Zinc in PDB 7ozo: Rna Polymerase II Dimer (Class 2)

Enzymatic activity of Rna Polymerase II Dimer (Class 2)

All present enzymatic activity of Rna Polymerase II Dimer (Class 2):
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Dimer (Class 2) (pdb code 7ozo). 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 Dimer (Class 2), PDB code: 7ozo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7ozo

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Zinc binding site 1 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:144.1
occ:1.00
 SG C:CYS90 2.3 96.2 1.0
SG C:CYS94 2.3 91.0 1.0
SG C:CYS97 2.3 91.7 1.0
SG C:CYS88 2.3 88.4 1.0
CB C:CYS97 3.0 91.7 1.0
CB C:CYS90 3.2 96.2 1.0
CB C:CYS94 3.4 91.0 1.0
CB C:CYS88 3.5 88.4 1.0
N C:CYS97 3.9 91.7 1.0
OE1 C:GLU96 3.9 92.0 1.0
CA C:CYS97 4.0 91.7 1.0
N C:CYS94 4.1 91.0 1.0
CA C:CYS94 4.3 91.0 1.0
N C:CYS90 4.3 96.2 1.0
CA C:CYS90 4.3 96.2 1.0
O C:GLU92 4.6 94.4 1.0
C C:GLU96 4.7 92.0 1.0
CA C:CYS88 4.8 88.4 1.0
O C:CYS94 4.8 91.0 1.0
C C:CYS94 4.8 91.0 1.0
N C:THR89 4.8 96.3 1.0
C C:CYS97 4.9 91.7 1.0
CB C:GLU96 4.9 92.0 1.0

Zinc binding site 2 out of 10 in 7ozo

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Zinc binding site 2 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:156.7
occ:1.00
 SG I:CYS17 2.3 113.6 1.0
SG I:CYS20 2.3 113.4 1.0
SG I:CYS42 2.3 115.5 1.0
SG I:CYS39 2.3 119.6 1.0
CB I:CYS39 3.0 119.6 1.0
CB I:CYS42 3.5 115.5 1.0
CB I:CYS17 3.8 113.6 1.0
OD1 I:ASN41 3.9 114.5 1.0
CB I:ASN22 3.9 109.0 1.0
CB I:CYS20 4.0 113.4 1.0
ND2 I:ASN41 4.0 114.5 1.0
N I:CYS20 4.2 113.4 1.0
N I:CYS42 4.3 115.5 1.0
CG I:ASN41 4.3 114.5 1.0
N I:ASN22 4.4 109.0 1.0
CA I:CYS42 4.4 115.5 1.0
CA I:CYS39 4.5 119.6 1.0
CA I:CYS20 4.5 113.4 1.0
CA I:ASN22 4.6 109.0 1.0
O I:CYS42 4.7 115.5 1.0
N I:ASN21 4.7 104.7 1.0
CG I:ASN22 4.7 109.0 1.0
C I:CYS20 4.8 113.4 1.0
CB I:GLU19 4.9 115.2 1.0
C I:CYS42 4.9 115.5 1.0
ND2 I:ASN22 5.0 109.0 1.0
O I:ASN22 5.0 109.0 1.0
CD2 I:LEU24 5.0 114.5 1.0

Zinc binding site 3 out of 10 in 7ozo

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Zinc binding site 3 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:148.9
occ:1.00
 SG I:CYS119 2.3 98.3 1.0
SG I:CYS114 2.3 90.3 1.0
SG I:CYS86 2.3 96.9 1.0
SG I:CYS89 2.3 99.6 1.0
CB I:CYS114 3.0 90.3 1.0
CB I:CYS89 3.0 99.6 1.0
CB I:CYS119 3.0 98.3 1.0
CB I:CYS86 3.2 96.9 1.0
N I:CYS89 4.1 99.6 1.0
CA I:CYS89 4.1 99.6 1.0
CB I:HIS121 4.4 88.1 1.0
CB I:ALA116 4.4 94.2 1.0
CA I:CYS114 4.4 90.3 1.0
CG I:LYS88 4.4 96.1 1.0
CA I:CYS119 4.5 98.3 1.0
CA I:CYS86 4.7 96.9 1.0
C I:LYS88 4.8 96.1 1.0

