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Zinc in PDB 4x67: Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions.

Enzymatic activity of Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions.

All present enzymatic activity of Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions.:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions., PDB code: 4x67 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 / 4.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.146, 220.798, 193.919, 90.00, 100.25, 90.00
R / Rfree (%) 24.2 / 28.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions. (pdb code 4x67). 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 Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions., PDB code: 4x67:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4x67

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Zinc binding site 1 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions.


Mono view


Stereo pair view

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

b:0.9
occ:1.00
 SG A:CYS110 1.9 0.2 1.0
SG A:CYS167 2.4 0.8 1.0
SG A:CYS148 3.2 0.5 1.0
O A:GLY166 3.3 0.0 1.0
O A:MET108 3.5 0.9 1.0
CB A:CYS110 3.6 0.8 1.0
O A:CYS107 3.7 0.5 1.0
CB A:CYS167 3.8 0.3 1.0
N A:CYS110 4.0 0.4 1.0
C A:GLY166 4.2 0.2 1.0
N A:GLY111 4.2 0.9 1.0
SG A:CYS107 4.3 0.5 1.0
CB A:CYS148 4.3 0.5 1.0
CA A:CYS110 4.3 0.4 1.0
O A:CYS167 4.4 0.7 1.0
CA A:CYS167 4.6 0.0 1.0
N A:CYS167 4.6 0.9 1.0
C A:MET108 4.7 0.3 1.0
C A:CYS110 4.8 0.6 1.0
C A:CYS167 4.9 0.9 1.0
C A:CYS107 4.9 0.4 1.0

Zinc binding site 2 out of 8 in 4x67

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Zinc binding site 2 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions.


Mono view


Stereo pair view

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

b:0.2
occ:1.00
 NE2 A:HIS80 2.3 0.6 1.0
SG A:CYS77 2.4 0.4 1.0
SG A:CYS70 2.7 0.3 1.0
CE1 A:HIS80 2.7 0.7 1.0
SG A:CYS67 2.7 0.1 1.0
CB A:CYS70 2.9 0.4 1.0
CB A:CYS67 3.1 0.2 1.0
OE1 A:GLN68 3.2 0.6 1.0
O A:CYS67 3.4 0.3 1.0
CD2 A:HIS80 3.7 0.6 1.0
CB A:CYS77 3.7 0.4 1.0
ND1 A:HIS80 4.0 0.3 1.0
CA A:CYS77 4.1 0.5 1.0
C A:CYS67 4.2 0.4 1.0
CA A:CYS67 4.2 0.2 1.0
CA A:CYS70 4.4 0.8 1.0
CD A:GLN68 4.4 0.6 1.0
CG A:HIS80 4.5 0.8 1.0
C A:CYS70 4.8 0.3 1.0
C A:CYS77 4.8 0.2 1.0
CD A:PRO78 4.9 0.8 1.0
O A:PRO78 5.0 0.5 1.0

Zinc binding site 3 out of 8 in 4x67

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Zinc binding site 3 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions.


Mono view


Stereo pair view

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

b:0.8
occ:1.00
 SG B:CYS1166 2.1 0.4 1.0
SG B:CYS1182 2.3 0.6 1.0
SG B:CYS1163 2.4 0.7 1.0
SG B:CYS1185 2.7 0.6 1.0
CB B:CYS1185 2.9 0.8 1.0
CB B:CYS1163 3.0 0.0 1.0
CB B:CYS1182 3.3 0.5 1.0
CB B:CYS1166 3.6 0.1 1.0
N B:CYS1166 4.0 0.5 1.0
O B:CYS1166 4.2 0.2 1.0
CA B:CYS1166 4.3 0.7 1.0
CA B:CYS1163 4.4 0.0 1.0
CA B:CYS1185 4.4 0.8 1.0
O B:CYS1182 4.4 0.8 1.0
CB B:ASN1187 4.5 0.7 1.0
C B:CYS1166 4.6 0.7 1.0
CA B:CYS1182 4.7 0.4 1.0
CB B:ILE1165 4.9 0.8 1.0
C B:CYS1182 4.9 0.6 1.0
CG2 B:ILE1165 4.9 0.1 1.0

