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Zinc in PDB 7nvu: Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna

Enzymatic activity of Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna

All present enzymatic activity of Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna:
2.3.1.48; 2.7.7.6; 3.6.4.12;

Other elements in 7nvu:

The structure of Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna (pdb code 7nvu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna, PDB code: 7nvu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7nvu

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Zinc binding site 1 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:45.5
occ:1.00
 NE2 A:HIS84 2.0 21.4 1.0
SG A:CYS74 2.3 39.9 1.0
SG A:CYS71 2.3 31.2 1.0
SG A:CYS81 2.3 31.8 1.0
CD2 A:HIS84 2.7 21.4 1.0
CB A:CYS71 3.0 31.2 1.0
CE1 A:HIS84 3.2 21.4 1.0
CB A:CYS74 3.4 39.9 1.0
CB A:CYS81 3.5 31.8 1.0
N A:CYS74 3.7 39.9 1.0
CG A:HIS84 4.0 21.4 1.0
CA A:CYS74 4.1 39.9 1.0
ND1 A:HIS84 4.2 21.4 1.0
CA A:CYS81 4.2 31.8 1.0
CB A:THR73 4.3 28.6 1.0
CA A:CYS71 4.5 31.2 1.0
CD A:PRO82 4.5 23.4 1.0
C A:THR73 4.7 28.6 1.0
N A:GLY83 4.7 17.7 1.0
C A:CYS74 4.8 39.9 1.0
C A:CYS81 4.9 31.8 1.0
CA A:THR73 4.9 28.6 1.0
OG1 A:THR73 4.9 28.6 1.0
N A:PRO82 4.9 23.4 1.0
N A:THR73 4.9 28.6 1.0
C A:CYS71 4.9 31.2 1.0
N A:ALA75 5.0 37.6 1.0

Zinc binding site 2 out of 10 in 7nvu

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Zinc binding site 2 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:107.2
occ:1.00
 SG A:CYS114 2.3 67.8 1.0
SG A:CYS184 2.3 79.4 1.0
SG A:CYS154 2.3 79.9 1.0
SG A:CYS111 2.4 64.5 1.0
O A:GLY183 2.9 74.9 1.0
CB A:CYS114 2.9 67.8 1.0
N A:CYS114 3.3 67.8 1.0
CB A:CYS154 3.4 79.9 1.0
CB A:CYS111 3.5 64.5 1.0
CA A:CYS114 3.7 67.8 1.0
O A:CYS184 3.9 79.4 1.0
CB A:CYS184 4.0 79.4 1.0
C A:GLY183 4.0 74.9 1.0
C A:CYS184 4.4 79.4 1.0
C A:PHE113 4.4 60.9 1.0
CB A:PHE113 4.5 60.9 1.0
CA A:CYS184 4.6 79.4 1.0
N A:CYS184 4.7 79.4 1.0
CA A:CYS154 4.8 79.9 1.0
N A:GLY183 4.8 74.9 1.0
CA A:PHE113 4.8 60.9 1.0
CA A:CYS111 4.9 64.5 1.0
N A:PHE113 4.9 60.9 1.0
CA A:GLY183 5.0 74.9 1.0
NE2 A:GLN188 5.0 70.5 1.0
C A:CYS114 5.0 67.8 1.0

Zinc binding site 3 out of 10 in 7nvu

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Zinc binding site 3 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:68.8
occ:1.00
 SG B:CYS1122 2.3 31.2 1.0
SG B:CYS1119 2.3 19.8 1.0
SG B:CYS1137 2.3 43.7 1.0
SG B:CYS1140 2.3 49.8 1.0
CB B:CYS1119 2.9 19.8 1.0
CB B:CYS1140 3.2 49.8 1.0
CB B:CYS1122 3.3 31.2 1.0
CB B:CYS1137 3.6 43.7 1.0
N B:CYS1122 3.6 31.2 1.0
O B:CYS1122 3.9 31.2 1.0
CA B:CYS1122 3.9 31.2 1.0
N B:CYS1140 4.3 49.8 1.0
C B:CYS1122 4.3 31.2 1.0
CA B:CYS1140 4.3 49.8 1.0
OD1 B:ASN1142 4.4 51.1 1.0
CA B:CYS1119 4.4 19.8 1.0
CB B:LEU1121 4.7 38.9 1.0
C B:LEU1121 4.7 38.9 1.0
C B:CYS1119 4.9 19.8 1.0
ND2 B:ASN1142 4.9 51.1 1.0
CA B:CYS1137 4.9 43.7 1.0
O B:CYS1137 5.0 43.7 1.0

