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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Go back to Zinc Binding Sites List in 8s55
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy