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Zinc in PDB 3how: Complete Rna Polymerase II Elongation Complex III with A T-U Mismatch and A Frayed Rna 3'-Uridine

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

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

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex III with A T-U Mismatch and A Frayed Rna 3'-Uridine, PDB code: 3how 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 / 3.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.645, 395.962, 283.476, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25.4

Other elements in 3how:

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

Zinc binding site 1 out of 8 in 3how

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


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

b:70.2
occ:1.00
 SG A:CYS110 2.3 96.2 1.0
SG A:CYS107 2.6 0.4 1.0
SG A:CYS167 2.6 0.5 1.0
SG A:CYS148 2.7 95.1 1.0
CB A:CYS110 3.3 93.9 1.0
CB A:CYS148 3.5 98.4 1.0
CB A:CYS107 3.5 0.3 1.0
O A:CYS167 3.6 0.8 1.0
N A:CYS110 3.8 94.7 1.0
O A:MET108 3.8 97.3 1.0
CB A:CYS167 4.0 0.1 1.0
CA A:CYS110 4.1 94.0 1.0
O A:GLY166 4.1 0.3 1.0
CB A:HIS109 4.5 99.9 1.0
C A:CYS167 4.5 0.5 1.0
N A:GLY111 4.6 93.1 1.0
O A:CYS107 4.7 98.4 1.0
ND2 A:ASN169 4.7 97.8 1.0
CA A:CYS167 4.8 0.6 1.0
C A:CYS107 4.8 98.7 1.0
CA A:CYS107 4.8 99.5 1.0
C A:CYS110 4.9 93.4 1.0
C A:HIS109 4.9 96.7 1.0
C A:GLY166 4.9 0.3 1.0
C A:MET108 4.9 97.5 1.0
CA A:CYS148 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 3how

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


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

b:35.7
occ:1.00
 SG A:CYS77 2.2 41.9 1.0
SG A:CYS70 2.3 63.6 1.0
NE2 A:HIS80 2.4 48.5 1.0
SG A:CYS67 2.4 67.7 1.0
CD2 A:HIS80 2.6 48.4 1.0
CB A:CYS70 3.1 71.7 1.0
CE1 A:HIS80 3.6 48.3 1.0
O A:CYS67 3.7 77.3 1.0
CB A:CYS67 3.7 72.2 1.0
CB A:CYS77 3.8 38.3 1.0
CG A:HIS80 3.9 48.5 1.0
OE1 A:GLN68 4.1 79.6 1.0
ND1 A:HIS80 4.4 46.2 1.0
CA A:CYS70 4.5 75.7 1.0
CD A:GLN68 4.6 80.5 1.0
C A:CYS67 4.6 76.9 1.0
O A:PRO78 4.6 40.5 1.0
CA A:CYS67 4.7 75.2 1.0
CA A:CYS77 4.7 39.6 1.0
C A:CYS70 4.9 77.1 1.0
O A:GLN71 5.0 81.6 1.0

Zinc binding site 3 out of 8 in 3how

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


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

b:32.6
occ:1.00
 SG B:CYS1166 2.2 32.2 1.0
SG B:CYS1182 2.3 49.1 1.0
SG B:CYS1163 2.5 44.9 1.0
SG B:CYS1185 2.5 55.3 1.0
CB B:CYS1185 2.6 52.6 1.0
CB B:CYS1163 3.0 44.6 1.0
CB B:CYS1166 3.7 41.2 1.0
CB B:CYS1182 3.7 54.4 1.0
N B:CYS1166 4.0 44.2 1.0
O B:CYS1166 4.0 49.1 1.0
CA B:CYS1185 4.1 54.3 1.0
O B:CYS1182 4.2 59.3 1.0
CA B:CYS1166 4.3 43.6 1.0
CA B:CYS1163 4.5 43.5 1.0
N B:CYS1185 4.5 55.4 1.0
C B:CYS1166 4.6 46.4 1.0
OG1 B:THR1170 4.7 46.0 1.0
CB B:THR1170 4.9 42.6 1.0
C B:CYS1185 4.9 54.6 1.0
CA B:CYS1182 5.0 55.4 1.0

Zinc binding site 4 out of 8 in 3how

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


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

b:27.2
occ:1.00
 SG C:CYS86 2.3 34.7 1.0
SG C:CYS88 2.3 33.4 1.0
SG C:CYS95 2.3 48.8 1.0
SG C:CYS92 2.4 46.0 1.0
CB C:CYS86 2.9 31.8 1.0
CB C:CYS95 3.0 50.1 1.0
N C:CYS92 3.2 48.0 1.0
CB C:CYS92 3.6 47.7 1.0
CB C:CYS88 3.7 36.4 1.0
CA C:CYS92 3.8 49.8 1.0
N C:CYS95 3.8 52.1 1.0
C C:HIS91 3.8 47.5 1.0
O C:CYS92 4.0 53.4 1.0
CA C:HIS91 4.0 47.6 1.0
CA C:CYS95 4.0 51.2 1.0
C C:CYS92 4.2 52.1 1.0
CA C:CYS86 4.3 32.9 1.0
N C:CYS88 4.4 33.5 1.0
CB C:LYS94 4.6 54.3 1.0
C C:LYS94 4.6 52.9 1.0
CA C:CYS88 4.7 37.0 1.0
C C:CYS86 4.7 33.0 1.0
O C:HIS91 4.7 47.8 1.0
N C:HIS91 4.8 49.5 1.0
N C:PHE87 4.9 33.2 1.0
N C:LYS94 4.9 54.2 1.0
CA C:LYS94 5.0 53.5 1.0

