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Zinc in PDB 4a93: Rna Polymerase II Elongation Complex Containing A Cpd Lesion

Enzymatic activity of Rna Polymerase II Elongation Complex Containing A Cpd Lesion

All present enzymatic activity of Rna Polymerase II Elongation Complex Containing A Cpd Lesion:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex Containing A Cpd Lesion, PDB code: 4a93 was solved by C.Walmacq, A.C.M.Cheung, M.L.Kireeva, L.Lubkowska, C.Ye, D.Gotte, J.N.Strathern, T.Carell, P.Cramer, M.Kashlev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.09 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.637, 391.519, 281.774, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.9

Other elements in 4a93:

The structure of Rna Polymerase II Elongation Complex Containing A Cpd Lesion 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 Rna Polymerase II Elongation Complex Containing A Cpd Lesion (pdb code 4a93). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion, PDB code: 4a93:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4a93

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.4
occ:1.00
 SG A:CYS148 2.3 0.2 1.0
SG A:CYS110 2.3 0.4 1.0
SG A:CYS107 2.3 0.8 1.0
SG A:CYS167 2.3 0.4 1.0
CB A:CYS167 2.5 0.8 1.0
CB A:CYS148 2.9 0.0 1.0
CB A:CYS110 3.1 0.4 1.0
CB A:CYS107 3.3 0.8 1.0
N A:CYS110 3.6 0.6 1.0
CA A:CYS167 3.9 0.3 1.0
CA A:CYS110 3.9 0.7 1.0
O A:GLY166 4.0 1.0 1.0
C A:CYS167 4.3 0.9 1.0
O A:CYS167 4.4 0.3 1.0
CA A:CYS148 4.4 0.8 1.0
ND1 A:HIS109 4.5 0.8 1.0
N A:CYS167 4.6 0.4 1.0
C A:GLY166 4.7 0.2 1.0
C A:HIS109 4.7 0.5 1.0
CB A:HIS109 4.7 0.8 1.0
CA A:CYS107 4.7 0.2 1.0
N A:GLY111 4.8 0.3 1.0
C A:CYS110 4.8 0.0 1.0
NE2 A:GLN171 4.8 0.4 1.0
O A:CYS148 4.9 0.3 1.0

Zinc binding site 2 out of 8 in 4a93

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:70.5
occ:1.00
 NE2 A:HIS80 2.1 89.4 1.0
SG A:CYS77 2.3 72.5 1.0
SG A:CYS70 2.3 68.4 1.0
SG A:CYS67 2.3 70.3 1.0
CD2 A:HIS80 2.4 78.4 1.0
CE1 A:HIS80 3.4 91.9 1.0
CB A:CYS70 3.5 0.9 1.0
CB A:CYS67 3.5 96.2 1.0
OG1 A:THR69 3.6 72.8 1.0
CG A:HIS80 3.7 72.0 1.0
CB A:CYS77 3.7 87.2 1.0
N A:CYS70 3.8 0.9 1.0
ND1 A:HIS80 4.2 78.5 1.0
CA A:CYS70 4.2 0.1 1.0
O A:PRO78 4.2 97.4 1.0
O A:LEU58 4.2 0.1 1.0
O A:CYS70 4.4 0.2 1.0
CA A:CYS77 4.5 85.3 1.0
C A:CYS70 4.6 0.6 1.0
CD A:PRO78 4.7 69.5 1.0
CB A:THR69 4.8 71.4 1.0
C A:THR69 4.9 0.0 1.0
CB A:HIS80 4.9 74.2 1.0
N A:THR69 4.9 81.3 1.0
O A:GLY79 4.9 87.8 1.0
CA A:CYS67 5.0 96.3 1.0
C A:CYS77 5.0 82.4 1.0

