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Zinc in PDB 3hoz: Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine

Enzymatic activity of Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine

All present enzymatic activity of Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine:
2.7.7.6;

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine, PDB code: 3hoz 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 (°) 221.427, 393.750, 281.818, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 25.3

Other elements in 3hoz:

The structure of Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine 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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine (pdb code 3hoz). 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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine, PDB code: 3hoz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3hoz

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Zinc binding site 1 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:89.0
occ:1.00
 SG A:CYS110 2.4 0.5 1.0
SG A:CYS167 2.6 0.7 1.0
SG A:CYS148 2.7 0.1 1.0
SG A:CYS107 2.7 0.6 1.0
CB A:CYS110 3.2 0.5 1.0
O A:CYS167 3.4 0.9 1.0
CB A:CYS148 3.4 0.8 1.0
CB A:CYS107 3.6 0.6 1.0
O A:MET108 3.8 0.3 1.0
N A:CYS110 3.8 0.5 1.0
O A:GLY166 3.9 0.9 1.0
CB A:CYS167 3.9 0.5 1.0
ND2 A:ASN169 4.0 0.6 1.0
CA A:CYS110 4.1 0.5 1.0
C A:CYS167 4.3 0.7 1.0
CB A:HIS109 4.6 0.6 1.0
CA A:CYS167 4.7 0.1 1.0
O A:CYS107 4.8 1.0 1.0
C A:GLY166 4.8 0.9 1.0
N A:GLY111 4.8 97.4 1.0
C A:CYS110 4.9 98.9 1.0
C A:HIS109 4.9 0.8 1.0
C A:CYS107 4.9 0.4 1.0
CA A:CYS107 4.9 0.2 1.0
CA A:CYS148 4.9 0.6 1.0

Zinc binding site 2 out of 8 in 3hoz

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Zinc binding site 2 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:31.4
occ:1.00
 NE2 A:HIS80 2.2 51.5 1.0
SG A:CYS77 2.3 50.0 1.0
SG A:CYS67 2.3 75.2 1.0
SG A:CYS70 2.3 77.0 1.0
CD2 A:HIS80 2.8 51.6 1.0
CE1 A:HIS80 3.5 51.1 1.0
CB A:CYS70 3.5 83.8 1.0
CB A:CYS77 3.5 48.0 1.0
CB A:CYS67 3.8 79.2 1.0
O A:CYS67 3.8 84.7 1.0
CG A:HIS80 4.1 52.4 1.0
OE1 A:GLN68 4.2 72.7 1.0
O A:PRO78 4.3 46.5 1.0
ND1 A:HIS80 4.4 50.7 1.0
CD A:GLN68 4.4 76.0 1.0
CA A:CYS77 4.5 48.2 1.0
NE2 A:GLN68 4.7 74.3 1.0
C A:CYS67 4.7 84.4 1.0
CA A:CYS67 4.8 82.7 1.0
CA A:CYS70 4.8 87.6 1.0
C A:CYS77 4.9 46.2 1.0
C A:CYS70 4.9 88.3 1.0
O A:GLN71 4.9 89.1 1.0

Zinc binding site 3 out of 8 in 3hoz

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Zinc binding site 3 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:30.8
occ:1.00
 SG B:CYS1166 2.3 36.3 1.0
SG B:CYS1182 2.4 45.9 1.0
CB B:CYS1185 2.5 62.1 1.0
SG B:CYS1185 2.5 64.0 1.0
SG B:CYS1163 2.6 47.2 1.0
CB B:CYS1163 3.0 47.5 1.0
CB B:CYS1166 3.8 43.3 1.0
CB B:CYS1182 3.9 52.3 1.0
O B:CYS1166 3.9 49.9 1.0
N B:CYS1166 3.9 47.1 1.0
CA B:CYS1185 4.0 62.7 1.0
O B:CYS1182 4.3 59.6 1.0
CA B:CYS1166 4.4 46.0 1.0
N B:CYS1185 4.5 61.9 1.0
CA B:CYS1163 4.5 46.4 1.0
C B:CYS1166 4.6 48.4 1.0
CB B:ILE1165 4.6 52.4 1.0
CB B:THR1170 4.8 35.9 1.0
OG1 B:THR1170 4.9 35.4 1.0
C B:CYS1185 4.9 64.2 1.0
CG2 B:THR1170 4.9 39.5 1.0

