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Zinc in PDB 5flm: Structure of Transcribing Mammalian Rna Polymerase II

Enzymatic activity of Structure of Transcribing Mammalian Rna Polymerase II

All present enzymatic activity of Structure of Transcribing Mammalian Rna Polymerase II:
2.7.7.6;

Other elements in 5flm:

The structure of Structure of Transcribing Mammalian Rna Polymerase II also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Transcribing Mammalian Rna Polymerase II (pdb code 5flm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Transcribing Mammalian Rna Polymerase II, PDB code: 5flm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5flm

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Zinc binding site 1 out of 8 in the Structure of Transcribing Mammalian 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 Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2488

b:0.1
occ:1.00
 NE2 A:HIS84 2.2 0.1 1.0
SG A:CYS74 2.4 0.3 1.0
SG A:CYS81 2.5 0.7 1.0
CD2 A:HIS84 2.6 0.1 1.0
SG A:CYS71 2.8 0.6 1.0
OG1 A:THR73 3.0 0.3 1.0
CE1 A:HIS84 3.4 0.1 1.0
CG A:HIS84 3.9 0.1 1.0
CB A:CYS81 3.9 0.7 1.0
CB A:CYS71 4.0 0.6 1.0
CB A:CYS74 4.1 0.3 1.0
ND1 A:HIS84 4.2 0.1 1.0
CB A:THR73 4.3 0.3 1.0
N A:CYS74 4.3 0.6 1.0
C A:THR73 4.6 0.0 1.0
CA A:CYS81 4.7 0.1 1.0
CA A:CYS74 4.7 0.6 1.0
N A:GLY83 4.8 0.5 1.0
CA A:THR73 4.9 0.0 1.0
CA A:GLY83 4.9 0.5 1.0
C A:GLY83 4.9 0.5 1.0
O A:GLY83 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 5flm

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Zinc binding site 2 out of 8 in the Structure of Transcribing Mammalian 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 Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2489

b:0.1
occ:1.00
 SG A:CYS111 2.4 0.5 1.0
CB A:CYS184 2.5 0.8 1.0
CB A:CYS114 2.5 0.7 1.0
SG A:CYS114 2.7 0.7 1.0
SG A:CYS184 2.7 0.8 1.0
SG A:CYS154 3.3 0.7 1.0
CB A:CYS111 3.3 0.5 1.0
O A:CYS184 3.5 0.2 1.0
O A:GLY183 3.6 0.3 1.0
CB A:CYS154 3.7 0.7 1.0
CA A:CYS184 3.8 0.2 1.0
C A:CYS184 4.0 0.2 1.0
CA A:CYS114 4.1 0.0 1.0
C A:GLY183 4.3 0.3 1.0
N A:CYS184 4.4 0.2 1.0
O A:PHE112 4.5 0.2 1.0
NE2 A:GLN188 4.6 0.9 1.0
N A:CYS114 4.7 0.0 1.0
CA A:CYS111 4.8 0.6 1.0
C A:CYS114 5.0 0.0 1.0

Zinc binding site 3 out of 8 in 5flm

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Zinc binding site 3 out of 8 in the Structure of Transcribing Mammalian 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 Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2175

b:0.1
occ:1.00
 SG B:CYS1137 2.4 0.7 1.0
SG B:CYS1140 2.4 1.0 1.0
SG B:CYS1122 2.5 0.6 1.0
SG B:CYS1119 2.6 0.6 1.0
CB B:CYS1140 2.6 1.0 1.0
CB B:CYS1119 3.4 0.6 1.0
CB B:CYS1137 3.5 0.7 1.0
CB B:CYS1122 3.8 0.6 1.0
N B:CYS1122 3.9 0.3 1.0
CA B:CYS1140 3.9 0.2 1.0
N B:CYS1140 4.1 0.2 1.0
CB B:ASN1142 4.3 0.6 1.0
CA B:CYS1122 4.4 0.3 1.0
ND2 B:ASN1142 4.6 0.6 1.0
CB B:LEU1121 4.7 0.9 1.0
C B:CYS1140 4.8 0.2 1.0
CA B:CYS1137 4.8 0.5 1.0
CA B:CYS1119 4.8 0.0 1.0
O B:CYS1122 4.9 0.3 1.0
O B:CYS1137 4.9 0.5 1.0
CG B:ASN1142 5.0 0.6 1.0