Zinc binding site 3 out of 8 in 4a93

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:75.3
occ:1.00
 SG B:CYS1166 2.3 0.3 1.0
SG B:CYS1185 2.3 80.3 1.0
SG B:CYS1163 2.4 92.6 1.0
SG B:CYS1182 2.4 57.1 1.0
CB B:CYS1163 2.9 86.8 1.0
CB B:CYS1185 3.0 53.6 1.0
CB B:CYS1166 3.0 90.6 1.0
O B:CYS1166 3.4 0.5 1.0
N B:CYS1166 3.4 89.4 1.0
CA B:CYS1166 3.7 88.9 1.0
CB B:CYS1182 3.9 92.9 1.0
C B:CYS1166 3.9 93.3 1.0
CA B:CYS1185 4.4 74.8 1.0
CA B:CYS1163 4.4 81.8 1.0
OG1 B:THR1170 4.5 82.3 1.0
C B:ILE1165 4.6 88.3 1.0
CB B:ILE1165 4.6 84.7 1.0
CB B:THR1170 4.7 78.7 1.0
N B:CYS1185 4.8 81.6 1.0
CG2 B:THR1170 4.8 55.3 1.0
N B:ILE1165 4.9 74.3 1.0
CA B:ILE1165 5.0 78.7 1.0
C B:CYS1163 5.0 80.3 1.0

Zinc binding site 4 out of 8 in 4a93

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:75.7
occ:1.00
 SG C:CYS88 2.3 64.9 1.0
SG C:CYS95 2.3 74.7 1.0
SG C:CYS86 2.3 0.2 1.0
SG C:CYS92 2.3 55.3 1.0
CB C:CYS86 2.8 83.9 1.0
CB C:CYS95 3.3 88.6 1.0
N C:CYS92 3.3 71.2 1.0
CB C:CYS92 3.4 70.1 1.0
CB C:CYS88 3.8 85.8 1.0
C C:HIS91 3.9 77.5 1.0
CA C:CYS92 4.0 71.1 1.0
CA C:HIS91 4.1 79.8 1.0
CA C:CYS86 4.1 83.7 1.0
N C:CYS88 4.2 70.7 1.0
O C:ASP90 4.2 93.2 1.0
N C:CYS95 4.3 92.5 1.0
C C:CYS86 4.3 80.0 1.0
CA C:CYS95 4.4 94.7 1.0
N C:PHE87 4.4 77.0 1.0
C C:CYS92 4.6 81.7 1.0
CA C:CYS88 4.6 77.9 1.0
CB C:LYS94 4.7 87.7 1.0
O C:HIS91 4.8 80.8 1.0
OG C:SER83 4.8 0.6 1.0
O C:CYS92 4.9 85.4 1.0
C C:LYS94 4.9 92.6 1.0
O C:CYS86 4.9 75.0 1.0
N C:LYS94 5.0 87.3 1.0
N C:HIS91 5.0 82.1 1.0
C C:ASP90 5.0 90.6 1.0

Zinc binding site 5 out of 8 in 4a93

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.1
occ:1.00
 SG I:CYS10 2.3 0.1 1.0
SG I:CYS7 2.3 0.3 1.0
SG I:CYS32 2.3 0.6 1.0
SG I:CYS29 2.4 0.3 1.0
CB I:CYS10 2.9 0.9 1.0
CB I:CYS29 3.0 0.4 1.0
CB I:CYS32 3.2 0.9 1.0
N I:CYS32 3.5 0.9 1.0
CB I:CYS7 3.6 0.5 1.0
N I:CYS10 3.7 0.2 1.0
CA I:CYS32 3.8 1.0 1.0
CA I:CYS10 4.0 0.5 1.0
CB I:TYR34 4.0 0.8 1.0
C I:CYS32 4.2 0.3 1.0
C I:THR31 4.3 0.2 1.0
N I:TYR34 4.5 0.5 1.0
CA I:CYS29 4.5 0.0 1.0
O I:ARG8 4.6 0.1 1.0
O I:CYS32 4.6 0.1 1.0
CB I:ASP9 4.7 0.4 1.0
N I:THR31 4.7 0.3 1.0
N I:SER33 4.8 0.3 1.0
C I:ASP9 4.8 0.8 1.0
CA I:THR31 4.9 0.5 1.0
CB I:THR31 4.9 0.4 1.0
CA I:TYR34 4.9 0.8 1.0
O I:THR31 5.0 1.0 1.0
CA I:CYS7 5.0 0.4 1.0

