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Zinc in PDB 6gyl: Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)

Enzymatic activity of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)

All present enzymatic activity of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist):
2.7.7.6; 3.6.4.12;

Other elements in 6gyl:

The structure of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) (pdb code 6gyl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist), PDB code: 6gyl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 6gyl

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Zinc binding site 1 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.0
occ:1.00
 SG A:CYS148 2.4 0.0 1.0
SG A:CYS107 2.4 0.0 1.0
SG A:CYS110 2.4 0.0 1.0
SG A:CYS167 2.4 0.0 1.0
CB A:CYS167 2.6 0.0 1.0
CB A:CYS148 2.9 0.0 1.0
CB A:CYS107 3.2 0.0 1.0
CB A:CYS110 3.7 0.0 1.0
NE2 A:GLN171 3.8 0.0 1.0
CA A:CYS167 4.1 0.0 1.0
N A:CYS110 4.1 0.0 1.0
N A:GLY168 4.2 0.0 1.0
CA A:CYS148 4.4 0.0 1.0
CA A:CYS110 4.5 0.0 1.0
O A:GLY166 4.5 0.0 1.0
CA A:CYS107 4.6 0.0 1.0
C A:CYS167 4.7 0.0 1.0
N A:CYS167 4.8 0.0 1.0
C A:GLY166 5.0 0.0 1.0

Zinc binding site 2 out of 10 in 6gyl

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Zinc binding site 2 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.0
occ:1.00
 SG A:CYS67 2.4 0.0 1.0
NE2 A:HIS80 2.4 0.0 1.0
SG A:CYS70 2.4 0.0 1.0
SG A:CYS77 2.4 0.0 1.0
CD2 A:HIS80 2.5 0.0 1.0
CB A:CYS70 2.7 0.0 1.0
CB A:CYS77 3.6 0.0 1.0
CE1 A:HIS80 3.6 0.0 1.0
CG A:HIS80 3.7 0.0 1.0
N A:CYS70 3.7 0.0 1.0
CA A:CYS70 3.8 0.0 1.0
CB A:CYS67 3.9 0.0 1.0
N A:GLY79 4.2 0.0 1.0
ND1 A:HIS80 4.2 0.0 1.0
CA A:CYS77 4.3 0.0 1.0
C A:GLY79 4.3 0.0 1.0
O A:GLY79 4.3 0.0 1.0
CA A:GLY79 4.4 0.0 1.0
CA A:GLY59 4.6 0.0 1.0
O A:LEU58 4.6 0.0 1.0
CD A:PRO78 4.6 0.0 1.0
O A:CYS67 4.7 0.0 1.0
C A:CYS77 4.8 0.0 1.0
N A:HIS80 4.8 0.0 1.0
C A:THR69 4.8 0.0 1.0
CB A:HIS80 4.9 0.0 1.0
C A:CYS70 4.9 0.0 1.0
N A:PRO78 4.9 0.0 1.0
CG2 A:THR69 4.9 0.0 1.0

Zinc binding site 3 out of 10 in 6gyl

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Zinc binding site 3 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.0
occ:1.00
 SG B:CYS1185 2.3 0.0 1.0
SG B:CYS1182 2.4 0.0 1.0
SG B:CYS1166 2.4 0.0 1.0
SG B:CYS1163 2.4 0.0 1.0
CB B:CYS1163 2.5 0.0 1.0
CB B:CYS1182 3.2 0.0 1.0
O B:CYS1166 3.7 0.0 1.0
CB B:CYS1185 3.8 0.0 1.0
CB B:CYS1166 3.9 0.0 1.0
N B:CYS1166 3.9 0.0 1.0
CA B:CYS1163 4.0 0.0 1.0
CA B:CYS1166 4.3 0.0 1.0
C B:CYS1166 4.4 0.0 1.0
C B:CYS1163 4.6 0.0 1.0
CA B:CYS1182 4.6 0.0 1.0
N B:CYS1163 4.7 0.0 1.0
C B:CYS1182 4.9 0.0 1.0
N B:ILE1165 4.9 0.0 1.0
N B:GLY1164 5.0 0.0 1.0
O B:CYS1182 5.0 0.0 1.0
CA B:CYS1185 5.0 0.0 1.0

