Zinc in PDB 8s5n: Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt

Enzymatic activity of Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt

All present enzymatic activity of Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt:
2.3.1.48; 2.7.7.6; 3.6.4.12;

Other elements in 8s5n:

The structure of Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt 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 Initially Transcribing Complex with An Ordered Rna of 12 Nt (pdb code 8s5n). 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 Initially Transcribing Complex with An Ordered Rna of 12 Nt, PDB code: 8s5n:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8s5n

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Zinc binding site 1 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:148.3
occ:1.00
 CE1 A:HIS84 1.3 60.0 1.0
ND1 A:HIS84 2.2 60.0 1.0
SG A:CYS74 2.3 66.5 1.0
SG A:CYS81 2.3 52.8 1.0
SG A:CYS71 2.3 66.9 1.0
NE2 A:HIS84 2.4 60.0 1.0
CB A:CYS71 3.2 66.9 1.0
CG A:HIS84 3.4 60.0 1.0
CD2 A:HIS84 3.4 60.0 1.0
CB A:CYS81 3.5 52.8 1.0
CB A:CYS74 3.9 66.5 1.0
N A:CYS74 4.5 66.5 1.0
CA A:CYS81 4.5 52.8 1.0
CA A:GLY63 4.7 54.8 1.0
CB A:HIS84 4.7 60.0 1.0
CA A:CYS71 4.7 66.9 1.0
CA A:CYS74 4.8 66.5 1.0
N A:HIS84 4.8 60.0 1.0
N A:GLY83 4.8 50.9 1.0
N A:GLY63 4.8 54.8 1.0

Zinc binding site 2 out of 10 in 8s5n

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Zinc binding site 2 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:159.2
occ:1.00
 SG A:CYS114 2.3 87.3 1.0
SG A:CYS154 2.3 106.9 1.0
SG A:CYS184 2.3 94.0 1.0
SG A:CYS111 2.3 84.0 1.0
CB A:CYS114 2.9 87.3 1.0
CB A:CYS154 3.2 106.9 1.0
O A:GLY183 3.3 96.7 1.0
N A:CYS114 3.6 87.3 1.0
CB A:CYS111 3.6 84.0 1.0
CB A:CYS184 3.7 94.0 1.0
C A:GLY183 3.8 96.7 1.0
CA A:CYS114 3.8 87.3 1.0
CA A:GLY183 4.4 96.7 1.0
N A:CYS184 4.4 94.0 1.0
CA A:CYS184 4.6 94.0 1.0
C A:PHE113 4.7 79.9 1.0
CA A:CYS154 4.7 106.9 1.0
N A:GLY183 4.7 96.7 1.0
CB A:PHE113 4.9 79.9 1.0
N A:PHE113 4.9 79.9 1.0
CA A:CYS111 4.9 84.0 1.0

Zinc binding site 3 out of 10 in 8s5n

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Zinc binding site 3 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:119.0
occ:1.00
 SG B:CYS1122 2.3 73.5 1.0
SG B:CYS1137 2.3 82.3 1.0
SG B:CYS1140 2.3 86.0 1.0
SG B:CYS1119 2.3 71.3 1.0
CB B:CYS1119 3.0 71.3 1.0
CB B:CYS1140 3.3 86.0 1.0
CB B:CYS1122 3.6 73.5 1.0
CB B:CYS1137 3.7 82.3 1.0
N B:CYS1122 3.9 73.5 1.0
O B:CYS1122 4.1 73.5 1.0
CA B:CYS1122 4.2 73.5 1.0
N B:CYS1140 4.4 86.0 1.0
CA B:CYS1140 4.5 86.0 1.0
CA B:CYS1119 4.5 71.3 1.0
C B:CYS1122 4.6 73.5 1.0
CB B:LEU1121 5.0 71.2 1.0

Zinc binding site 4 out of 10 in 8s5n

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Zinc binding site 4 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:114.4
occ:1.00
 SG C:CYS97 2.3 58.6 1.0
SG C:CYS88 2.3 67.4 1.0
SG C:CYS90 2.3 69.9 1.0
SG C:CYS94 2.3 58.0 1.0
CB C:CYS90 2.8 69.9 1.0
CB C:CYS88 2.9 67.4 1.0
CB C:CYS94 3.8 58.0 1.0
N C:CYS90 3.8 69.9 1.0
CA C:CYS90 3.9 69.9 1.0
CB C:CYS97 4.0 58.6 1.0
N C:CYS97 4.1 58.6 1.0
N C:CYS94 4.3 58.0 1.0
CA C:CYS88 4.4 67.4 1.0
CA C:CYS97 4.6 58.6 1.0
CA C:CYS94 4.6 58.0 1.0
O C:CYS94 4.6 58.0 1.0
C C:CYS88 4.7 67.4 1.0
O C:CYS97 4.7 58.6 1.0
N C:THR89 4.7 72.8 1.0
CB C:GLU96 4.7 61.7 1.0
C C:CYS94 4.9 58.0 1.0
C C:GLU96 5.0 61.7 1.0
C C:CYS90 5.0 69.9 1.0
C C:CYS97 5.0 58.6 1.0

