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Zinc in PDB 6gyk: Structure of A Yeast Closed Complex (Core CC1)

Enzymatic activity of Structure of A Yeast Closed Complex (Core CC1)

All present enzymatic activity of Structure of A Yeast Closed Complex (Core CC1):
2.7.7.6; 3.6.4.12;

Other elements in 6gyk:

The structure of Structure of A Yeast Closed Complex (Core CC1) 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 (Core CC1) (pdb code 6gyk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of A Yeast Closed Complex (Core CC1), PDB code: 6gyk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6gyk

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Zinc binding site 1 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Yeast Closed Complex (Core CC1) 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 4.9 0.0 1.0

Zinc binding site 2 out of 9 in 6gyk

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Zinc binding site 2 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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 9 in 6gyk

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Zinc binding site 3 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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 9 in 6gyk

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Zinc binding site 4 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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
CA C:CYS88 4.6 0.0 1.0
CB C:LYS94 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 9 in 6gyk

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Zinc binding site 5 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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 9 in 6gyk

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Zinc binding site 6 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


Mono view


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 (Core CC1) 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 9 in 6gyk

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Zinc binding site 7 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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 9 in 6gyk

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Zinc binding site 8 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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 9 in 6gyk

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Zinc binding site 9 out of 9 in the Structure of A Yeast Closed Complex (Core CC1)


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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 (Core CC1) 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

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 22:04:59 2024

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