Zinc binding site 4 out of 10 in 6gyl

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Zinc binding site 4 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.0
occ:1.00
 SG C:CYS95 2.3 0.0 1.0
SG C:CYS86 2.3 0.0 1.0
SG C:CYS88 2.3 0.0 1.0
SG C:CYS92 2.4 0.0 1.0
CB C:CYS86 2.8 0.0 1.0
CB C:CYS92 3.5 0.0 1.0
CB C:CYS88 3.7 0.0 1.0
N C:CYS92 3.7 0.0 1.0
CB C:CYS95 4.0 0.0 1.0
C C:HIS91 4.1 0.0 1.0
CA C:CYS92 4.2 0.0 1.0
CA C:CYS86 4.2 0.0 1.0
CA C:HIS91 4.4 0.0 1.0
N C:CYS88 4.4 0.0 1.0
N C:CYS95 4.4 0.0 1.0
C C:CYS86 4.5 0.0 1.0
O C:CYS92 4.6 0.0 1.0
CB C:LYS94 4.6 0.0 1.0
CA C:CYS88 4.6 0.0 1.0
C C:CYS92 4.7 0.0 1.0
O C:HIS91 4.7 0.0 1.0
O C:CYS86 4.8 0.0 1.0
CA C:CYS95 4.9 0.0 1.0
O C:ASP90 5.0 0.0 1.0

Zinc binding site 5 out of 10 in 6gyl

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Zinc binding site 5 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.0
occ:1.00
 SG I:CYS32 2.3 0.0 1.0
SG I:CYS29 2.3 0.0 1.0
SG I:CYS7 2.4 0.0 1.0
SG I:CYS10 2.4 0.0 1.0
CB I:CYS10 2.4 0.0 1.0
CB I:CYS7 3.2 0.0 1.0
CB I:CYS29 3.3 0.0 1.0
OG1 I:THR31 3.4 0.0 1.0
CB I:CYS32 3.6 0.0 1.0
CA I:CYS10 3.8 0.0 1.0
N I:CYS10 4.2 0.0 1.0
O I:ARG8 4.2 0.0 1.0
N I:CYS32 4.2 0.0 1.0
CA I:CYS32 4.5 0.0 1.0
CB I:THR31 4.6 0.0 1.0
ND2 I:ASN12 4.6 0.0 1.0
CA I:CYS7 4.7 0.0 1.0
CB I:TYR34 4.7 0.0 1.0
C I:CYS10 4.7 0.0 1.0
CA I:CYS29 4.7 0.0 1.0
N I:ASN11 4.9 0.0 1.0

Zinc binding site 6 out of 10 in 6gyl

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Zinc binding site 6 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.0
occ:1.00
 SG I:CYS103 2.5 0.0 1.0
SG I:CYS78 2.5 0.0 1.0
SG I:CYS75 2.5 0.0 1.0
SG I:CYS106 2.5 0.0 1.0
CB I:CYS103 2.8 0.0 1.0
CB I:CYS75 3.0 0.0 1.0
OG I:SER105 3.6 0.0 1.0
CB I:CYS78 3.9 0.0 1.0
CB I:CYS106 4.0 0.0 1.0
N I:CYS78 4.1 0.0 1.0
N I:CYS106 4.3 0.0 1.0
CA I:CYS103 4.3 0.0 1.0
CB I:HIS108 4.4 0.0 1.0
CA I:CYS75 4.5 0.0 1.0
CA I:CYS78 4.6 0.0 1.0
CA I:CYS106 4.7 0.0 1.0
CE1 I:PHE110 4.7 0.0 1.0
CB I:LYS77 4.8 0.0 1.0
N I:HIS108 4.8 0.0 1.0
CB I:SER80 4.9 0.0 1.0
CB I:SER105 5.0 0.0 1.0

Zinc binding site 7 out of 10 in 6gyl

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Zinc binding site 7 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.0
occ:1.00
 SG J:CYS10 2.3 0.0 1.0
SG J:CYS45 2.3 0.0 1.0
SG J:CYS7 2.4 0.0 1.0
SG J:CYS46 2.4 0.0 1.0
N J:CYS46 2.6 0.0 1.0
C J:CYS45 3.0 0.0 1.0
CA J:CYS46 3.1 0.0 1.0
CB J:CYS45 3.2 0.0 1.0
CB J:CYS46 3.3 0.0 1.0
O J:CYS45 3.5 0.0 1.0
CB J:CYS7 3.6 0.0 1.0
CB J:CYS10 3.6 0.0 1.0
CA J:CYS45 3.7 0.0 1.0
N J:CYS10 3.8 0.0 1.0
CB J:SER9 4.3 0.0 1.0
CA J:CYS10 4.4 0.0 1.0
N J:CYS45 4.5 0.0 1.0
C J:CYS46 4.6 0.0 1.0
N J:SER9 4.8 0.0 1.0
C J:SER9 4.9 0.0 1.0
CA J:SER9 4.9 0.0 1.0
N J:GLY11 5.0 0.0 1.0
NE J:ARG43 5.0 0.0 1.0