Zinc binding site 4 out of 8 in 4x67

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Zinc binding site 4 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at 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 Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:78.5
occ:1.00
 SG C:CYS88 2.1 60.0 1.0
SG C:CYS92 2.2 66.6 1.0
SG C:CYS95 2.3 69.0 1.0
SG C:CYS86 2.5 64.7 1.0
CB C:CYS86 2.8 61.5 1.0
CB C:CYS95 3.2 66.3 1.0
CB C:CYS92 3.5 67.8 1.0
CB C:CYS88 3.5 59.4 1.0
N C:CYS92 3.6 71.8 1.0
C C:HIS91 3.9 70.5 1.0
N C:CYS95 4.0 63.4 1.0
CA C:CYS92 4.1 72.8 1.0
O C:HIS91 4.1 73.9 1.0
CA C:CYS95 4.2 64.8 1.0
CA C:CYS86 4.3 65.6 1.0
O C:ASP90 4.4 63.1 1.0
N C:CYS88 4.5 61.6 1.0
CA C:HIS91 4.5 67.2 1.0
CB C:LYS94 4.6 70.6 1.0
CA C:CYS88 4.6 62.5 1.0
C C:LYS94 4.6 60.7 1.0
C C:CYS86 4.7 61.5 1.0
C C:CYS92 4.9 71.5 1.0
CA C:LYS94 5.0 66.2 1.0

Zinc binding site 5 out of 8 in 4x67

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Zinc binding site 5 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at 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 Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.1
occ:1.00
 SG I:CYS32 2.1 0.7 1.0
SG I:CYS29 2.2 88.7 1.0
SG I:CYS10 2.3 92.6 1.0
SG I:CYS7 2.7 1.0 1.0
CB I:CYS10 2.9 96.9 1.0
CB I:CYS29 3.1 95.4 1.0
CB I:CYS32 3.4 0.6 1.0
N I:CYS32 3.6 96.5 1.0
N I:CYS10 3.8 0.6 1.0
CA I:CYS10 3.9 98.6 1.0
CA I:CYS32 4.0 0.0 1.0
CB I:CYS7 4.2 0.9 1.0
CB I:TYR34 4.2 78.5 1.0
CB I:THR31 4.2 97.8 1.0
O I:ARG8 4.4 0.1 1.0
O I:CYS29 4.4 1.0 1.0
CA I:CYS29 4.5 95.3 1.0
C I:THR31 4.5 95.0 1.0
CB I:ASP9 4.5 95.9 1.0
N I:TYR34 4.6 74.4 1.0
C I:CYS32 4.6 95.1 1.0
C I:CYS29 4.7 97.2 1.0
OG1 I:THR31 4.7 0.4 1.0
N I:THR31 4.7 86.3 1.0
CA I:THR31 4.8 88.8 1.0
N I:SER33 4.8 89.0 1.0
C I:ASP9 4.9 1.0 1.0