Zinc binding site 4 out of 8 in 3hoz

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Zinc binding site 4 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:40.8
occ:1.00
 SG C:CYS86 2.3 40.5 1.0
SG C:CYS88 2.3 35.1 1.0
SG C:CYS95 2.3 47.7 1.0
SG C:CYS92 2.4 53.7 1.0
CB C:CYS86 3.1 39.7 1.0
N C:CYS92 3.1 52.4 1.0
CB C:CYS95 3.1 52.5 1.0
CB C:CYS92 3.5 53.8 1.0
CB C:CYS88 3.7 40.4 1.0
CA C:CYS92 3.8 54.4 1.0
C C:HIS91 3.8 52.2 1.0
N C:CYS95 3.9 54.3 1.0
CA C:HIS91 3.9 52.2 1.0
CA C:CYS95 4.2 53.2 1.0
O C:CYS92 4.2 56.7 1.0
C C:CYS92 4.3 56.1 1.0
N C:CYS88 4.4 36.7 1.0
CA C:CYS86 4.5 39.0 1.0
C C:LYS94 4.5 55.4 1.0
CB C:LYS94 4.5 58.3 1.0
CA C:CYS88 4.7 41.3 1.0
O C:HIS91 4.7 52.5 1.0
C C:CYS86 4.8 37.8 1.0
N C:HIS91 4.8 54.0 1.0
N C:LYS94 4.9 58.0 1.0
CA C:LYS94 4.9 56.9 1.0
CB C:HIS91 4.9 49.5 1.0
O C:ASP90 5.0 56.6 1.0

Zinc binding site 5 out of 8 in 3hoz

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Zinc binding site 5 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:76.3
occ:1.00
 SG I:CYS10 2.2 85.7 1.0
SG I:CYS32 2.2 83.2 1.0
SG I:CYS7 2.4 72.4 1.0
SG I:CYS29 2.4 88.5 1.0
CB I:CYS32 3.0 81.3 1.0
CB I:CYS29 3.2 87.7 1.0
N I:CYS32 3.6 83.7 1.0
CB I:CYS7 3.8 80.3 1.0
CB I:CYS10 3.8 86.1 1.0
CA I:CYS32 3.8 81.5 1.0
O I:CYS10 3.9 84.7 1.0
N I:CYS10 4.0 87.7 1.0
O I:ARG8 4.2 86.2 1.0
CA I:CYS10 4.2 86.0 1.0
C I:CYS10 4.3 84.6 1.0
CB I:THR31 4.4 87.7 1.0
C I:CYS32 4.5 80.0 1.0
OG1 I:THR31 4.5 88.9 1.0
CB I:TYR34 4.5 64.3 1.0
C I:THR31 4.6 86.5 1.0
CA I:CYS29 4.7 87.3 1.0
CB I:ASP9 4.8 90.3 1.0
N I:THR31 4.9 86.5 1.0
CA I:THR31 4.9 87.0 1.0

Zinc binding site 6 out of 8 in 3hoz

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Zinc binding site 6 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:1.0
occ:1.00
 SG I:CYS75 2.5 1.0 1.0
SG I:CYS106 2.6 0.8 1.0
CB I:CYS75 2.8 0.2 1.0
SG I:CYS78 2.9 0.9 1.0
SG I:CYS103 3.1 0.1 1.0
CB I:HIS108 3.4 0.8 1.0
CB I:CYS103 3.4 0.5 1.0
N I:CYS78 3.6 0.3 1.0
CD2 I:HIS108 4.0 0.4 1.0
CG I:HIS108 4.0 0.6 1.0
CB I:CYS78 4.1 0.7 1.0
CB I:CYS106 4.2 0.8 1.0
CB I:LYS77 4.3 0.7 1.0
N I:LYS77 4.3 0.1 1.0
CA I:CYS75 4.3 0.8 1.0
CA I:CYS78 4.3 0.3 1.0
C I:LYS77 4.5 0.7 1.0
CA I:LYS77 4.5 0.2 1.0
CA I:HIS108 4.6 0.7 1.0
N I:HIS108 4.7 0.1 1.0
CD I:PRO76 4.7 0.6 1.0
C I:CYS75 4.7 0.8 1.0
N I:PRO76 4.8 0.7 1.0
C I:CYS78 4.8 1.0 1.0
O I:HIS108 4.9 0.4 1.0
N I:HIS79 4.9 0.8 1.0
CA I:CYS103 4.9 0.8 1.0
O I:SER105 5.0 0.6 1.0

Zinc binding site 7 out of 8 in 3hoz

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Zinc binding site 7 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:53.7
occ:1.00
 SG J:CYS46 2.4 70.5 1.0
SG J:CYS10 2.4 62.9 1.0
SG J:CYS45 2.4 54.3 1.0
SG J:CYS7 2.4 58.3 1.0
CB J:CYS7 3.1 57.0 1.0
N J:CYS46 3.1 60.5 1.0
CB J:CYS46 3.3 63.7 1.0
CB J:CYS45 3.4 56.6 1.0
CA J:CYS46 3.4 62.6 1.0
C J:CYS45 3.5 58.9 1.0
CB J:CYS10 3.5 62.8 1.0
N J:CYS10 3.6 60.5 1.0
O J:CYS45 4.0 59.3 1.0
CA J:CYS10 4.0 61.5 1.0
CA J:CYS45 4.0 57.3 1.0
CA J:CYS7 4.5 55.9 1.0
CB J:SER9 4.6 57.6 1.0
C J:CYS10 4.6 61.4 1.0
C J:SER9 4.7 58.7 1.0
NE J:ARG43 4.7 60.5 1.0
CB J:LYS12 4.8 67.4 1.0
N J:GLY11 4.8 62.4 1.0
N J:CYS45 4.8 57.3 1.0
C J:CYS46 4.9 62.6 1.0
O J:CYS7 5.0 58.2 1.0
NH2 J:ARG43 5.0 59.9 1.0
C J:CYS7 5.0 56.5 1.0
N J:LYS12 5.0 66.2 1.0

Zinc binding site 8 out of 8 in 3hoz

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Zinc binding site 8 out of 8 in the Complete Rna Polymerase II Elongation Complex IV with A T-U Mismatch and A Frayed Rna 3'-Guanine


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 IV with A T-U Mismatch and A Frayed Rna 3'-Guanine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.9
occ:1.00
 SG L:CYS34 2.3 99.8 1.0
SG L:CYS48 2.5 1.0 1.0
CB L:CYS51 2.6 0.6 1.0
SG L:CYS31 2.8 99.1 1.0
CB L:CYS48 2.9 0.4 1.0
SG L:CYS51 3.2 0.7 1.0
N L:CYS51 3.3 0.6 1.0
O L:CYS51 3.4 0.5 1.0
CA L:CYS51 3.4 0.3 1.0
CB L:CYS31 3.4 99.3 1.0
C L:CYS51 3.8 0.3 1.0
CB L:CYS34 3.9 0.2 1.0
CA L:CYS48 4.3 0.9 1.0
C L:ASP50 4.5 0.4 1.0
OG L:SER36 4.6 0.3 1.0
O L:CYS34 4.6 0.9 1.0
C L:CYS48 4.7 0.1 1.0
CB L:ASP50 4.7 0.8 1.0
N L:CYS34 4.7 0.7 1.0
CA L:CYS31 4.7 98.8 1.0
CA L:CYS34 4.7 0.8 1.0
C L:CYS34 4.9 0.8 1.0
N L:LYS49 4.9 0.1 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 06:32:26 2024

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