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Zinc in PDB 7b7u: Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2

Enzymatic activity of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2

All present enzymatic activity of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2:
2.7.7.6; 3.1.3.16;

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 (pdb code 7b7u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2, PDB code: 7b7u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7b7u

Go back to Zinc Binding Sites List in 7b7u
Zinc binding site 1 out of 6 in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:146.9
occ:1.00
 SG C:CYS94 2.3 99.7 1.0
SG C:CYS90 2.3 119.5 1.0
SG C:CYS88 2.3 114.2 1.0
SG C:CYS97 2.3 94.2 1.0
CB C:CYS97 3.1 94.2 1.0
CB C:CYS90 3.4 119.5 1.0
CB C:CYS88 3.5 114.2 1.0
CB C:CYS94 3.5 99.7 1.0
N C:CYS94 3.9 99.7 1.0
N C:CYS97 4.0 94.2 1.0
CA C:CYS97 4.1 94.2 1.0
CA C:CYS94 4.2 99.7 1.0
CA C:CYS90 4.5 119.5 1.0
N C:CYS90 4.5 119.5 1.0
O C:CYS94 4.6 99.7 1.0
C C:PHE93 4.7 101.5 1.0
C C:GLU96 4.7 96.9 1.0
O C:GLU91 4.7 117.0 1.0
CA C:CYS88 4.8 114.2 1.0
C C:CYS94 4.8 99.7 1.0
OE1 C:GLU96 4.9 96.9 1.0
C C:CYS88 4.9 114.2 1.0
C C:CYS97 4.9 94.2 1.0

Zinc binding site 2 out of 6 in 7b7u

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Zinc binding site 2 out of 6 in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:142.6
occ:1.00
 CB I:CYS39 1.9 111.1 1.0
SG I:CYS20 2.3 109.6 1.0
SG I:CYS17 2.3 108.8 1.0
SG I:CYS39 2.3 111.1 1.0
CB I:CYS17 2.7 108.8 1.0
CA I:CYS39 3.4 111.1 1.0
CB I:CYS42 3.7 106.5 1.0
CB I:CYS20 3.8 109.6 1.0
OD1 I:ASN41 3.9 106.0 1.0
N I:CYS39 4.0 111.1 1.0
C I:CYS39 4.2 111.1 1.0
CA I:CYS17 4.2 108.8 1.0
OE1 I:GLU19 4.2 111.1 1.0
O I:CYS39 4.4 111.1 1.0
SG I:CYS42 4.4 106.5 1.0
CD2 I:LEU24 4.4 103.5 1.0
CB I:TYR44 4.6 102.8 1.0
N I:CYS42 4.6 106.5 1.0
CA I:CYS42 4.7 106.5 1.0
CB I:ASN22 4.7 105.0 1.0
O I:MET23 4.7 105.6 1.0
O I:ASN22 5.0 105.0 1.0
N I:CYS17 5.0 108.8 1.0
CA I:CYS20 5.0 109.6 1.0

Zinc binding site 3 out of 6 in 7b7u

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Zinc binding site 3 out of 6 in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:149.2
occ:1.00
 CB I:CYS119 0.8 134.6 1.0
CA I:CYS119 2.0 134.6 1.0
SG I:CYS119 2.3 134.6 1.0
C I:CYS119 2.6 134.6 1.0
N I:GLY120 2.7 119.3 1.0
N I:CYS119 2.8 134.6 1.0
CB I:ALA116 3.0 114.5 1.0
O I:CYS119 3.6 134.6 1.0
CA I:GLY120 4.0 119.3 1.0
C I:HIS118 4.1 126.8 1.0
CA I:ALA116 4.3 114.5 1.0
NZ I:LYS88 4.4 110.2 1.0
O I:GLY120 4.4 119.3 1.0
C I:GLY120 4.5 119.3 1.0
C I:ALA116 4.5 114.5 1.0
SG I:CYS89 4.6 112.1 1.0
O I:HIS118 4.7 126.8 1.0
N I:PRO117 4.9 120.5 1.0
O I:ALA116 4.9 114.5 1.0
O I:PRO117 5.0 120.5 1.0
SG I:CYS114 5.0 100.8 1.0
N I:ALA116 5.0 114.5 1.0