Zinc binding site 5 out of 8 in 3how

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


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

b:74.5
occ:1.00
 SG I:CYS32 2.2 70.0 1.0
SG I:CYS10 2.2 76.1 1.0
SG I:CYS7 2.4 75.0 1.0
SG I:CYS29 2.4 73.7 1.0
CB I:CYS29 3.1 75.6 1.0
CB I:CYS32 3.4 71.5 1.0
CB I:CYS10 3.8 77.4 1.0
CB I:CYS7 3.8 80.1 1.0
N I:CYS10 3.8 79.1 1.0
O I:ARG8 3.9 82.8 1.0
N I:CYS32 4.1 76.4 1.0
CB I:TYR34 4.1 60.4 1.0
CA I:CYS10 4.2 77.5 1.0
CA I:CYS32 4.3 73.8 1.0
CB I:ASP9 4.5 79.8 1.0
C I:CYS10 4.5 76.6 1.0
CA I:CYS29 4.6 76.7 1.0
C I:CYS32 4.7 72.6 1.0
O I:CYS10 4.8 76.6 1.0
CB I:THR31 4.8 80.0 1.0
N I:TYR34 4.8 64.3 1.0
C I:ASP9 5.0 80.9 1.0

Zinc binding site 6 out of 8 in 3how

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


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

b:0.2
occ:1.00
 SG I:CYS75 2.5 0.0 1.0
SG I:CYS106 2.6 92.9 1.0
SG I:CYS78 2.8 94.9 1.0
SG I:CYS103 3.1 0.8 1.0
CB I:CYS75 3.1 0.8 1.0
CB I:HIS108 3.5 0.1 1.0
CB I:CYS103 3.6 0.1 1.0
N I:CYS78 3.6 0.4 1.0
CB I:LYS77 3.9 0.3 1.0
CB I:CYS78 4.1 0.4 1.0
CB I:CYS106 4.2 99.0 1.0
CG I:HIS108 4.2 0.6 1.0
N I:LYS77 4.2 0.9 1.0
CA I:LYS77 4.3 0.2 1.0
C I:LYS77 4.3 0.3 1.0
CA I:CYS78 4.3 0.9 1.0
CD2 I:HIS108 4.3 0.6 1.0
O I:SER105 4.4 0.3 1.0
CA I:CYS75 4.5 0.1 1.0
N I:HIS108 4.6 0.0 1.0
CA I:HIS108 4.6 0.2 1.0
CG I:LYS77 4.8 98.9 1.0
N I:HIS79 4.9 0.1 1.0
C I:CYS75 4.9 0.8 1.0
CD I:PRO76 4.9 0.2 1.0
O I:HIS108 4.9 0.2 1.0
N I:PRO76 5.0 1.0 1.0

Zinc binding site 7 out of 8 in 3how

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


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

b:39.5
occ:1.00
 SG J:CYS10 2.3 56.5 1.0
SG J:CYS7 2.3 56.7 1.0
SG J:CYS45 2.3 42.5 1.0
SG J:CYS46 2.4 61.4 1.0
N J:CYS46 3.0 49.4 1.0
CB J:CYS7 3.1 51.1 1.0
CA J:CYS46 3.2 51.5 1.0
C J:CYS45 3.2 47.6 1.0
CB J:CYS46 3.3 52.6 1.0
CB J:CYS45 3.4 44.6 1.0
CB J:CYS10 3.5 57.6 1.0
O J:CYS45 3.6 48.3 1.0
N J:CYS10 3.6 55.2 1.0
CA J:CYS45 3.9 45.9 1.0
CA J:CYS10 4.0 56.6 1.0
CB J:SER9 4.5 52.0 1.0
CA J:CYS7 4.6 48.8 1.0
C J:CYS10 4.6 56.5 1.0
C J:CYS46 4.7 51.8 1.0
NE J:ARG43 4.7 52.8 1.0
NH2 J:ARG43 4.8 53.3 1.0
C J:SER9 4.8 52.9 1.0
N J:GLY11 4.8 57.6 1.0
N J:CYS45 4.8 46.0 1.0
CB J:LYS12 4.8 63.7 1.0
O J:CYS7 4.9 49.2 1.0
C J:CYS7 4.9 48.3 1.0
N J:LYS12 4.9 62.1 1.0
CA J:SER9 5.0 50.7 1.0

Zinc binding site 8 out of 8 in 3how

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


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

b:87.0
occ:1.00
 SG L:CYS34 2.3 94.0 1.0
SG L:CYS48 2.5 0.8 1.0
CB L:CYS51 2.7 0.6 1.0
CB L:CYS48 2.7 0.9 1.0
SG L:CYS31 2.8 0.7 1.0
O L:CYS51 3.2 0.9 1.0
N L:CYS51 3.3 0.0 1.0
SG L:CYS51 3.4 1.0 1.0
CA L:CYS51 3.4 0.2 1.0
CB L:CYS31 3.5 100.0 1.0
C L:CYS51 3.8 0.6 1.0
CB L:CYS34 3.9 0.7 1.0
CA L:CYS48 4.2 0.5 1.0
O L:CYS34 4.4 0.6 1.0
C L:ASP50 4.5 0.8 1.0
C L:CYS48 4.5 0.7 1.0
OG L:SER36 4.6 0.7 1.0
N L:LYS49 4.7 0.3 1.0
CB L:ASP50 4.7 0.6 1.0
CA L:CYS34 4.8 0.7 1.0
N L:CYS34 4.8 0.7 1.0
CA L:CYS31 4.9 99.1 1.0
N L:ASP50 4.9 0.2 1.0
OE1 L:GLU33 4.9 0.2 1.0
C L:CYS34 4.9 0.8 1.0
N L:CYS48 5.0 0.1 1.0
CA L:ASP50 5.0 0.7 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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