Zinc binding site 4 out of 8 in 5flm

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Zinc binding site 4 out of 8 in the Structure of Transcribing Mammalian 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 Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1272

b:0.1
occ:1.00
 SG C:CYS94 2.2 1.0 1.0
SG C:CYS90 2.3 0.1 1.0
SG C:CYS88 2.4 0.1 1.0
SG C:CYS97 2.5 0.5 1.0
N C:CYS94 3.0 0.6 1.0
CB C:CYS94 3.0 1.0 1.0
CA C:CYS94 3.6 0.6 1.0
C C:PHE93 3.7 0.4 1.0
CB C:CYS97 3.7 0.5 1.0
CB C:CYS88 3.9 0.1 1.0
O C:GLU92 4.0 0.8 1.0
CA C:PHE93 4.1 0.4 1.0
CB C:CYS90 4.1 0.1 1.0
O C:CYS90 4.4 0.5 1.0
C C:CYS94 4.4 0.6 1.0
O C:CYS94 4.4 0.6 1.0
N C:CYS97 4.4 0.8 1.0
O C:GLU91 4.5 0.3 1.0
N C:CYS90 4.5 0.5 1.0
O C:PHE93 4.5 0.4 1.0
N C:PHE93 4.6 0.4 1.0
C C:GLU92 4.6 0.8 1.0
CA C:CYS90 4.7 0.5 1.0
C C:CYS90 4.7 0.5 1.0
CA C:CYS97 4.7 0.8 1.0

Zinc binding site 5 out of 8 in 5flm

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Zinc binding site 5 out of 8 in the Structure of Transcribing Mammalian 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 Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1126

b:0.1
occ:1.00
 SG I:CYS42 2.4 0.8 1.0
SG I:CYS20 2.5 0.9 1.0
SG I:CYS17 2.5 0.5 1.0
SG I:CYS39 2.5 0.3 1.0
CB I:CYS17 3.0 0.5 1.0
CB I:CYS39 3.0 0.3 1.0
N I:CYS20 3.9 0.2 1.0
CB I:CYS42 4.0 0.8 1.0
CB I:CYS20 4.0 0.9 1.0
CA I:CYS20 4.4 0.2 1.0
CA I:CYS17 4.5 0.9 1.0
CB I:GLU19 4.5 0.2 1.0
CA I:CYS39 4.5 0.3 1.0
N I:CYS42 4.5 0.9 1.0
CB I:ASN22 4.6 0.4 1.0
N I:ASN22 4.7 0.2 1.0
N I:ASN21 4.7 0.4 1.0
ND2 I:ASN22 4.8 0.4 1.0
CB I:TYR44 4.8 0.5 1.0
N I:GLU19 4.8 0.9 1.0
CA I:CYS42 4.8 0.9 1.0
C I:CYS20 4.9 0.2 1.0
OE1 I:GLU19 4.9 0.2 1.0
C I:GLU19 4.9 0.9 1.0
CA I:GLU19 5.0 0.9 1.0

Zinc binding site 6 out of 8 in 5flm

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Zinc binding site 6 out of 8 in the Structure of Transcribing Mammalian Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1127

b:0.1
occ:1.00
 SG I:CYS86 2.3 0.4 1.0
SG I:CYS89 2.3 0.6 1.0
SG I:CYS114 2.3 0.3 1.0
SG I:CYS119 2.3 0.5 1.0
CB I:CYS86 2.8 0.4 1.0
CB I:CYS114 3.3 0.3 1.0
CB I:CYS119 3.3 0.5 1.0
CB I:CYS89 3.9 0.6 1.0
N I:CYS89 4.1 0.2 1.0
CA I:CYS86 4.3 0.4 1.0
CB I:HIS91 4.4 0.6 1.0
CA I:CYS89 4.5 0.2 1.0
N I:HIS91 4.6 0.5 1.0
O I:THR115 4.7 0.4 1.0
CB I:HIS121 4.7 0.5 1.0
CA I:CYS114 4.7 0.3 1.0
CA I:CYS119 4.8 0.7 1.0
N I:GLY90 4.8 0.3 1.0
CB I:LYS88 4.9 0.6 1.0
C I:CYS89 4.9 0.2 1.0
C I:CYS86 5.0 0.4 1.0