Zinc binding site 4 out of 6 in 7b7u

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Zinc binding site 4 out of 6 in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:98.4
occ:1.00
 SG J:CYS10 2.3 66.1 1.0
SG J:CYS45 2.3 69.8 1.0
SG J:CYS7 2.3 64.7 1.0
SG J:CYS44 2.3 70.5 1.0
CB J:CYS10 3.5 66.1 1.0
N J:CYS45 3.5 69.8 1.0
CB J:CYS45 3.7 69.8 1.0
CA J:CYS45 3.8 69.8 1.0
CB J:CYS44 3.9 70.5 1.0
N J:CYS10 4.0 66.1 1.0
CB J:LYS12 4.0 63.1 1.0
CB J:CYS7 4.0 64.7 1.0
NE J:ARG42 4.1 69.2 1.0
C J:CYS44 4.1 70.5 1.0
N J:LYS12 4.2 63.1 1.0
CA J:CYS10 4.2 66.1 1.0
N J:GLY11 4.3 62.1 1.0
NH2 J:ARG42 4.3 69.2 1.0
CA J:CYS44 4.6 70.5 1.0
CZ J:ARG42 4.7 69.2 1.0
C J:CYS10 4.7 66.1 1.0
CA J:LYS12 4.7 63.1 1.0
O J:CYS44 4.8 70.5 1.0
O J:CYS7 4.8 64.7 1.0
CB J:ARG42 4.8 69.2 1.0

Zinc binding site 5 out of 6 in 7b7u

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Zinc binding site 5 out of 6 in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:168.8
occ:1.00
 SG L:CYS22 2.3 138.4 1.0
SG L:CYS39 2.3 147.0 1.0
SG L:CYS19 2.3 135.1 1.0
SG L:CYS36 2.3 145.5 1.0
CB L:CYS39 2.7 147.0 1.0
CB L:CYS19 3.1 135.1 1.0
CB L:CYS36 3.3 145.5 1.0
CB L:CYS22 3.4 138.4 1.0
OG1 L:THR24 3.8 134.6 1.0
N L:CYS22 4.1 138.4 1.0
CA L:CYS39 4.2 147.0 1.0
CA L:CYS22 4.3 138.4 1.0
CA L:CYS19 4.6 135.1 1.0
CB L:TYR41 4.7 136.5 1.0
O L:TYR41 4.7 136.5 1.0
CA L:CYS36 4.7 145.5 1.0
O L:ARG37 4.7 145.9 1.0
N L:HIS23 4.8 131.6 1.0
C L:CYS22 4.8 138.4 1.0
ND2 L:ASN26 4.9 138.9 1.0
N L:GLY20 4.9 135.7 1.0
C L:CYS39 4.9 147.0 1.0
N L:CYS39 5.0 147.0 1.0

Zinc binding site 6 out of 6 in 7b7u

Go back to Zinc Binding Sites List in 7b7u
Zinc binding site 6 out of 6 in the Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn701

b:187.4
occ:1.00
 SG M:CYS100 2.3 149.0 1.0
SG M:CYS105 2.3 145.3 1.0
SG M:CYS140 2.3 154.2 1.0
SG M:CYS136 2.3 151.3 1.0
CB M:CYS100 2.9 149.0 1.0
CB M:CYS140 3.1 154.2 1.0
CB M:CYS105 3.8 145.3 1.0
CB M:CYS136 3.9 151.3 1.0
NZ M:LYS107 4.0 137.4 1.0
OG M:SER137 4.0 150.9 1.0
N M:CYS136 4.1 151.3 1.0
N M:SER137 4.2 150.9 1.0
CA M:CYS100 4.3 149.0 1.0
CA M:CYS136 4.5 151.3 1.0
CA M:CYS140 4.6 154.2 1.0
CB M:TYR102 4.6 151.6 1.0
CE M:LYS107 4.7 137.4 1.0
C M:CYS136 4.8 151.3 1.0
CB M:SER137 4.9 150.9 1.0
O M:SER137 5.0 150.9 1.0

Reference:

I.Finau, C.Dienemann, S.Aibara, S.Schilbach, P.Cramer. Cryo-Em Structure of Mammalian Rna Polymerase II in Complex with Human RPAP2 To Be Published.
DOI: 10.1038/S42003-021-02088-Z
Page generated: Tue Oct 29 17:28:19 2024

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