Zinc binding site 8 out of 10 in 6gyl

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Zinc binding site 8 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 SG L:CYS31 2.3 0.0 1.0
SG L:CYS48 2.3 0.0 1.0
SG L:CYS51 2.3 0.0 1.0
SG L:CYS34 2.4 0.0 1.0
CB L:CYS31 3.0 0.0 1.0
CB L:CYS48 3.6 0.0 1.0
CB L:CYS34 3.7 0.0 1.0
OG L:SER36 3.7 0.0 1.0
CB L:CYS51 3.8 0.0 1.0
O L:LYS49 4.0 0.0 1.0
N L:CYS51 4.4 0.0 1.0
N L:CYS34 4.4 0.0 1.0
CA L:CYS31 4.5 0.0 1.0
CA L:CYS51 4.6 0.0 1.0
CA L:CYS34 4.6 0.0 1.0
O L:CYS51 4.8 0.0 1.0
CG L:GLU33 4.8 0.0 1.0
CB L:SER36 4.9 0.0 1.0
C L:LYS49 4.9 0.0 1.0
C L:CYS51 5.0 0.0 1.0
CA L:CYS48 5.0 0.0 1.0

Zinc binding site 9 out of 10 in 6gyl

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Zinc binding site 9 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:0.0
occ:1.00
 SG M:CYS27 2.3 0.0 1.0
SG M:CYS48 2.4 0.0 1.0
SG M:CYS45 2.4 0.0 1.0
SG M:CYS24 2.4 0.0 1.0
CB M:CYS45 2.7 0.0 1.0
CB M:CYS24 3.0 0.0 1.0
CB M:CYS27 3.7 0.0 1.0
CB M:CYS48 3.8 0.0 1.0
N M:CYS48 3.9 0.0 1.0
CA M:CYS45 4.2 0.0 1.0
CA M:CYS48 4.4 0.0 1.0
CA M:CYS24 4.5 0.0 1.0
CB M:LEU50 4.6 0.0 1.0
CB M:LEU47 4.6 0.0 1.0
N M:CYS27 4.6 0.0 1.0
C M:CYS45 4.7 0.0 1.0
N M:LEU50 4.7 0.0 1.0
O M:LEU50 4.8 0.0 1.0
O M:CYS45 4.8 0.0 1.0
CA M:CYS27 4.8 0.0 1.0
N M:GLY49 4.9 0.0 1.0
C M:CYS48 4.9 0.0 1.0
N M:LEU47 4.9 0.0 1.0
CD1 M:LEU52 4.9 0.0 1.0
C M:LEU47 5.0 0.0 1.0
N M:CYS45 5.0 0.0 1.0

Zinc binding site 10 out of 10 in 6gyl

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Zinc binding site 10 out of 10 in the Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of A Yeast Closed Complex with Distorted Dna (Core Ccdist) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn601

b:0.0
occ:1.00
 SG W:CYS124 2.4 0.0 1.0
SG W:CYS152 2.4 0.0 1.0
SG W:CYS149 2.4 0.0 1.0
SG W:CYS127 2.4 0.0 1.0
CB W:CYS152 3.1 0.0 1.0
CB W:CYS127 3.4 0.0 1.0
CB W:CYS149 3.5 0.0 1.0
CB W:CYS124 3.6 0.0 1.0
N W:CYS152 3.7 0.0 1.0
N W:CYS127 3.8 0.0 1.0
CA W:CYS152 4.0 0.0 1.0
CB W:LEU151 4.0 0.0 1.0
CA W:CYS127 4.2 0.0 1.0
C W:LEU151 4.4 0.0 1.0
OH W:TYR131 4.4 0.0 1.0
CE1 W:TYR131 4.6 0.0 1.0
CB W:ILE126 4.6 0.0 1.0
CA W:LEU151 4.6 0.0 1.0
C W:ILE126 4.8 0.0 1.0
CA W:CYS149 4.8 0.0 1.0
N W:LEU151 4.8 0.0 1.0
CZ W:TYR131 4.9 0.0 1.0
CA W:CYS124 5.0 0.0 1.0

Reference:

C.Dienemann, B.Schwalb, S.Schilbach, P.Cramer. Promoter Distortion and Opening in the Rna Polymerase II Cleft. Mol. Cell V. 73 97 2019.
ISSN: ISSN 1097-4164
PubMed: 30472190
DOI: 10.1016/J.MOLCEL.2018.10.014
Page generated: Mon Oct 28 22:05:45 2024

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