Zinc in PDB 8s55: Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)

Enzymatic activity of Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)

All present enzymatic activity of Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure):
2.7.7.6; 3.6.4.12;

Other elements in 8s55:

The structure of Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) (pdb code 8s55). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure), PDB code: 8s55:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 8s55

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Zinc binding site 1 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:205.8
occ:1.00
 NE2 A:HIS84 2.1 162.6 1.0
SG A:CYS81 2.3 161.1 1.0
SG A:CYS71 2.3 171.1 1.0
SG A:CYS74 2.3 166.5 1.0
CE1 A:HIS84 3.0 162.6 1.0
CD2 A:HIS84 3.0 162.6 1.0
CB A:CYS71 3.0 171.1 1.0
CB A:CYS81 3.5 161.1 1.0
ND1 A:HIS84 4.0 162.6 1.0
CB A:CYS74 4.1 166.5 1.0
CG A:HIS84 4.1 162.6 1.0
OG1 A:THR73 4.2 167.2 1.0
CA A:CYS81 4.4 161.1 1.0
CA A:GLY63 4.4 166.8 1.0
CA A:CYS71 4.5 171.1 1.0
C A:GLY63 4.5 166.8 1.0
CA A:GLY76 4.6 170.1 1.0
O A:GLY63 4.7 166.8 1.0
N A:CYS74 4.7 166.5 1.0
CA A:CYS74 4.8 166.5 1.0
O A:CYS74 4.9 166.5 1.0
C A:CYS74 4.9 166.5 1.0
O A:GLN62 5.0 167.4 1.0
C A:CYS81 5.0 161.1 1.0

Zinc binding site 2 out of 9 in 8s55

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Zinc binding site 2 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:249.3
occ:1.00
 CB A:CYS114 2.0 212.9 1.0
SG A:CYS114 2.3 212.9 1.0
SG A:CYS184 2.3 226.1 1.0
SG A:CYS111 2.3 213.0 1.0
CB A:CYS184 2.9 226.1 1.0
CA A:CYS114 3.4 212.9 1.0
CB A:CYS111 3.5 213.0 1.0
SG A:CYS154 3.6 222.4 1.0
O A:PHE112 3.9 207.8 1.0
O A:CYS184 4.0 226.1 1.0
N A:CYS114 4.0 212.9 1.0
CB A:CYS154 4.2 222.4 1.0
CA A:CYS184 4.3 226.1 1.0
C A:CYS114 4.5 212.9 1.0
C A:CYS184 4.6 226.1 1.0
C A:CYS111 4.6 213.0 1.0
C A:PHE113 4.6 209.8 1.0
CA A:CYS111 4.7 213.0 1.0
O A:PHE113 4.8 209.8 1.0
O A:GLY183 4.8 229.4 1.0
O A:CYS111 4.8 213.0 1.0
C A:PHE112 4.9 207.8 1.0
N A:PHE112 5.0 207.8 1.0

Zinc binding site 3 out of 9 in 8s55

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Zinc binding site 3 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:215.7
occ:1.00
 SG B:CYS1122 2.3 167.9 1.0
SG B:CYS1140 2.3 181.9 1.0
SG B:CYS1137 2.3 174.4 1.0
SG B:CYS1119 2.3 170.3 1.0
CB B:CYS1119 2.8 170.3 1.0
CB B:CYS1140 3.5 181.9 1.0
CB B:CYS1122 3.5 167.9 1.0
CB B:CYS1137 3.6 174.4 1.0
N B:CYS1122 3.9 167.9 1.0
O B:CYS1122 4.1 167.9 1.0
CA B:CYS1122 4.2 167.9 1.0
CA B:CYS1119 4.3 170.3 1.0
C B:CYS1122 4.4 167.9 1.0
N B:CYS1140 4.6 181.9 1.0
CA B:CYS1140 4.6 181.9 1.0
O B:ARG1138 4.8 172.3 1.0
C B:CYS1119 4.9 170.3 1.0
CA B:CYS1137 4.9 174.4 1.0

