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Zinc in PDB 7f4g: Structure of RPAP2-Bound Rna Polymerase II

Enzymatic activity of Structure of RPAP2-Bound Rna Polymerase II

All present enzymatic activity of Structure of RPAP2-Bound Rna Polymerase II:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of RPAP2-Bound Rna Polymerase II (pdb code 7f4g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of RPAP2-Bound Rna Polymerase II, PDB code: 7f4g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7f4g

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Zinc binding site 1 out of 5 in the Structure of RPAP2-Bound Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of RPAP2-Bound Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:107.6
occ:1.00
 SG I:CYS17 2.2 88.6 1.0
SG I:CYS39 2.3 97.0 1.0
SG I:CYS20 2.4 90.5 1.0
SG I:CYS42 2.8 101.3 1.0
CB I:CYS17 2.9 88.6 1.0
CB I:CYS39 3.0 97.0 1.0
CB I:CYS42 3.6 101.3 1.0
CB I:CYS20 3.7 90.5 1.0
N I:CYS20 3.8 90.5 1.0
CA I:CYS20 4.2 90.5 1.0
N I:CYS42 4.2 101.3 1.0
CA I:CYS17 4.3 88.6 1.0
CA I:CYS39 4.5 97.0 1.0
N I:ASN21 4.5 86.5 1.0
CA I:CYS42 4.5 101.3 1.0
CB I:TYR44 4.7 96.0 1.0
C I:ASN41 4.7 98.2 1.0
C I:CYS20 4.7 90.5 1.0
N I:ASN22 4.7 85.7 1.0
N I:GLU19 4.7 95.5 1.0
CB I:ASN41 4.8 98.2 1.0
CB I:GLU19 4.8 95.5 1.0
N I:ASN41 4.8 98.2 1.0
C I:GLU19 4.9 95.5 1.0
CB I:ASN22 4.9 85.7 1.0
CA I:ASN41 5.0 98.2 1.0

Zinc binding site 2 out of 5 in 7f4g

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Zinc binding site 2 out of 5 in the Structure of RPAP2-Bound Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of RPAP2-Bound Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:97.9
occ:1.00
 SG I:CYS89 2.1 88.5 1.0
SG I:CYS114 2.2 73.8 1.0
SG I:CYS119 2.3 84.5 1.0
SG I:CYS86 2.3 86.9 1.0
CB I:CYS86 2.8 86.9 1.0
CB I:CYS114 2.9 73.8 1.0
CB I:CYS119 3.3 84.5 1.0
CB I:CYS89 3.7 88.5 1.0
N I:CYS89 4.0 88.5 1.0
CA I:CYS86 4.3 86.9 1.0
CA I:CYS114 4.3 73.8 1.0
CB I:HIS91 4.4 84.1 1.0
CA I:CYS89 4.4 88.5 1.0
CB I:HIS121 4.4 76.5 1.0
CA I:CYS119 4.7 84.5 1.0
CB I:LYS88 4.7 87.4 1.0
N I:HIS121 4.7 76.5 1.0
CB I:ALA116 4.8 82.0 1.0
N I:HIS91 4.8 84.1 1.0
C I:CYS114 4.9 73.8 1.0
C I:CYS86 4.9 86.9 1.0
C I:CYS119 5.0 84.5 1.0
C I:CYS89 5.0 88.5 1.0
N I:GLY120 5.0 78.4 1.0
N I:GLY90 5.0 87.6 1.0

