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Zinc in PDB 4x6a: Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions

Enzymatic activity of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions

All present enzymatic activity of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions, PDB code: 4x6a was solved by L.Wang, J.Chong, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.96
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.550, 220.334, 191.563, 90.00, 97.00, 90.00
R / Rfree (%) 24.9 / 29.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions (pdb code 4x6a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions, PDB code: 4x6a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4x6a

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Zinc binding site 1 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.6
occ:1.00
 SG A:CYS110 1.9 0.5 1.0
SG A:CYS167 2.5 0.6 1.0
SG A:CYS148 3.0 0.3 1.0
CB A:CYS110 3.6 0.4 1.0
O A:GLY166 3.7 0.4 1.0
O A:MET108 3.8 0.1 1.0
CB A:CYS167 4.0 0.0 1.0
CB A:CYS148 4.1 0.1 1.0
O A:CYS107 4.1 0.9 1.0
N A:CYS110 4.2 0.2 1.0
C A:GLY166 4.2 0.1 1.0
O A:CYS167 4.2 0.3 1.0
SG A:CYS107 4.2 0.6 1.0
CA A:CYS110 4.3 0.6 1.0
N A:GLY111 4.3 0.8 1.0
N A:CYS167 4.6 0.0 1.0
CA A:CYS167 4.6 0.7 1.0
C A:CYS110 4.7 0.4 1.0
C A:CYS167 4.8 0.5 1.0

Zinc binding site 2 out of 8 in 4x6a

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Zinc binding site 2 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.7
occ:1.00
 SG A:CYS70 2.1 0.6 1.0
SG A:CYS77 2.5 0.5 1.0
NE2 A:HIS80 2.7 0.6 1.0
CB A:CYS70 2.7 1.0 1.0
CE1 A:HIS80 3.0 0.4 1.0
CB A:CYS67 3.1 0.7 1.0
NE2 A:GLN68 3.4 0.5 1.0
SG A:CYS67 3.5 0.9 1.0
CB A:CYS77 3.6 0.7 1.0
CA A:CYS77 3.9 0.2 1.0
CD2 A:HIS80 3.9 0.7 1.0
O A:CYS67 4.0 0.0 1.0
CA A:CYS70 4.2 0.6 1.0
ND1 A:HIS80 4.3 0.9 1.0
CA A:CYS67 4.4 0.9 1.0
C A:CYS70 4.5 0.1 1.0
C A:CYS67 4.6 0.0 1.0
CD A:PRO78 4.6 0.2 1.0
C A:CYS77 4.7 0.3 1.0
CD A:GLN68 4.7 0.6 1.0
CG A:HIS80 4.8 1.0 1.0
O A:CYS70 4.8 0.4 1.0
N A:PRO78 5.0 0.9 1.0

Zinc binding site 3 out of 8 in 4x6a

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Zinc binding site 3 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.2
occ:1.00
 SG B:CYS1166 2.0 0.1 1.0
SG B:CYS1182 2.2 0.8 1.0
SG B:CYS1163 2.3 0.5 1.0
CB B:CYS1163 3.0 0.1 1.0
CB B:CYS1185 3.0 0.7 1.0
SG B:CYS1185 3.1 0.5 1.0
CB B:CYS1182 3.1 0.3 1.0
CB B:CYS1166 3.8 0.5 1.0
O B:CYS1182 4.2 0.8 1.0
N B:CYS1166 4.2 0.2 1.0
CB B:ASN1187 4.2 0.5 1.0
O B:CYS1166 4.3 0.3 1.0
CA B:CYS1182 4.4 0.8 1.0
CA B:CYS1166 4.4 0.1 1.0
CA B:CYS1163 4.5 0.8 1.0
CA B:CYS1185 4.5 0.7 1.0
C B:CYS1182 4.7 0.2 1.0
C B:CYS1166 4.7 0.3 1.0
OD1 B:ASN1187 4.9 0.1 1.0
CG B:ASN1187 5.0 0.6 1.0