Zinc binding site 4 out of 9 in 8s55

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Zinc binding site 4 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:210.3
occ:1.00
 CB C:CYS90 2.0 164.6 1.0
SG C:CYS97 2.3 145.8 1.0
SG C:CYS94 2.3 150.6 1.0
SG C:CYS90 2.4 164.6 1.0
SG C:CYS88 2.4 156.7 1.0
CB C:CYS97 3.3 145.8 1.0
CB C:CYS88 3.4 156.7 1.0
CB C:CYS94 3.4 150.6 1.0
CA C:CYS90 3.5 164.6 1.0
N C:CYS94 3.7 150.6 1.0
CA C:CYS94 4.0 150.6 1.0
N C:CYS90 4.0 164.6 1.0
N C:CYS97 4.2 145.8 1.0
O C:CYS94 4.3 150.6 1.0
CA C:CYS97 4.4 145.8 1.0
C C:CYS90 4.4 164.6 1.0
C C:CYS94 4.5 150.6 1.0
C C:PHE93 4.5 143.8 1.0
O C:CYS90 4.7 164.6 1.0
CA C:CYS88 4.7 156.7 1.0
CA C:PHE93 4.8 143.8 1.0
C C:CYS88 4.9 156.7 1.0
C C:GLU96 5.0 147.2 1.0

Zinc binding site 5 out of 9 in 8s55

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Zinc binding site 5 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:271.6
occ:1.00
 SG I:CYS42 2.3 246.7 1.0
SG I:CYS39 2.3 239.1 1.0
CB I:CYS42 2.4 246.7 1.0
N I:CYS42 2.7 246.7 1.0
SG I:CYS20 3.0 232.7 1.0
C I:ASN41 3.0 235.8 1.0
CA I:CYS42 3.1 246.7 1.0
CB I:ASN41 3.3 235.8 1.0
O I:ASN41 3.5 235.8 1.0
CA I:ASN41 3.6 235.8 1.0
CB I:CYS39 3.8 239.1 1.0
CB I:ASN22 3.8 225.3 1.0
ND2 I:ASN41 3.9 235.8 1.0
CB I:CYS20 4.0 232.7 1.0
N I:ASN41 4.1 235.8 1.0
SG I:CYS17 4.1 227.7 1.0
CG I:ASN41 4.1 235.8 1.0
C I:CYS42 4.2 246.7 1.0
CG I:ASN22 4.4 225.3 1.0
ND2 I:ASN22 4.4 225.3 1.0
O I:CYS42 4.8 246.7 1.0
N I:ASP43 5.0 244.0 1.0

Zinc binding site 6 out of 9 in 8s55

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Zinc binding site 6 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:220.6
occ:1.00
 SG I:CYS119 2.3 183.8 1.0
SG I:CYS89 2.3 182.7 1.0
SG I:CYS86 2.3 181.1 1.0
SG I:CYS114 2.3 175.6 1.0
CB I:CYS86 2.9 181.1 1.0
CB I:CYS114 3.1 175.6 1.0
CB I:CYS119 3.3 183.8 1.0
O I:CYS89 3.9 182.7 1.0
CB I:CYS89 3.9 182.7 1.0
N I:CYS89 4.1 182.7 1.0
CA I:CYS86 4.4 181.1 1.0
CA I:CYS89 4.4 182.7 1.0
C I:CYS89 4.5 182.7 1.0
CB I:HIS91 4.5 177.9 1.0
CA I:CYS114 4.6 175.6 1.0
CB I:ALA116 4.7 178.6 1.0
N I:GLY120 4.7 174.7 1.0
CA I:CYS119 4.7 183.8 1.0
C I:CYS86 4.9 181.1 1.0

