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Zinc in PDB 3hou: Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch

Enzymatic activity of Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch

All present enzymatic activity of Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch:
2.7.7.6;

Protein crystallography data

The structure of Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch, PDB code: 3hou 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) 40.00 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 394.264, 221.614, 283.446, 90.00, 90.90, 90.00
R / Rfree (%) 23.3 / 25.2

Other elements in 3hou:

The structure of Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch (pdb code 3hou). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch, PDB code: 3hou:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 3hou

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Zinc binding site 1 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9984

b:70.3
occ:1.00
 SG A:CYS110 2.3 81.8 1.0
SG A:CYS107 2.5 86.0 1.0
SG A:CYS148 2.6 83.2 1.0
SG A:CYS167 2.7 98.2 1.0
CB A:CYS110 3.0 82.1 1.0
O A:CYS167 3.3 93.8 1.0
CB A:CYS107 3.4 83.6 1.0
CB A:CYS148 3.4 85.4 1.0
O A:MET108 3.8 84.7 1.0
N A:CYS110 3.9 83.2 1.0
CB A:CYS167 3.9 95.8 1.0
CA A:CYS110 4.0 81.8 1.0
O A:GLY166 4.1 95.2 1.0
ND2 A:ASN169 4.3 86.7 1.0
C A:CYS167 4.3 93.5 1.0
O A:CYS107 4.6 82.3 1.0
CA A:CYS107 4.7 82.1 1.0
CA A:CYS167 4.7 94.9 1.0
C A:CYS107 4.7 82.3 1.0
N A:GLY111 4.7 79.7 1.0
C A:CYS110 4.7 80.5 1.0
CA A:CYS148 4.9 86.8 1.0
C A:GLY166 4.9 95.6 1.0
ND1 A:HIS109 4.9 91.7 1.0
C A:HIS109 4.9 85.5 1.0

Zinc binding site 2 out of 16 in 3hou

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Zinc binding site 2 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn9985

b:40.5
occ:1.00
 NE2 A:HIS80 2.2 39.7 1.0
SG A:CYS70 2.2 58.1 1.0
SG A:CYS77 2.2 37.3 1.0
SG A:CYS67 2.2 47.9 1.0
CD2 A:HIS80 2.6 39.7 1.0
CB A:CYS70 3.2 65.1 1.0
CE1 A:HIS80 3.5 40.3 1.0
CB A:CYS77 3.7 27.9 1.0
CB A:CYS67 3.9 58.3 1.0
CG A:HIS80 3.9 40.5 1.0
O A:CYS67 4.1 68.2 1.0
OE1 A:GLN68 4.3 48.1 1.0
ND1 A:HIS80 4.3 40.1 1.0
O A:PRO78 4.3 34.7 1.0
CA A:CYS77 4.4 31.1 1.0
CD A:GLN68 4.6 54.0 1.0
CA A:CYS70 4.6 68.6 1.0
NE2 A:GLN68 4.9 53.8 1.0
C A:CYS67 4.9 65.9 1.0
C A:CYS77 5.0 29.5 1.0
CA A:CYS67 5.0 63.6 1.0
C A:CYS70 5.0 69.9 1.0

Zinc binding site 3 out of 16 in 3hou

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Zinc binding site 3 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn9986

b:33.2
occ:1.00
 SG B:CYS1166 2.3 26.9 1.0
SG B:CYS1182 2.4 41.3 1.0
SG B:CYS1185 2.6 42.0 1.0
SG B:CYS1163 2.6 32.8 1.0
CB B:CYS1185 2.7 39.5 1.0
CB B:CYS1163 3.0 32.7 1.0
CB B:CYS1182 3.8 44.2 1.0
CB B:CYS1166 4.0 33.7 1.0
CA B:CYS1185 4.1 41.2 1.0
N B:CYS1166 4.3 36.9 1.0
O B:CYS1182 4.3 48.5 1.0
O B:CYS1166 4.3 42.4 1.0
OG1 B:THR1170 4.5 34.1 1.0
N B:CYS1185 4.5 41.4 1.0
CA B:CYS1163 4.6 32.0 1.0
CB B:THR1170 4.6 33.5 1.0
CA B:CYS1166 4.7 37.2 1.0
CB B:ILE1165 4.8 35.7 1.0
CG2 B:THR1170 4.9 35.6 1.0
C B:CYS1166 5.0 40.2 1.0