Zinc binding site 3 out of 5 in 7f4g

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Zinc binding site 3 out of 5 in the Structure of RPAP2-Bound Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of RPAP2-Bound Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:54.8
occ:1.00
 SG J:CYS10 2.2 37.0 1.0
SG J:CYS45 2.3 40.1 1.0
SG J:CYS7 2.3 32.5 1.0
SG J:CYS44 2.3 40.0 1.0
CB J:CYS10 3.1 37.0 1.0
CB J:CYS7 3.2 32.5 1.0
N J:CYS45 3.5 40.1 1.0
CB J:CYS45 3.5 40.1 1.0
CA J:CYS45 3.7 40.1 1.0
N J:CYS10 3.7 37.0 1.0
CB J:CYS44 3.7 40.0 1.0
C J:CYS44 3.8 40.0 1.0
CA J:CYS10 4.0 37.0 1.0
O J:CYS44 4.2 40.0 1.0
NE J:ARG42 4.3 41.8 1.0
CA J:CYS44 4.4 40.0 1.0
NH2 J:ARG42 4.5 41.8 1.0
N J:GLY11 4.6 33.4 1.0
CA J:CYS7 4.6 32.5 1.0
CB J:THR9 4.6 34.8 1.0
C J:CYS10 4.7 37.0 1.0
C J:THR9 4.8 34.8 1.0
CB J:LYS12 4.8 35.0 1.0
N J:LYS12 4.9 35.0 1.0
CZ J:ARG42 4.9 41.8 1.0
C J:CYS7 4.9 32.5 1.0
CB J:ARG42 5.0 41.8 1.0
N J:THR9 5.0 34.8 1.0

Zinc binding site 4 out of 5 in 7f4g

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Zinc binding site 4 out of 5 in the Structure of RPAP2-Bound Rna Polymerase II


Mono view


Stereo pair view

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

b:115.6
occ:1.00
 O L:GLU38 1.9 94.6 1.0
C L:GLU38 2.1 94.6 1.0
CG L:GLU38 2.2 94.6 1.0
N L:CYS39 2.6 88.9 1.0
CB L:GLU38 3.0 94.6 1.0
CB L:CYS39 3.0 88.9 1.0
CA L:CYS39 3.0 88.9 1.0
CA L:GLU38 3.1 94.6 1.0
O L:ARG37 3.4 90.0 1.0
CD L:GLU38 3.5 94.6 1.0
SG L:CYS22 3.9 82.4 1.0
N L:GLU38 4.0 94.6 1.0
OE2 L:GLU38 4.0 94.6 1.0
C L:ARG37 4.1 90.0 1.0
OE1 L:GLU38 4.3 94.6 1.0
SG L:CYS36 4.5 84.4 1.0
SG L:CYS39 4.5 88.9 1.0
C L:CYS39 4.6 88.9 1.0
CB L:CYS22 4.6 82.4 1.0
CG2 L:THR24 5.0 82.6 1.0

Zinc binding site 5 out of 5 in 7f4g

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Zinc binding site 5 out of 5 in the Structure of RPAP2-Bound Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of RPAP2-Bound Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn800

b:186.6
occ:1.00
 SG R:CYS140 2.2 175.8 1.0
SG R:CYS105 2.4 177.9 1.0
SG R:CYS100 2.4 173.1 1.0
SG R:CYS136 2.7 172.3 1.0
CB R:CYS105 2.7 177.9 1.0
CB R:CYS140 2.8 175.8 1.0
CB R:CYS100 3.1 173.1 1.0
OG R:SER137 3.9 173.1 1.0
CB R:CYS136 3.9 172.3 1.0
N R:CYS136 4.0 172.3 1.0
N R:SER137 4.1 173.1 1.0
CA R:CYS105 4.2 177.9 1.0
CA R:CYS140 4.3 175.8 1.0
CA R:CYS136 4.5 172.3 1.0
CA R:CYS100 4.5 173.1 1.0
C R:CYS105 4.7 177.9 1.0
CB R:TYR102 4.7 177.8 1.0
C R:CYS136 4.8 172.3 1.0
CB R:SER137 4.8 173.1 1.0
O R:SER137 4.8 173.1 1.0
CB R:LYS107 4.9 173.0 1.0
CA R:SER137 5.0 173.1 1.0
CD R:LYS107 5.0 173.0 1.0
CB R:PHE135 5.0 168.0 1.0

Reference:

X.Chen, Y.Qi, X.Wang, J.Li, D.Zhao, Y.Xu. Structure of RPAP2-Bound Rna Polymerase II To Be Published.
Page generated: Tue Oct 29 20:11:57 2024

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