Zinc binding site 7 out of 9 in 8s55

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Zinc binding site 7 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:160.8
occ:1.00
 SG J:CYS44 2.3 128.5 1.0
SG J:CYS45 2.3 130.3 1.0
SG J:CYS10 2.3 125.9 1.0
SG J:CYS7 2.3 126.1 1.0
CB J:CYS7 3.1 126.1 1.0
OG1 J:THR9 3.2 121.4 1.0
N J:CYS45 3.4 130.3 1.0
CB J:CYS44 3.7 128.5 1.0
CB J:CYS45 3.7 130.3 1.0
CB J:CYS10 3.7 125.9 1.0
CA J:CYS45 3.8 130.3 1.0
C J:CYS44 3.9 128.5 1.0
NH2 J:ARG42 3.9 129.1 1.0
N J:CYS10 4.0 125.9 1.0
CA J:CYS44 4.4 128.5 1.0
CA J:CYS10 4.4 125.9 1.0
N J:GLY11 4.5 122.7 1.0
CA J:CYS7 4.6 126.1 1.0
O J:CYS44 4.6 128.5 1.0
CB J:THR9 4.7 121.4 1.0
N J:LYS12 4.9 125.9 1.0
CB J:LYS12 4.9 125.9 1.0
N J:CYS44 5.0 128.5 1.0
C J:CYS7 5.0 126.1 1.0

Zinc binding site 8 out of 9 in 8s55

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Zinc binding site 8 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:215.5
occ:1.00
 SG L:CYS22 2.3 181.8 1.0
SG L:CYS36 2.3 179.5 1.0
SG L:CYS19 2.3 174.7 1.0
SG L:CYS39 2.3 182.9 1.0
CB L:CYS39 3.2 182.9 1.0
CB L:CYS19 3.6 174.7 1.0
N L:CYS39 3.6 182.9 1.0
CB L:CYS22 3.7 181.8 1.0
CB L:CYS36 3.8 179.5 1.0
CA L:CYS39 3.9 182.9 1.0
N L:CYS22 4.2 181.8 1.0
N L:GLY40 4.3 176.1 1.0
CA L:CYS22 4.4 181.8 1.0
C L:CYS39 4.5 182.9 1.0
CB L:GLU38 4.6 184.6 1.0
N L:HIS23 4.7 171.9 1.0
C L:GLU38 4.7 184.6 1.0
C L:CYS22 4.8 181.8 1.0
OG1 L:THR24 4.8 174.4 1.0
N L:TYR41 4.9 173.5 1.0
CA L:CYS19 4.9 174.7 1.0

Zinc binding site 9 out of 9 in 8s55

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Zinc binding site 9 out of 9 in the Rna Polymerase II Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure)


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 Early Elongation Complex Bound to Tfiie and Tfiif - State A (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn501

b:377.4
occ:1.00
 CB W:CYS154 1.6 352.1 1.0
SG W:CYS129 2.3 352.3 1.0
SG W:CYS157 2.3 346.5 1.0
SG W:CYS154 2.3 352.1 1.0
CB W:CYS129 2.8 352.3 1.0
CE2 W:PHE136 3.1 344.4 1.0
CA W:CYS154 3.1 352.1 1.0
N W:CYS154 3.7 352.1 1.0
CZ W:PHE136 3.8 344.4 1.0
CD2 W:PHE136 4.0 344.4 1.0
C W:CYS154 4.0 352.1 1.0
SG W:CYS132 4.1 349.4 1.0
CB W:CYS157 4.1 346.5 1.0
CG2 W:THR159 4.2 343.9 1.0
CA W:CYS129 4.3 352.3 1.0
O W:CYS154 4.4 352.1 1.0
N W:CYS157 4.5 346.5 1.0
CB W:CYS132 4.7 349.4 1.0
CA W:CYS157 4.8 346.5 1.0
O W:THR159 4.9 343.9 1.0
N W:HIS158 4.9 337.3 1.0
N W:THR155 4.9 338.5 1.0
N W:CYS129 5.0 352.3 1.0
C W:ARG153 5.0 342.6 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 10:48:37 2024

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