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Zinc in PDB 5oik: Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex

Enzymatic activity of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex

All present enzymatic activity of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex:
2.7.7.6;

Other elements in 5oik:

The structure of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex (pdb code 5oik). 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 An Rna Polymerase II-Dsif Transcription Elongation Complex, PDB code: 5oik:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5oik

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Zinc binding site 1 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:0.1
occ:1.00
 SG A:CYS81 2.2 0.1 1.0
SG A:CYS71 2.3 0.4 1.0
SG A:CYS74 2.4 0.8 1.0
NE2 A:HIS84 2.8 1.0 1.0
CD2 A:HIS84 3.0 1.0 1.0
OG1 A:THR73 3.2 0.3 1.0
CB A:CYS71 3.7 0.4 1.0
CB A:CYS81 3.8 0.1 1.0
CB A:CYS74 4.0 0.8 1.0
CE1 A:HIS84 4.0 1.0 1.0
N A:CYS74 4.2 0.3 1.0
CG A:HIS84 4.3 1.0 1.0
CB A:THR73 4.4 0.3 1.0
C A:THR73 4.5 0.9 1.0
CA A:CYS81 4.5 0.3 1.0
CA A:CYS74 4.5 0.3 1.0
O A:CYS74 4.5 0.3 1.0
C A:CYS74 4.8 0.3 1.0
ND1 A:HIS84 4.8 1.0 1.0
CA A:THR73 4.8 0.9 1.0
N A:THR73 4.8 0.9 1.0
CA A:GLY76 4.9 0.4 1.0
N A:GLY83 5.0 0.6 1.0

Zinc binding site 2 out of 8 in 5oik

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Zinc binding site 2 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.1
occ:1.00
 SG A:CYS111 2.3 0.1 1.0
SG A:CYS114 2.3 0.3 1.0
CB A:CYS184 2.4 0.0 1.0
SG A:CYS184 2.5 0.0 1.0
O A:CYS184 3.1 0.9 1.0
SG A:CYS154 3.4 0.6 1.0
O A:GLY183 3.4 0.6 1.0
CB A:CYS111 3.5 0.1 1.0
CA A:CYS184 3.6 0.9 1.0
CB A:CYS114 3.6 0.3 1.0
C A:CYS184 3.8 0.9 1.0
CB A:CYS154 3.8 0.6 1.0
N A:CYS114 4.1 0.3 1.0
C A:GLY183 4.2 0.6 1.0
N A:CYS184 4.3 0.9 1.0
NE2 A:GLN188 4.4 0.1 1.0
CA A:CYS114 4.5 0.3 1.0
CA A:CYS111 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 5oik

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Zinc binding site 3 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:0.1
occ:1.00
 SG B:CYS1122 2.3 0.3 1.0
SG B:CYS1140 2.4 0.2 1.0
SG B:CYS1119 2.4 0.1 1.0
SG B:CYS1137 2.4 0.8 1.0
CB B:CYS1140 2.7 0.2 1.0
CB B:CYS1119 3.4 0.1 1.0
CB B:CYS1122 3.6 0.3 1.0
CB B:CYS1137 3.6 0.8 1.0
N B:CYS1122 3.6 0.6 1.0
CA B:CYS1140 4.0 0.7 1.0
CA B:CYS1122 4.2 0.6 1.0
N B:CYS1140 4.2 0.7 1.0
CB B:LEU1121 4.3 0.2 1.0
CB B:ASN1142 4.6 0.9 1.0
O B:CYS1122 4.6 0.6 1.0
C B:LEU1121 4.7 0.7 1.0
N B:LEU1121 4.7 0.7 1.0
C B:CYS1122 4.8 0.6 1.0
CA B:LEU1121 4.8 0.7 1.0
CA B:CYS1119 4.9 0.6 1.0
ND2 B:ASN1142 4.9 0.9 1.0
C B:CYS1140 4.9 0.7 1.0
CA B:CYS1137 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 5oik

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Zinc binding site 4 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.1
occ:1.00
 SG I:CYS17 2.3 0.5 1.0
SG I:CYS42 2.4 0.7 1.0
SG I:CYS20 2.5 0.6 1.0
SG I:CYS39 2.7 0.2 1.0
CB I:CYS39 2.7 0.2 1.0
CB I:CYS17 3.0 0.5 1.0
CB I:CYS42 4.0 0.7 1.0
N I:CYS20 4.0 0.9 1.0
CB I:CYS20 4.1 0.6 1.0
CA I:CYS39 4.3 0.1 1.0
CB I:TYR44 4.4 0.7 1.0
CA I:CYS17 4.5 0.2 1.0
N I:CYS42 4.6 0.9 1.0
CA I:CYS20 4.6 0.9 1.0
CB I:GLU19 4.8 0.1 1.0
CA I:CYS42 4.8 0.9 1.0
N I:GLU19 4.9 0.2 1.0
N I:ASN22 4.9 0.5 1.0
CB I:ASN22 4.9 0.3 1.0
N I:ASN21 4.9 0.9 1.0
N I:CYS39 4.9 0.1 1.0
CD2 I:TYR44 5.0 0.7 1.0
C I:CYS39 5.0 0.1 1.0
C I:CYS20 5.0 0.9 1.0