Zinc binding site 6 out of 8 in 4a93

Go back to Zinc Binding Sites List in 4a93
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.5
occ:1.00
 SG I:CYS78 2.3 0.1 1.0
SG I:CYS103 2.3 0.3 1.0
SG I:CYS75 2.3 0.9 1.0
SG I:CYS106 2.3 0.5 1.0
CB I:CYS75 2.6 0.2 1.0
CB I:CYS103 3.1 0.0 1.0
N I:CYS78 3.4 0.3 1.0
CB I:CYS78 3.5 0.3 1.0
CB I:CYS106 3.5 0.5 1.0
CA I:CYS78 3.7 0.5 1.0
C I:CYS78 3.9 0.6 1.0
CB I:SER80 4.0 0.5 1.0
CA I:CYS75 4.1 0.2 1.0
N I:SER80 4.2 0.8 1.0
N I:HIS79 4.3 0.1 1.0
C I:LYS77 4.3 0.9 1.0
O I:CYS78 4.3 1.0 1.0
N I:CYS106 4.3 0.3 1.0
CA I:CYS106 4.5 0.2 1.0
CA I:CYS103 4.5 0.2 1.0
CB I:LYS77 4.6 0.6 1.0
OG I:SER105 4.7 0.6 1.0
CA I:SER80 4.7 1.0 1.0
N I:LYS77 4.8 0.8 1.0
CA I:LYS77 4.8 0.7 1.0
N I:CYS75 4.9 0.8 1.0
C I:CYS75 4.9 0.2 1.0
O I:SER80 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 4a93

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


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 Elongation Complex Containing A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:90.5
occ:1.00
 SG J:CYS46 2.3 73.6 1.0
SG J:CYS45 2.3 0.6 1.0
SG J:CYS10 2.3 89.1 1.0
SG J:CYS7 2.3 0.9 1.0
N J:CYS46 3.0 93.8 1.0
CB J:CYS45 3.1 88.5 1.0
CB J:CYS10 3.3 85.7 1.0
C J:CYS45 3.4 91.2 1.0
CB J:CYS7 3.5 0.8 1.0
CB J:CYS46 3.5 97.0 1.0
CA J:CYS46 3.5 97.2 1.0
N J:CYS10 3.6 84.8 1.0
CA J:CYS45 3.8 91.2 1.0
CA J:CYS10 4.0 85.6 1.0
O J:CYS45 4.0 90.6 1.0
NH2 J:ARG43 4.0 0.3 1.0
CB J:SER9 4.3 95.1 1.0
O J:ARG43 4.4 0.7 1.0
N J:CYS45 4.5 98.3 1.0
N J:GLY11 4.6 87.7 1.0
C J:SER9 4.6 88.2 1.0
NE J:ARG43 4.7 0.7 1.0
CZ J:ARG43 4.8 0.0 1.0
C J:CYS10 4.8 86.0 1.0
OG J:SER9 4.8 96.1 1.0
CA J:SER9 4.8 92.3 1.0
N J:SER9 4.9 93.8 1.0
CA J:CYS7 4.9 97.4 1.0
CB J:ARG43 4.9 0.3 1.0

Zinc binding site 8 out of 8 in 4a93

Go back to Zinc Binding Sites List in 4a93
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Containing A Cpd Lesion


Mono view


Stereo pair view

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

b:0.9
occ:1.00
 CB L:CYS51 1.9 0.6 1.0
SG L:CYS48 2.3 97.3 1.0
SG L:CYS51 2.3 0.8 1.0
SG L:CYS34 2.3 0.0 1.0
SG L:CYS31 2.3 0.9 1.0
CB L:CYS48 3.3 0.3 1.0
CB L:CYS34 3.3 0.7 1.0
CA L:CYS51 3.4 0.0 1.0
CB L:CYS31 3.5 0.4 1.0
N L:CYS51 4.0 0.0 1.0
N L:CYS34 4.1 0.0 1.0
C L:CYS51 4.2 0.0 1.0
CA L:CYS34 4.2 0.6 1.0
OG L:SER36 4.5 0.7 1.0
O L:CYS51 4.5 0.2 1.0
CG L:GLU33 4.5 1.0 1.0
CA L:CYS48 4.8 0.1 1.0
N L:SER35 4.8 0.8 1.0
C L:CYS34 4.8 0.3 1.0
CA L:CYS31 4.9 0.7 1.0
OE2 L:GLU33 4.9 0.9 1.0

Reference:

C.Walmacq, A.C.Cheung, M.L.Kireeva, L.Lubkowska, C.Ye, D.Gotte, J.N.Strathern, T.Carell, P.Cramer, M.Kashlev. Mechanism of Translesion Transcription By Rna Polymerase II and Its Role in Cellular Resistance to Dna Damage. Mol.Cell V. 46 18 2012.
ISSN: ISSN 1097-2765
PubMed: 22405652
DOI: 10.1016/J.MOLCEL.2012.02.006
Page generated: Sat Oct 26 19:08:14 2024

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