Zinc binding site 5 out of 10 in 8s5n

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Zinc binding site 5 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:142.3
occ:1.00
 SG I:CYS42 2.3 107.6 1.0
SG I:CYS20 2.3 104.3 1.0
SG I:CYS39 2.3 106.9 1.0
SG I:CYS17 2.3 110.6 1.0
CB I:CYS39 3.0 106.9 1.0
CB I:CYS17 3.7 110.6 1.0
OE1 I:GLU19 3.8 103.9 1.0
CB I:CYS42 3.9 107.6 1.0
CB I:CYS20 3.9 104.3 1.0
OD1 I:ASN41 4.0 105.2 1.0
N I:CYS20 4.0 104.3 1.0
CB I:ASN22 4.2 103.9 1.0
O I:ASN41 4.2 105.2 1.0
CA I:CYS20 4.4 104.3 1.0
N I:ASN22 4.4 103.9 1.0
CA I:CYS39 4.5 106.9 1.0
N I:ASN21 4.5 103.0 1.0
C I:ASN41 4.5 105.2 1.0
C I:CYS20 4.6 104.3 1.0
CA I:ASN22 4.8 103.9 1.0
N I:ASN41 4.9 105.2 1.0
CA I:CYS42 4.9 107.6 1.0
N I:ARG40 4.9 106.6 1.0
N I:CYS42 4.9 107.6 1.0
CB I:GLU19 5.0 103.9 1.0
CD I:GLU19 5.0 103.9 1.0

Zinc binding site 6 out of 10 in 8s5n

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Zinc binding site 6 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:125.3
occ:1.00
 SG I:CYS114 2.3 61.1 1.0
SG I:CYS89 2.3 88.0 1.0
SG I:CYS86 2.3 78.2 1.0
SG I:CYS119 2.3 82.9 1.0
CB I:CYS114 3.1 61.1 1.0
CB I:CYS86 3.2 78.2 1.0
CB I:CYS89 3.2 88.0 1.0
CB I:CYS119 3.6 82.9 1.0
N I:CYS89 3.7 88.0 1.0
CA I:CYS89 4.0 88.0 1.0
CB I:ALA116 4.4 75.2 1.0
O I:CYS119 4.5 82.9 1.0
CB I:HIS91 4.5 73.7 1.0
C I:CYS89 4.5 88.0 1.0
CA I:CYS114 4.6 61.1 1.0
CB I:HIS121 4.6 71.7 1.0
N I:GLY90 4.6 80.5 1.0
CA I:CYS86 4.7 78.2 1.0
N I:HIS91 4.7 73.7 1.0
CB I:LYS88 4.8 79.4 1.0
CA I:CYS119 4.9 82.9 1.0
C I:LYS88 4.9 79.4 1.0
C I:CYS119 5.0 82.9 1.0

Zinc binding site 7 out of 10 in 8s5n

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Zinc binding site 7 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:65.1
occ:1.00
 SG J:CYS10 2.3 33.4 1.0
SG J:CYS44 2.3 36.4 1.0
SG J:CYS45 2.3 36.6 1.0
SG J:CYS7 2.3 33.0 1.0
CB J:CYS7 3.0 33.0 1.0
N J:CYS45 3.2 36.6 1.0
CB J:CYS44 3.3 36.4 1.0
CB J:CYS10 3.5 33.4 1.0
CB J:CYS45 3.6 36.6 1.0
C J:CYS44 3.7 36.4 1.0
CA J:CYS45 3.7 36.6 1.0
NH1 J:ARG42 3.9 35.7 1.0
N J:CYS10 4.0 33.4 1.0
CA J:CYS44 4.1 36.4 1.0
CA J:CYS10 4.4 33.4 1.0
O J:CYS44 4.4 36.4 1.0
CA J:CYS7 4.5 33.0 1.0
CB J:LYS12 4.6 32.4 1.0
N J:GLY11 4.6 33.1 1.0
N J:CYS44 4.7 36.4 1.0
N J:LYS12 4.8 32.4 1.0
CB J:THR9 4.9 33.0 1.0