Zinc binding site 4 out of 10 in 7nvu

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Zinc binding site 4 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:59.9
occ:1.00
 SG C:CYS90 2.2 51.0 1.0
SG C:CYS94 2.3 25.3 1.0
SG C:CYS88 2.3 30.8 1.0
SG C:CYS97 2.4 23.6 1.0
CB C:CYS90 3.1 51.0 1.0
CB C:CYS94 3.3 25.3 1.0
CB C:CYS88 3.3 30.8 1.0
CB C:CYS97 3.4 23.6 1.0
N C:CYS94 3.7 25.3 1.0
CA C:CYS94 4.0 25.3 1.0
N C:CYS97 4.1 23.6 1.0
N C:CYS90 4.2 51.0 1.0
CA C:CYS90 4.2 51.0 1.0
C C:PHE93 4.3 25.8 1.0
CA C:CYS97 4.4 23.6 1.0
O C:CYS94 4.4 25.3 1.0
C C:CYS94 4.4 25.3 1.0
CA C:CYS88 4.6 30.8 1.0
O C:GLU91 4.7 50.9 1.0
C C:GLU96 4.7 27.6 1.0
CA C:PHE93 4.8 25.8 1.0
O C:PHE93 4.8 25.8 1.0
CB C:GLU96 4.8 27.6 1.0
C C:CYS88 4.8 30.8 1.0
C C:CYS90 4.9 51.0 1.0
N C:GLU96 4.9 27.6 1.0

Zinc binding site 5 out of 10 in 7nvu

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Zinc binding site 5 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:100.4
occ:1.00
 SG I:CYS17 2.2 76.7 1.0
CB I:CYS42 2.3 88.3 1.0
SG I:CYS20 2.3 83.4 1.0
SG I:CYS39 2.5 81.1 1.0
SG I:CYS42 2.6 88.3 1.0
CB I:CYS39 3.4 81.1 1.0
CB I:CYS20 3.5 83.4 1.0
CB I:CYS17 3.6 76.7 1.0
N I:CYS20 3.7 83.4 1.0
CA I:CYS42 3.7 88.3 1.0
CA I:CYS20 4.0 83.4 1.0
N I:CYS42 4.2 88.3 1.0
CB I:ASN22 4.3 68.5 1.0
C I:CYS20 4.4 83.4 1.0
CB I:GLU19 4.5 86.6 1.0
N I:ASN22 4.5 68.5 1.0
N I:ASN21 4.6 76.8 1.0
C I:CYS42 4.7 88.3 1.0
CB I:TYR44 4.8 81.4 1.0
C I:GLU19 4.8 86.6 1.0
ND2 I:ASN22 4.8 68.5 1.0
C I:ASN41 4.8 85.4 1.0
CA I:CYS39 4.8 81.1 1.0
CA I:CYS17 4.9 76.7 1.0
CA I:ASN22 5.0 68.5 1.0

Zinc binding site 6 out of 10 in 7nvu

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Zinc binding site 6 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:89.5
occ:1.00
 SG I:CYS89 2.3 76.3 1.0
SG I:CYS119 2.3 63.4 1.0
SG I:CYS114 2.3 48.4 1.0
SG I:CYS86 2.3 60.4 1.0
CB I:CYS86 2.9 60.4 1.0
CB I:CYS114 3.1 48.4 1.0
CB I:CYS89 3.5 76.3 1.0
CB I:CYS119 3.5 63.4 1.0
N I:CYS89 3.9 76.3 1.0
O I:CYS119 4.2 63.4 1.0
CA I:CYS89 4.2 76.3 1.0
CB I:HIS91 4.4 58.6 1.0
CB I:HIS121 4.4 48.7 1.0
CB I:ALA116 4.4 58.4 1.0
CA I:CYS86 4.4 60.4 1.0
CA I:CYS114 4.5 48.4 1.0
N I:HIS91 4.7 58.6 1.0
CA I:CYS119 4.8 63.4 1.0
C I:CYS119 4.8 63.4 1.0
N I:GLY90 4.8 74.9 1.0
C I:CYS89 4.8 76.3 1.0
CB I:LYS88 4.9 62.1 1.0

Zinc binding site 7 out of 10 in 7nvu

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Zinc binding site 7 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:31.2
occ:1.00
 SG J:CYS45 2.2 20.7 1.0
SG J:CYS10 2.3 20.7 1.0
SG J:CYS44 2.3 2.8 1.0
SG J:CYS7 2.3 20.7 1.0
CB J:CYS7 3.2 20.7 1.0
N J:CYS45 3.3 20.7 1.0
CB J:CYS10 3.5 20.7 1.0
CB J:CYS45 3.6 20.7 1.0
CB J:CYS44 3.6 2.8 1.0
CA J:CYS45 3.7 20.7 1.0
C J:CYS44 3.8 2.8 1.0
N J:CYS10 3.8 20.7 1.0
NE J:ARG42 4.0 2.9 1.0
CA J:CYS10 4.2 20.7 1.0
CA J:CYS44 4.3 2.8 1.0
O J:CYS44 4.4 2.8 1.0
NH2 J:ARG42 4.5 2.9 1.0
CB J:THR9 4.5 20.7 1.0
CB J:LYS12 4.6 20.7 1.0
CA J:CYS7 4.6 20.7 1.0
CB J:ARG42 4.7 2.9 1.0
CZ J:ARG42 4.8 2.9 1.0
N J:GLY11 4.9 20.7 1.0
C J:THR9 4.9 20.7 1.0
C J:CYS10 4.9 20.7 1.0
N J:LYS12 4.9 20.7 1.0
CD J:ARG42 4.9 2.9 1.0
N J:CYS44 4.9 2.8 1.0
N J:THR9 5.0 20.7 1.0