Zinc binding site 6 out of 8 in 4x67

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Zinc binding site 6 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at 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 Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:74.6
occ:1.00
 SG I:CYS103 2.1 81.3 1.0
SG I:CYS106 2.2 95.9 1.0
SG I:CYS75 2.4 91.6 1.0
SG I:CYS78 2.4 80.0 1.0
CB I:CYS78 2.4 75.8 1.0
CB I:CYS103 2.8 76.7 1.0
CB I:CYS75 3.3 87.5 1.0
N I:CYS78 3.5 79.7 1.0
CA I:CYS78 3.6 80.7 1.0
CB I:CYS106 3.9 91.6 1.0
CB I:HIS108 4.0 80.8 1.0
N I:CYS106 4.1 77.5 1.0
CA I:CYS103 4.3 67.8 1.0
OG I:SER80 4.4 96.3 1.0
CA I:CYS106 4.5 82.6 1.0
N I:HIS79 4.6 85.6 1.0
CA I:CYS75 4.6 85.6 1.0
C I:CYS78 4.7 81.1 1.0
C I:CYS103 4.7 72.7 1.0
CD2 I:HIS108 4.7 78.4 1.0
CG I:HIS108 4.7 79.3 1.0
O I:CYS75 4.7 89.2 1.0
C I:LYS77 4.8 81.6 1.0
N I:HIS108 4.8 74.3 1.0
N I:SER105 4.8 84.3 1.0
C I:CYS75 4.9 86.7 1.0
C I:CYS106 4.9 86.0 1.0
C I:SER105 4.9 73.6 1.0
CB I:SER105 5.0 80.5 1.0

Zinc binding site 7 out of 8 in 4x67

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Zinc binding site 7 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at 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 Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:61.4
occ:1.00
 SG J:CYS10 2.0 47.6 1.0
SG J:CYS46 2.0 59.4 1.0
SG J:CYS45 2.3 57.7 1.0
CB J:CYS10 2.5 43.0 1.0
SG J:CYS7 2.6 59.1 1.0
N J:CYS46 2.6 50.1 1.0
CA J:CYS46 2.8 49.6 1.0
CB J:CYS46 2.8 53.0 1.0
C J:CYS45 3.3 49.6 1.0
CB J:CYS7 3.5 48.9 1.0
CA J:CYS10 3.6 40.1 1.0
N J:CYS10 3.6 38.6 1.0
CB J:CYS45 3.7 54.5 1.0
O J:CYS45 3.9 50.2 1.0
CA J:CYS45 4.1 52.7 1.0
C J:CYS46 4.3 51.6 1.0
N J:GLY11 4.4 44.0 1.0
CG J:ARG43 4.4 63.2 1.0
OG J:SER9 4.5 42.3 1.0
C J:CYS10 4.5 44.9 1.0
N J:CYS45 4.7 53.5 1.0
CA J:CYS7 4.8 45.7 1.0
C J:SER9 4.8 39.1 1.0
O J:CYS7 4.9 42.9 1.0
CD1 B:ILE1006 5.0 48.6 1.0

Zinc binding site 8 out of 8 in 4x67

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Zinc binding site 8 out of 8 in the Crystal Structure of Elongating Yeast Rna Polymerase II Stalled at 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 Elongating Yeast Rna Polymerase II Stalled at Oxidative Cyclopurine Dna Lesions. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:1.0
occ:1.00
 SG L:CYS51 2.0 0.5 1.0
SG L:CYS48 2.4 0.9 1.0
SG L:CYS34 2.5 0.3 1.0
SG L:CYS31 2.7 0.6 1.0
CB L:CYS31 3.2 0.6 1.0
CB L:CYS48 3.4 0.4 1.0
CB L:CYS51 3.7 0.3 1.0
CB L:CYS34 3.8 0.8 1.0
O L:CYS51 4.0 1.0 1.0
C L:CYS51 4.1 0.8 1.0
O L:LYS49 4.3 0.7 1.0
CA L:CYS51 4.4 0.7 1.0
N L:CYS34 4.5 0.8 1.0
N L:GLY52 4.6 0.3 1.0
N L:CYS51 4.6 0.3 1.0
N L:LYS49 4.7 0.1 1.0
C L:GLU33 4.7 0.1 1.0
CA L:CYS31 4.7 0.6 1.0
CB L:GLU33 4.7 1.0 1.0
CA L:CYS34 4.7 0.7 1.0
CB L:SER36 4.8 0.6 1.0
CA L:CYS48 4.9 0.4 1.0
N L:GLU33 5.0 0.4 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 10:18:57 2024

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