Zinc binding site 7 out of 8 in 5flm

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Zinc binding site 7 out of 8 in the Structure of Transcribing Mammalian Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1068

b:0.1
occ:1.00
 SG J:CYS10 2.4 95.3 1.0
SG J:CYS45 2.6 0.2 1.0
SG J:CYS44 2.6 0.5 1.0
N J:CYS45 2.6 97.0 1.0
SG J:CYS7 2.8 98.6 1.0
C J:CYS44 2.9 97.9 1.0
CA J:CYS45 3.1 97.0 1.0
CB J:CYS44 3.3 0.5 1.0
O J:CYS44 3.3 97.9 1.0
CB J:CYS45 3.4 0.2 1.0
CA J:CYS44 3.6 97.9 1.0
CB J:CYS10 3.7 95.3 1.0
CB J:CYS7 3.8 98.6 1.0
N J:CYS10 4.1 93.8 1.0
NE J:ARG42 4.3 0.3 1.0
N J:CYS44 4.4 97.9 1.0
C J:CYS45 4.5 97.0 1.0
CA J:CYS10 4.5 93.8 1.0
CG J:ARG42 4.6 0.3 1.0
O J:ARG42 4.7 100.0 1.0
CB J:THR9 4.7 92.6 1.0
CD J:ARG42 4.9 0.3 1.0

Zinc binding site 8 out of 8 in 5flm

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Zinc binding site 8 out of 8 in the Structure of Transcribing Mammalian Rna Polymerase II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Transcribing Mammalian Rna Polymerase II within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1059

b:0.1
occ:1.00
 SG L:CYS19 2.3 0.6 1.0
SG L:CYS39 2.3 0.7 1.0
SG L:CYS22 2.4 0.8 1.0
SG L:CYS36 2.4 0.0 1.0
CB L:CYS19 2.7 0.6 1.0
CB L:CYS36 3.2 0.0 1.0
OG1 L:THR24 3.3 0.9 1.0
CB L:CYS39 3.7 0.7 1.0
N L:CYS22 3.8 0.7 1.0
CB L:CYS22 3.9 0.8 1.0
CA L:CYS19 4.2 0.2 1.0
CA L:CYS22 4.3 0.7 1.0
O L:THR24 4.4 1.0 1.0
N L:THR24 4.4 1.0 1.0
N L:HIS23 4.4 0.8 1.0
O L:ARG37 4.4 0.1 1.0
CA L:CYS36 4.6 0.9 1.0
C L:CYS22 4.6 0.7 1.0
CB L:THR24 4.6 0.9 1.0
CB L:GLU21 4.8 0.4 1.0
C L:CYS36 4.8 0.9 1.0
N L:GLU21 4.8 0.9 1.0
N L:CYS39 4.8 0.1 1.0
CA L:CYS39 4.9 0.1 1.0
C L:GLU21 4.9 0.9 1.0
C L:CYS19 5.0 0.2 1.0
CA L:THR24 5.0 1.0 1.0
O L:CYS36 5.0 0.9 1.0
CB L:TYR41 5.0 0.2 1.0
CE L:MET44 5.0 0.6 1.0

Reference:

C.Bernecky, F.Herzog, W.Baumeister, J.M.Plitzko, P.Cramer. Structure of Transcribing Mammalian Rna Polymerase II Nature V. 529 551 2016.
ISSN: ISSN 0028-0836
PubMed: 26789250
DOI: 10.1038/NATURE16482
Page generated: Sun Oct 27 16:18:33 2024

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