Zinc binding site 8 out of 10 in 7nvu

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Zinc binding site 8 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


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 Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:78.3
occ:1.00
 SG L:CYS36 2.2 31.2 1.0
SG L:CYS22 2.3 38.2 1.0
SG L:CYS39 2.3 47.9 1.0
SG L:CYS19 2.3 31.6 1.0
CB L:CYS19 2.9 31.6 1.0
CB L:CYS36 3.1 31.2 1.0
CB L:CYS22 3.2 38.2 1.0
CB L:CYS39 3.7 47.9 1.0
N L:CYS22 3.8 38.2 1.0
CA L:CYS22 4.0 38.2 1.0
N L:CYS39 4.1 47.9 1.0
CB L:TYR41 4.2 26.3 1.0
CA L:CYS39 4.4 47.9 1.0
CA L:CYS19 4.4 31.6 1.0
OG1 L:THR24 4.5 39.9 1.0
C L:CYS22 4.6 38.2 1.0
CA L:CYS36 4.6 31.2 1.0
N L:TYR41 4.6 26.3 1.0
N L:HIS23 4.7 45.0 1.0
CB L:THR24 4.7 39.9 1.0
N L:GLY40 4.8 34.6 1.0
C L:CYS39 4.9 47.9 1.0
C L:GLU21 5.0 39.9 1.0

Zinc binding site 9 out of 10 in 7nvu

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Zinc binding site 9 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:90.7
occ:1.00
 CE1 M:HIS18 1.8 75.4 1.0
NE2 M:HIS18 2.2 75.4 1.0
SG M:CYS37 2.2 54.5 1.0
ND1 M:HIS18 2.3 75.4 1.0
SG M:CYS34 2.3 46.8 1.0
SG M:CYS15 2.4 62.9 1.0
CD2 M:HIS18 2.9 75.4 1.0
CG M:HIS18 2.9 75.4 1.0
CB M:CYS34 3.1 46.8 1.0
CB M:CYS37 3.1 54.5 1.0
CB M:CYS15 3.5 62.9 1.0
N M:CYS37 3.6 54.5 1.0
CA M:CYS37 3.9 54.5 1.0
CB M:HIS18 4.1 75.4 1.0
CB M:LEU39 4.4 34.2 1.0
CA M:CYS34 4.6 46.8 1.0
C M:CYS37 4.6 54.5 1.0
CB M:GLU36 4.6 59.8 1.0
N M:GLY38 4.7 38.6 1.0
N M:LEU39 4.7 34.2 1.0
C M:GLU36 4.7 59.8 1.0
CA M:CYS15 4.9 62.9 1.0

Zinc binding site 10 out of 10 in 7nvu

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Zinc binding site 10 out of 10 in the Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rna Polymerase II Core Pre-Initiation Complex with Open Promoter Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn501

b:129.7
occ:1.00
 CB W:CYS154 1.8 114.8 1.0
SG W:CYS157 2.3 112.8 1.0
SG W:CYS154 2.3 114.8 1.0
SG W:CYS129 2.3 113.6 1.0
CB W:CYS129 2.9 113.6 1.0
CA W:CYS154 3.3 114.8 1.0
CE2 W:PHE136 3.4 119.3 1.0
N W:CYS154 3.9 114.8 1.0
CZ W:PHE136 4.0 119.3 1.0
CB W:CYS157 4.1 112.8 1.0
C W:CYS154 4.1 114.8 1.0
CG2 W:THR159 4.1 111.7 1.0
O W:CYS154 4.3 114.8 1.0
CD2 W:PHE136 4.3 119.3 1.0
N W:CYS157 4.4 112.8 1.0
CA W:CYS129 4.4 113.6 1.0
SG W:CYS132 4.5 106.7 1.0
CB W:CYS132 4.7 106.7 1.0
CA W:CYS157 4.7 112.8 1.0
N W:HIS158 4.8 114.2 1.0
O W:THR159 5.0 111.7 1.0
N W:THR155 5.0 116.0 1.0

Reference:

S.Aibara, S.Schilbach, P.Cramer. Structures of Mammalian Rna Polymerase II Pre-Initiation Complexes. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902107
DOI: 10.1038/S41586-021-03554-8
Page generated: Fri Aug 22 02:39:35 2025

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