Zinc binding site 4 out of 10 in 7ozo

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Zinc binding site 4 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:88.0
occ:1.00
 SG J:CYS45 2.3 47.5 1.0
SG J:CYS44 2.3 44.3 1.0
SG J:CYS10 2.3 45.3 1.0
SG J:CYS7 2.3 53.1 1.0
CB J:CYS7 3.0 53.1 1.0
N J:CYS45 3.4 47.5 1.0
CB J:CYS44 3.6 44.3 1.0
CB J:CYS45 3.7 47.5 1.0
CA J:CYS45 3.8 47.5 1.0
C J:CYS44 3.9 44.3 1.0
CB J:CYS10 3.9 45.3 1.0
N J:CYS10 4.1 45.3 1.0
CA J:CYS44 4.3 44.3 1.0
CB J:THR9 4.4 40.5 1.0
O J:CYS44 4.5 44.3 1.0
CA J:CYS7 4.5 53.1 1.0
CA J:CYS10 4.6 45.3 1.0
NH2 J:ARG42 4.6 48.3 1.0
CB J:LYS12 4.7 56.4 1.0
CB J:ARG42 4.8 48.3 1.0
N J:GLY11 4.8 52.2 1.0
CZ J:ARG42 4.8 48.3 1.0
N J:LYS12 4.9 56.4 1.0
OG1 J:THR9 5.0 40.5 1.0
N J:CYS44 5.0 44.3 1.0

Zinc binding site 5 out of 10 in 7ozo

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Zinc binding site 5 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:217.9
occ:1.00
 SG L:CYS22 2.3 128.0 1.0
SG L:CYS36 2.3 126.3 1.0
SG L:CYS39 2.3 128.8 1.0
SG L:CYS19 2.3 121.8 1.0
CB L:CYS19 2.9 121.8 1.0
CB L:CYS22 3.3 128.0 1.0
CB L:CYS36 3.3 126.3 1.0
CB L:CYS39 3.4 128.8 1.0
N L:CYS22 3.7 128.0 1.0
CA L:CYS22 4.0 128.0 1.0
N L:CYS39 4.2 128.8 1.0
OG1 L:THR24 4.2 121.0 1.0
OE1 L:GLU38 4.3 129.5 1.0
CA L:CYS19 4.4 121.8 1.0
CA L:CYS39 4.4 128.8 1.0
CB L:GLU38 4.6 129.5 1.0
CB L:GLU21 4.7 122.7 1.0
C L:GLU38 4.7 129.5 1.0
CA L:CYS36 4.8 126.3 1.0
C L:GLU21 4.8 122.7 1.0
C L:CYS22 4.8 128.0 1.0
N L:HIS23 4.8 118.8 1.0
CB L:TYR41 4.9 119.6 1.0
N L:GLU21 4.9 122.7 1.0
C L:CYS19 5.0 121.8 1.0

Zinc binding site 6 out of 10 in 7ozo

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Zinc binding site 6 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn301

b:144.1
occ:1.00
 SG O:CYS90 2.3 94.8 1.0
SG O:CYS94 2.3 91.4 1.0
SG O:CYS97 2.3 87.5 1.0
SG O:CYS88 2.3 89.3 1.0
CB O:CYS97 3.0 87.5 1.0
CB O:CYS90 3.2 94.8 1.0
CB O:CYS94 3.4 91.4 1.0
CB O:CYS88 3.5 89.3 1.0
N O:CYS97 3.9 87.5 1.0
OE1 O:GLU96 3.9 89.5 1.0
CA O:CYS97 4.0 87.5 1.0
N O:CYS94 4.1 91.4 1.0
CA O:CYS94 4.3 91.4 1.0
N O:CYS90 4.3 94.8 1.0
CA O:CYS90 4.3 94.8 1.0
O O:GLU92 4.6 94.0 1.0
C O:GLU96 4.7 89.5 1.0
CA O:CYS88 4.8 89.3 1.0
O O:CYS94 4.8 91.4 1.0
C O:CYS94 4.8 91.4 1.0
N O:THR89 4.8 95.7 1.0
C O:CYS97 4.9 87.5 1.0
CB O:GLU96 4.9 89.5 1.0

Zinc binding site 7 out of 10 in 7ozo

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Zinc binding site 7 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn201

b:154.1
occ:1.00
 SG U:CYS17 2.3 114.4 1.0
SG U:CYS42 2.3 119.1 1.0
SG U:CYS20 2.3 114.0 1.0
SG U:CYS39 2.3 117.4 1.0
CB U:CYS39 3.0 117.4 1.0
CB U:CYS42 3.5 119.1 1.0
CB U:CYS17 3.8 114.4 1.0
OD1 U:ASN41 3.9 113.5 1.0
CB U:ASN22 3.9 110.1 1.0
CB U:CYS20 4.0 114.0 1.0
ND2 U:ASN41 4.0 113.5 1.0
N U:CYS20 4.2 114.0 1.0
N U:CYS42 4.3 119.1 1.0
CG U:ASN41 4.3 113.5 1.0
N U:ASN22 4.4 110.1 1.0
CA U:CYS42 4.4 119.1 1.0
CA U:CYS39 4.5 117.4 1.0
CA U:CYS20 4.5 114.0 1.0
CA U:ASN22 4.7 110.1 1.0
O U:CYS42 4.7 119.1 1.0
N U:ASN21 4.7 104.6 1.0
CG U:ASN22 4.7 110.1 1.0
C U:CYS20 4.8 114.0 1.0
CB U:GLU19 4.9 115.4 1.0
C U:CYS42 4.9 119.1 1.0
O U:ASN22 5.0 110.1 1.0
ND2 U:ASN22 5.0 110.1 1.0
CD2 U:LEU24 5.0 115.5 1.0