Zinc binding site 4 out of 16 in 3hou

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Zinc binding site 4 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn9987

b:28.3
occ:1.00
 SG C:CYS86 2.2 27.8 1.0
SG C:CYS95 2.3 35.7 1.0
SG C:CYS92 2.4 38.6 1.0
SG C:CYS88 2.4 28.3 1.0
CB C:CYS86 2.9 27.2 1.0
CB C:CYS95 3.1 36.7 1.0
N C:CYS92 3.3 40.0 1.0
CB C:CYS92 3.6 40.3 1.0
CB C:CYS88 3.7 29.0 1.0
C C:HIS91 3.8 39.3 1.0
CA C:HIS91 3.9 38.6 1.0
CA C:CYS92 3.9 42.9 1.0
N C:CYS95 4.0 39.2 1.0
CA C:CYS95 4.2 37.3 1.0
CA C:CYS86 4.3 29.0 1.0
N C:CYS88 4.3 27.9 1.0
C C:CYS92 4.5 45.2 1.0
C C:LYS94 4.5 41.5 1.0
C C:CYS86 4.5 29.5 1.0
CB C:LYS94 4.5 44.5 1.0
O C:CYS92 4.6 46.1 1.0
CA C:CYS88 4.6 31.4 1.0
O C:HIS91 4.7 40.2 1.0
N C:HIS91 4.8 38.9 1.0
O C:CYS86 4.9 29.8 1.0
CB C:HIS91 4.9 35.4 1.0
N C:LYS94 4.9 43.3 1.0
CA C:SER83 4.9 35.2 1.0
CA C:LYS94 4.9 42.8 1.0
N C:PHE87 5.0 28.9 1.0

Zinc binding site 5 out of 16 in 3hou

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Zinc binding site 5 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn9988

b:65.0
occ:1.00
 SG I:CYS10 2.2 69.4 1.0
SG I:CYS32 2.3 60.1 1.0
SG I:CYS29 2.4 62.5 1.0
SG I:CYS7 2.5 54.8 1.0
CB I:CYS29 3.1 65.0 1.0
CB I:CYS32 3.3 60.2 1.0
N I:CYS32 3.6 63.7 1.0
CB I:CYS10 3.7 71.5 1.0
CB I:CYS7 3.8 64.4 1.0
N I:CYS10 4.0 73.3 1.0
CA I:CYS32 4.0 60.9 1.0
CA I:CYS10 4.1 71.4 1.0
O I:CYS10 4.2 69.9 1.0
C I:CYS10 4.3 70.0 1.0
CB I:THR31 4.3 68.2 1.0
CB I:TYR34 4.4 44.6 1.0
O I:ARG8 4.5 72.9 1.0
C I:THR31 4.6 66.5 1.0
CA I:CYS29 4.6 65.5 1.0
C I:CYS32 4.7 59.4 1.0
CB I:ASN12 4.8 69.1 1.0
N I:THR31 4.8 67.6 1.0
CA I:THR31 4.8 67.3 1.0
CB I:ASP9 4.9 74.1 1.0

Zinc binding site 6 out of 16 in 3hou

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Zinc binding site 6 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn9989

b:0.6
occ:1.00
 SG I:CYS75 2.5 95.2 1.0
SG I:CYS106 2.5 88.3 1.0
CB I:CYS75 2.7 97.5 1.0
SG I:CYS78 2.9 95.0 1.0
SG I:CYS103 3.1 90.5 1.0
CB I:CYS103 3.3 89.6 1.0
CB I:HIS108 3.4 90.9 1.0
N I:CYS78 3.6 97.9 1.0
CB I:LYS77 3.8 94.2 1.0
CB I:CYS106 3.9 90.8 1.0
N I:LYS77 4.1 97.3 1.0
CB I:CYS78 4.1 97.4 1.0
CG I:HIS108 4.2 92.0 1.0
CA I:CYS75 4.2 98.1 1.0
C I:LYS77 4.2 97.3 1.0
CA I:LYS77 4.2 96.4 1.0
CD2 I:HIS108 4.2 92.2 1.0
CA I:CYS78 4.3 97.8 1.0
N I:HIS108 4.5 90.0 1.0
C I:CYS75 4.6 98.1 1.0
CA I:HIS108 4.6 90.2 1.0
CG I:LYS77 4.7 92.2 1.0
N I:PRO76 4.7 98.2 1.0
CD I:PRO76 4.8 98.1 1.0
CA I:CYS103 4.8 88.5 1.0
C I:CYS78 4.9 98.4 1.0
N I:HIS79 4.9 99.2 1.0
O I:SER105 4.9 93.8 1.0

Zinc binding site 7 out of 16 in 3hou

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Zinc binding site 7 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn9990

b:52.0
occ:1.00
 SG J:CYS10 2.3 33.2 1.0
SG J:CYS45 2.4 32.8 1.0
SG J:CYS7 2.4 37.8 1.0
SG J:CYS46 2.4 51.0 1.0
N J:CYS46 3.1 46.3 1.0
CB J:CYS7 3.2 37.0 1.0
CB J:CYS46 3.3 47.9 1.0
CA J:CYS46 3.3 47.9 1.0
C J:CYS45 3.4 44.5 1.0
CB J:CYS45 3.7 39.5 1.0
CB J:CYS10 3.7 37.0 1.0
O J:CYS45 3.7 44.8 1.0
N J:CYS10 3.8 34.6 1.0
CA J:CYS45 4.2 42.4 1.0
CA J:CYS10 4.2 37.0 1.0
CB J:LYS12 4.5 51.5 1.0
NE J:ARG43 4.5 39.0 1.0
N J:GLY11 4.6 41.1 1.0
CA J:CYS7 4.6 36.5 1.0
N J:LYS12 4.7 49.7 1.0
NH2 J:ARG43 4.7 35.2 1.0
C J:CYS10 4.7 38.0 1.0
CB J:SER9 4.7 32.1 1.0
C J:CYS46 4.8 48.8 1.0
CZ J:ARG43 4.9 38.6 1.0
C J:SER9 5.0 32.2 1.0
CG J:ARG43 5.0 43.1 1.0
N J:CYS45 5.0 44.1 1.0

Zinc binding site 8 out of 16 in 3hou

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Zinc binding site 8 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


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 I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn9991

b:90.1
occ:1.00
 SG L:CYS34 2.3 79.8 1.0
CB L:CYS51 2.6 0.8 1.0
SG L:CYS48 2.6 98.8 1.0
SG L:CYS31 2.7 93.6 1.0
CB L:CYS48 2.8 97.7 1.0
CB L:CYS31 3.3 89.4 1.0
O L:CYS51 3.3 0.4 1.0
N L:CYS51 3.4 0.7 1.0
CA L:CYS51 3.4 0.5 1.0
SG L:CYS51 3.4 0.8 1.0
C L:CYS51 3.8 0.2 1.0
CB L:CYS34 3.9 85.9 1.0
CA L:CYS48 4.2 98.9 1.0
OG L:SER36 4.4 88.1 1.0
C L:ASP50 4.5 0.5 1.0
C L:CYS48 4.5 100.0 1.0
O L:CYS34 4.6 88.4 1.0
N L:LYS49 4.6 0.3 1.0
CA L:CYS31 4.7 87.7 1.0
CA L:CYS34 4.8 87.6 1.0
N L:CYS34 4.9 89.3 1.0
O L:LYS49 4.9 0.2 1.0
C L:LYS49 4.9 0.1 1.0
N L:ASP50 5.0 0.6 1.0
N L:CYS48 5.0 98.3 1.0
CB L:ASP50 5.0 0.1 1.0

Zinc binding site 9 out of 16 in 3hou

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Zinc binding site 9 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn9992

b:74.8
occ:1.00
 SG M:CYS110 2.4 83.0 1.0
SG M:CYS167 2.6 0.9 1.0
SG M:CYS148 2.7 85.2 1.0
SG M:CYS107 2.7 84.9 1.0
CB M:CYS110 2.7 80.5 1.0
O M:CYS167 3.4 0.2 1.0
CB M:CYS107 3.7 83.3 1.0
CB M:CYS148 3.7 89.1 1.0
O M:GLY166 3.8 0.9 1.0
CA M:CYS110 3.9 80.2 1.0
CB M:CYS167 3.9 0.1 1.0
N M:CYS110 4.0 81.5 1.0
O M:MET108 4.2 84.9 1.0
ND2 M:ASN169 4.4 92.4 1.0
C M:CYS167 4.4 100.0 1.0
C M:CYS110 4.6 79.7 1.0
C M:GLY166 4.6 0.7 1.0
CA M:CYS167 4.6 0.6 1.0
N M:GLY111 4.7 79.2 1.0
O M:CYS107 4.9 80.5 1.0
ND1 M:HIS109 4.9 90.8 1.0
N M:CYS167 4.9 0.8 1.0

Zinc binding site 10 out of 16 in 3hou

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Zinc binding site 10 out of 16 in the Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Complete Rna Polymerase II Elongation Complex I with A T-U Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn9993

b:37.7
occ:1.00
 NE2 M:HIS80 2.2 37.5 1.0
SG M:CYS70 2.2 61.8 1.0
SG M:CYS77 2.2 42.2 1.0
SG M:CYS67 2.3 57.8 1.0
CD2 M:HIS80 2.7 39.6 1.0
CB M:CYS70 3.1 69.4 1.0
CE1 M:HIS80 3.5 39.3 1.0
CB M:CYS77 3.7 38.2 1.0
CB M:CYS67 3.9 65.7 1.0
CG M:HIS80 4.0 38.8 1.0
O M:CYS67 4.1 74.0 1.0
OE1 M:GLN68 4.1 61.7 1.0
ND1 M:HIS80 4.3 37.7 1.0
O M:PRO78 4.4 41.0 1.0
CA M:CYS77 4.4 38.6 1.0
CD M:GLN68 4.5 65.3 1.0
CA M:CYS70 4.5 72.6 1.0
NE2 M:GLN68 4.8 64.2 1.0
C M:CYS67 4.9 72.7 1.0
C M:CYS70 4.9 74.2 1.0
CA M:CYS67 4.9 71.0 1.0
O M:GLN71 4.9 75.4 1.0
C M:CYS77 5.0 36.9 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 06:30:17 2024

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