Zinc binding site 4 out of 8 in 4x6a

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Zinc binding site 4 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.6
occ:1.00
 SG C:CYS88 1.9 0.8 1.0
SG C:CYS95 2.3 0.3 1.0
SG C:CYS92 2.3 0.1 1.0
SG C:CYS86 2.7 0.9 1.0
CB C:CYS86 2.8 0.8 1.0
CB C:CYS92 3.1 0.7 1.0
CB C:CYS95 3.5 0.5 1.0
CB C:CYS88 3.5 0.5 1.0
N C:CYS92 3.7 0.1 1.0
C C:HIS91 3.9 1.0 1.0
CA C:CYS92 4.0 0.5 1.0
O C:HIS91 4.1 0.6 1.0
N C:CYS88 4.2 0.3 1.0
CA C:CYS86 4.2 0.4 1.0
N C:CYS95 4.4 0.9 1.0
CA C:CYS88 4.4 0.1 1.0
O C:CYS92 4.4 1.0 1.0
O C:ASP90 4.5 0.2 1.0
CA C:CYS95 4.5 1.0 1.0
C C:CYS86 4.6 0.7 1.0
O C:CYS88 4.6 0.2 1.0
C C:CYS92 4.6 0.7 1.0
CA C:HIS91 4.6 0.1 1.0
N C:PHE87 4.7 0.9 1.0
C C:CYS88 4.9 0.8 1.0
C C:LYS94 4.9 0.3 1.0
CB C:LYS94 5.0 1.0 1.0

Zinc binding site 5 out of 8 in 4x6a

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Zinc binding site 5 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.3
occ:1.00
 SG I:CYS10 2.2 0.2 1.0
SG I:CYS32 2.3 0.4 1.0
SG I:CYS7 2.5 0.3 1.0
SG I:CYS29 2.5 0.6 1.0
CB I:CYS10 2.8 0.3 1.0
CB I:CYS29 3.1 0.9 1.0
N I:CYS10 3.5 0.6 1.0
CB I:CYS32 3.7 1.0 1.0
CA I:CYS10 3.7 0.4 1.0
N I:CYS32 3.8 0.0 1.0
CB I:TYR34 4.0 0.4 1.0
CB I:CYS7 4.1 0.5 1.0
CB I:ASP9 4.2 0.7 1.0
O I:ARG8 4.2 0.7 1.0
CB I:THR31 4.2 0.3 1.0
CA I:CYS32 4.3 0.1 1.0
CA I:CYS29 4.6 0.6 1.0
C I:ASP9 4.6 0.6 1.0
N I:TYR34 4.7 0.5 1.0
O I:CYS29 4.7 0.6 1.0
CG2 I:THR31 4.7 0.5 1.0
C I:CYS10 4.8 0.2 1.0
C I:THR31 4.8 0.7 1.0
C I:CYS32 4.9 0.3 1.0
N I:ASN11 4.9 0.6 1.0
CG I:TYR34 4.9 1.0 1.0
C I:CYS29 4.9 0.9 1.0
N I:SER33 5.0 0.5 1.0
CA I:THR31 5.0 0.8 1.0
CA I:ASP9 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 4x6a

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Zinc binding site 6 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.5
occ:1.00
 SG I:CYS75 2.2 0.6 1.0
SG I:CYS103 2.2 0.5 1.0
SG I:CYS106 2.3 0.9 1.0
SG I:CYS78 2.4 0.4 1.0
O I:LYS77 2.9 0.3 1.0
CB I:CYS103 3.2 0.9 1.0
CB I:CYS75 3.3 0.2 1.0
CB I:CYS78 3.7 0.7 1.0
CB I:CYS106 3.8 1.0 1.0
C I:LYS77 4.1 0.8 1.0
N I:CYS106 4.2 0.9 1.0
CB I:HIS108 4.3 0.5 1.0
CB I:LYS77 4.3 0.0 1.0
OG I:SER80 4.4 0.2 1.0
CA I:CYS106 4.6 0.7 1.0
CA I:CYS103 4.6 0.3 1.0
N I:HIS79 4.6 0.7 1.0
CA I:CYS75 4.7 0.6 1.0
O I:CYS75 4.8 0.6 1.0
CA I:CYS78 4.9 0.3 1.0
C I:CYS75 4.9 0.6 1.0
CA I:LYS77 4.9 0.2 1.0
C I:SER105 4.9 0.5 1.0
CB I:SER105 5.0 0.4 1.0
N I:CYS78 5.0 0.8 1.0
CD2 I:HIS108 5.0 0.1 1.0
N I:SER80 5.0 0.9 1.0

Zinc binding site 7 out of 8 in 4x6a

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Zinc binding site 7 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.9
occ:1.00
 SG J:CYS46 2.1 0.6 1.0
SG J:CYS45 2.3 0.5 1.0
SG J:CYS10 2.3 0.2 1.0
CB J:CYS10 2.5 0.9 1.0
CB J:CYS46 2.6 0.7 1.0
N J:CYS46 2.6 0.1 1.0
SG J:CYS7 2.7 0.0 1.0
CA J:CYS46 2.7 0.5 1.0
C J:CYS45 3.5 0.7 1.0
CB J:CYS7 3.6 0.8 1.0
CA J:CYS10 3.8 0.2 1.0
CB J:CYS45 3.8 0.7 1.0
N J:CYS10 3.9 1.0 1.0
O J:CYS45 4.1 1.0 1.0
CA J:CYS45 4.2 0.6 1.0
C J:CYS46 4.3 0.3 1.0
NE J:ARG43 4.4 0.0 1.0
N J:GLY11 4.5 0.8 1.0
C J:CYS10 4.6 0.3 1.0
CD J:ARG43 4.7 0.0 1.0
N J:CYS45 4.7 0.1 1.0
CB J:ARG43 4.8 0.5 1.0
OG J:SER9 5.0 0.3 1.0
CA J:CYS7 5.0 0.6 1.0
N J:ARG47 5.0 0.6 1.0

Zinc binding site 8 out of 8 in 4x6a

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Zinc binding site 8 out of 8 in the Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Yeast Rna Polymerase II Encountering Oxidative Cyclopurine Dna Lesions within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.4
occ:1.00
 SG L:CYS34 2.1 0.8 1.0
SG L:CYS48 2.2 0.7 1.0
SG L:CYS31 2.4 0.7 1.0
SG L:CYS51 2.8 0.7 1.0
CB L:CYS51 2.8 0.9 1.0
CB L:CYS31 2.9 0.3 1.0
CB L:CYS48 3.5 0.4 1.0
O L:CYS51 3.5 0.9 1.0
CB L:CYS34 3.7 0.4 1.0
CA L:CYS51 4.0 0.5 1.0
N L:CYS34 4.1 0.7 1.0
C L:CYS51 4.2 0.2 1.0
CA L:CYS31 4.4 1.0 1.0
CA L:CYS34 4.5 0.6 1.0
N L:CYS51 4.5 0.0 1.0
N L:SER35 4.8 0.3 1.0
CA L:CYS48 4.9 0.4 1.0
CB L:SER36 4.9 0.6 1.0
C L:CYS31 4.9 0.1 1.0

Reference:

C.Walmacq, L.Wang, J.Chong, K.Scibelli, L.Lubkowska, A.Gnatt, P.J.Brooks, D.Wang, M.Kashlev. Mechanism of Rna Polymerase II Bypass of Oxidative Cyclopurine Dna Lesions. Proc.Natl.Acad.Sci.Usa V. 112 E410 2015.
ISSN: ESSN 1091-6490
PubMed: 25605892
DOI: 10.1073/PNAS.1415186112
Page generated: Sun Oct 27 10:19:51 2024

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