Zinc binding site 8 out of 10 in 7ozo

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Zinc binding site 8 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn202

b:150.2
occ:1.00
 SG U:CYS119 2.3 99.3 1.0
SG U:CYS114 2.3 92.6 1.0
SG U:CYS89 2.3 100.4 1.0
SG U:CYS86 2.3 98.1 1.0
CB U:CYS114 3.0 92.6 1.0
CB U:CYS89 3.0 100.4 1.0
CB U:CYS119 3.0 99.3 1.0
CB U:CYS86 3.2 98.1 1.0
N U:CYS89 4.1 100.4 1.0
CA U:CYS89 4.1 100.4 1.0
CB U:HIS121 4.4 90.2 1.0
CB U:ALA116 4.4 95.8 1.0
CA U:CYS114 4.4 92.6 1.0
CG U:LYS88 4.4 99.9 1.0
CA U:CYS119 4.5 99.3 1.0
CA U:CYS86 4.7 98.1 1.0
C U:LYS88 4.8 99.9 1.0

Zinc binding site 9 out of 10 in 7ozo

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Zinc binding site 9 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn101

b:80.4
occ:1.00
 SG V:CYS45 2.3 47.6 1.0
SG V:CYS44 2.3 45.2 1.0
SG V:CYS10 2.3 45.1 1.0
SG V:CYS7 2.3 51.0 1.0
CB V:CYS7 3.0 51.0 1.0
N V:CYS45 3.4 47.6 1.0
CB V:CYS44 3.6 45.2 1.0
CB V:CYS45 3.7 47.6 1.0
CA V:CYS45 3.8 47.6 1.0
C V:CYS44 3.9 45.2 1.0
CB V:CYS10 3.9 45.1 1.0
N V:CYS10 4.1 45.1 1.0
CA V:CYS44 4.3 45.2 1.0
CB V:THR9 4.4 40.0 1.0
O V:CYS44 4.5 45.2 1.0
CA V:CYS7 4.5 51.0 1.0
CA V:CYS10 4.6 45.1 1.0
NH2 V:ARG42 4.6 47.9 1.0
CB V:LYS12 4.7 55.2 1.0
CB V:ARG42 4.8 47.9 1.0
N V:GLY11 4.8 51.2 1.0
CZ V:ARG42 4.8 47.9 1.0
N V:LYS12 4.9 55.2 1.0
OG1 V:THR9 5.0 40.0 1.0
N V:CYS44 5.0 45.2 1.0

Zinc binding site 10 out of 10 in 7ozo

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Zinc binding site 10 out of 10 in the Rna Polymerase II Dimer (Class 2)


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 Dimer (Class 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Zn101

b:207.2
occ:1.00
 SG X:CYS22 2.3 126.5 1.0
SG X:CYS36 2.3 125.8 1.0
SG X:CYS39 2.3 125.6 1.0
SG X:CYS19 2.3 118.9 1.0
CB X:CYS19 2.9 118.9 1.0
CB X:CYS22 3.3 126.5 1.0
CB X:CYS36 3.3 125.8 1.0
CB X:CYS39 3.4 125.6 1.0
N X:CYS22 3.7 126.5 1.0
CA X:CYS22 4.0 126.5 1.0
N X:CYS39 4.2 125.6 1.0
OG1 X:THR24 4.2 118.9 1.0
OE1 X:GLU38 4.3 128.4 1.0
CA X:CYS19 4.4 118.9 1.0
CA X:CYS39 4.4 125.6 1.0
CB X:GLU38 4.6 128.4 1.0
CB X:GLU21 4.7 121.6 1.0
C X:GLU38 4.7 128.4 1.0
CA X:CYS36 4.8 125.8 1.0
C X:GLU21 4.8 121.6 1.0
C X:CYS22 4.8 126.5 1.0
N X:HIS23 4.8 116.9 1.0
CB X:TYR41 4.9 119.2 1.0
N X:GLU21 4.9 121.6 1.0
C X:CYS19 5.0 118.9 1.0

Reference:

S.Aibara, C.Dienemann, P.Cramer. Structure of An Inactive Rna Polymerase II Dimer. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 34530439
DOI: 10.1093/NAR/GKAB783
Page generated: Wed Oct 30 08:55:00 2024

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