 0.1 1.0
C L:CYS48 4.6 0.8 1.0
OG L:SER36 4.6 96.0 1.0
OE1 L:GLU33 4.7 98.2 1.0
CA L:CYS34 4.8 91.0 1.0
N L:CYS34 4.8 92.1 1.0
CA L:CYS31 4.8 91.9 1.0
N L:CYS48 4.8 0.3 1.0
CA L:ASP50 4.9 0.8 1.0
C L:CYS34 4.9 92.7 1.0
N L:ASP50 4.9 0.3 1.0
N L:GLY52 5.0 0.1 1.0
N L:LYS49 5.0 0.8 1.0

Reference:

J.F.Sydow, F.Brueckner, A.C.M.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, P.Cramer. Structural Basis of Transcription: Mismatch-Specific Fidelity Mechanisms and Paused Rna Polymerase II with Frayed Rna. Mol.Cell V. 34 710 2009.
ISSN: ISSN 1097-2765
PubMed: 19560423
DOI: 10.1016/J.MOLCEL.2009.06.002
Page generated: Sat Oct 26 06:32:25 2024

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