Zinc binding site 8 out of 10 in 8s5n

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Zinc binding site 8 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:88.2
occ:1.00
 SG L:CYS39 2.3 64.9 1.0
SG L:CYS36 2.3 65.2 1.0
SG L:CYS22 2.3 62.2 1.0
SG L:CYS19 2.3 58.1 1.0
CB L:CYS19 2.9 58.1 1.0
CB L:CYS36 3.3 65.2 1.0
CB L:CYS39 3.7 64.9 1.0
CB L:CYS22 3.8 62.2 1.0
N L:CYS22 3.9 62.2 1.0
N L:CYS39 4.1 64.9 1.0
OG1 L:THR24 4.2 60.0 1.0
CA L:CYS19 4.4 58.1 1.0
CA L:CYS22 4.4 62.2 1.0
CB L:TYR41 4.5 56.5 1.0
CA L:CYS39 4.5 64.9 1.0
CB L:GLU21 4.6 62.6 1.0
N L:GLU21 4.7 62.6 1.0
CA L:CYS36 4.7 65.2 1.0
N L:TYR41 4.9 56.5 1.0
C L:GLU21 4.9 62.6 1.0
N L:GLY40 4.9 61.1 1.0
C L:CYS39 4.9 64.9 1.0
N L:HIS23 5.0 61.1 1.0
CA L:GLU21 5.0 62.6 1.0

Zinc binding site 9 out of 10 in 8s5n

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Zinc binding site 9 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:160.8
occ:1.00
 ND1 M:HIS18 2.1 128.8 1.0
SG M:CYS15 2.3 122.7 1.0
SG M:CYS34 2.3 113.0 1.0
SG M:CYS37 2.3 118.5 1.0
CE1 M:HIS18 3.1 128.8 1.0
CG M:HIS18 3.2 128.8 1.0
CB M:CYS34 3.3 113.0 1.0
CB M:HIS18 3.5 128.8 1.0
CB M:CYS15 3.5 122.7 1.0
CB M:CYS37 3.9 118.5 1.0
N M:CYS37 4.1 118.5 1.0
O M:PRO16 4.1 118.1 1.0
NE2 M:HIS18 4.2 128.8 1.0
CD2 M:HIS18 4.3 128.8 1.0
CD1 M:LEU39 4.3 107.8 1.0
CA M:CYS37 4.5 118.5 1.0
CB M:GLU36 4.6 117.3 1.0
CA M:CYS34 4.7 113.0 1.0
N M:GLY38 4.8 112.1 1.0
CA M:HIS18 4.8 128.8 1.0
CA M:CYS15 4.8 122.7 1.0
C M:GLU36 4.9 117.3 1.0
N M:GLU36 4.9 117.3 1.0
CG M:LEU39 4.9 107.8 1.0
N M:HIS18 4.9 128.8 1.0
N M:LEU39 5.0 107.8 1.0
C M:CYS37 5.0 118.5 1.0

Zinc binding site 10 out of 10 in 8s5n

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Zinc binding site 10 out of 10 in the Rna Polymerase II Core Initially Transcribing Complex with An Ordered Rna of 12 Nt


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 Initially Transcribing Complex with An Ordered Rna of 12 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn501

b:253.3
occ:1.00
 CB W:CYS154 2.0 170.1 1.0
SG W:CYS129 2.3 268.0 1.0
SG W:CYS157 2.3 178.6 1.0
SG W:CYS154 2.3 170.1 1.0
CB W:CYS129 3.1 268.0 1.0
CE2 W:PHE136 3.4 184.4 1.0
CA W:CYS154 3.6 170.1 1.0
SG W:CYS132 3.9 300.8 1.0
CB W:CYS157 3.9 178.6 1.0
CZ W:PHE136 4.0 184.4 1.0
CD2 W:PHE136 4.2 184.4 1.0
N W:CYS154 4.2 170.1 1.0
N W:CYS157 4.2 178.6 1.0
C W:CYS154 4.3 170.1 1.0
CA W:CYS129 4.6 268.0 1.0
CA W:CYS157 4.7 178.6 1.0
O W:CYS154 4.7 170.1 1.0
OG1 W:THR159 4.9 183.6 1.0
N W:PHE156 4.9 158.9 1.0
CB W:PHE156 4.9 158.9 1.0

Reference:

Y.Zhan, F.Grabbe, E.Oberbeckmann, C.Dienemann, P.Cramer. Three-Step Mechanism of Promoter Escape By Rna Polymerase II To Be Published.
Page generated: Thu Oct 31 10:48:52 2024

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