Zinc binding site 5 out of 8 in 5oik

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Zinc binding site 5 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.1
occ:1.00
 SG I:CYS119 2.2 0.9 1.0
SG I:CYS86 2.3 0.4 1.0
SG I:CYS89 2.3 0.9 1.0
SG I:CYS114 2.4 0.8 1.0
CB I:CYS86 3.0 0.4 1.0
CB I:CYS119 3.4 0.9 1.0
CB I:CYS114 3.5 0.8 1.0
CB I:CYS89 3.9 0.9 1.0
CB I:HIS91 3.9 0.2 1.0
N I:CYS89 4.0 0.9 1.0
CA I:CYS89 4.5 0.9 1.0
CA I:CYS86 4.5 0.1 1.0
N I:HIS91 4.5 0.6 1.0
O I:THR115 4.6 0.6 1.0
CA I:CYS119 4.8 0.4 1.0
CB I:HIS121 4.8 0.9 1.0
N I:GLY90 4.8 0.9 1.0
C I:CYS89 4.9 0.9 1.0
CA I:HIS91 4.9 0.6 1.0
CA I:CYS114 4.9 0.7 1.0
CG I:HIS91 5.0 0.2 1.0
CB I:LYS88 5.0 0.3 1.0

Zinc binding site 6 out of 8 in 5oik

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Zinc binding site 6 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.1
occ:1.00
 SG J:CYS10 2.1 78.1 1.0
SG J:CYS7 2.3 75.7 1.0
SG J:CYS44 2.3 83.7 1.0
SG J:CYS45 2.4 86.5 1.0
CB J:CYS7 3.2 75.7 1.0
N J:CYS45 3.2 72.0 1.0
CB J:CYS10 3.3 78.1 1.0
CB J:CYS44 3.4 83.7 1.0
C J:CYS44 3.5 75.6 1.0
CA J:CYS45 3.6 72.0 1.0
CB J:CYS45 3.6 86.5 1.0
N J:CYS10 3.7 72.3 1.0
O J:CYS44 3.9 75.6 1.0
CA J:CYS10 4.1 72.3 1.0
CA J:CYS44 4.1 75.6 1.0
N J:GLY11 4.4 71.7 1.0
CA J:CYS7 4.6 66.3 1.0
C J:CYS10 4.7 72.3 1.0
NH2 J:ARG42 4.7 77.0 1.0
CB J:LYS12 4.8 68.2 1.0
C J:CYS7 4.8 66.3 1.0
N J:LYS12 4.8 71.0 1.0
CB J:THR9 4.8 71.2 1.0
C J:THR9 4.9 67.8 1.0
N J:CYS44 4.9 75.6 1.0
O J:CYS7 4.9 66.3 1.0

Zinc binding site 7 out of 8 in 5oik

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Zinc binding site 7 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.1
occ:1.00
 SG L:CYS22 2.2 0.8 1.0
SG L:CYS39 2.2 0.8 1.0
SG L:CYS36 2.3 0.2 1.0
SG L:CYS19 2.4 0.0 1.0
CB L:CYS36 2.7 0.2 1.0
CB L:CYS19 3.0 0.0 1.0
CB L:CYS39 3.3 0.8 1.0
O L:ARG37 3.7 0.3 1.0
CB L:CYS22 3.9 0.8 1.0
OG1 L:THR24 3.9 0.1 1.0
CA L:CYS36 4.0 0.4 1.0
N L:CYS39 4.2 0.8 1.0
C L:CYS36 4.2 0.4 1.0
N L:CYS22 4.3 0.2 1.0
O L:CYS36 4.3 0.4 1.0
CA L:CYS39 4.4 0.8 1.0
CA L:CYS19 4.4 0.3 1.0
CA L:CYS22 4.6 0.2 1.0
C L:ARG37 4.7 0.3 1.0
C L:GLU38 4.7 0.1 1.0
CB L:TYR41 4.9 0.1 1.0
N L:ARG37 4.9 0.3 1.0
N L:CYS36 4.9 0.4 1.0
N L:GLY40 4.9 0.0 1.0
CE L:MET44 5.0 0.6 1.0

Zinc binding site 8 out of 8 in 5oik

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Zinc binding site 8 out of 8 in the Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of An Rna Polymerase II-Dsif Transcription Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:0.1
occ:1.00
 SG Y:CYS33 2.3 0.5 1.0
SG Y:CYS16 2.4 0.9 1.0
SG Y:CYS36 2.4 0.2 1.0
SG Y:CYS19 2.4 0.5 1.0
CB Y:CYS16 3.2 0.9 1.0
CB Y:CYS19 3.2 0.5 1.0
CB Y:CYS36 3.3 0.2 1.0
CB Y:CYS33 3.5 0.5 1.0
N Y:CYS19 3.7 0.2 1.0
N Y:CYS36 3.9 0.6 1.0
CA Y:CYS19 4.0 0.2 1.0
CB Y:ASN35 4.3 0.1 1.0
CA Y:CYS36 4.3 0.6 1.0
CA Y:CYS16 4.6 0.5 1.0
CB Y:LEU18 4.6 0.9 1.0
CD1 Y:LEU40 4.6 0.6 1.0
C Y:LEU18 4.7 0.2 1.0
C Y:ASN35 4.8 0.1 1.0
CB Y:LEU21 4.8 0.6 1.0
ND2 Y:ASN35 4.8 0.1 1.0
C Y:CYS19 4.8 0.2 1.0
CA Y:CYS33 4.9 0.9 1.0
CA Y:ASN35 4.9 0.1 1.0
N Y:ASN35 4.9 0.1 1.0
N Y:SER20 4.9 0.7 1.0
CA Y:LEU18 5.0 0.2 1.0
N Y:LEU18 5.0 0.2 1.0

Reference:

C.Bernecky, J.M.Plitzko, P.Cramer. Structure of A Transcribing Rna Polymerase II-Dsif Complex Reveals A Multidentate Dna-Rna Clamp. Nat. Struct. Mol. Biol. V. 24 809 2017.
ISSN: ESSN 1545-9985
PubMed: 28892040
DOI: 10.1038/NSMB.3465
Page generated: Wed Dec 16 06:38:40 2020

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