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Zinc in PDB 6a5l: Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna

Enzymatic activity of Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna

All present enzymatic activity of Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna:
2.7.7.6;

Other elements in 6a5l:

The structure of Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna (pdb code 6a5l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna, PDB code: 6a5l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6a5l

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.1
occ:1.00
 NE2 A:HIS80 2.1 86.7 1.0
CB A:CYS70 2.2 0.8 1.0
SG A:CYS77 2.2 91.9 1.0
SG A:CYS70 2.3 0.8 1.0
CE1 A:HIS80 2.7 86.7 1.0
N A:CYS70 2.8 0.8 1.0
CA A:CYS70 3.0 0.8 1.0
CD2 A:HIS80 3.3 86.7 1.0
CB A:CYS77 3.5 91.9 1.0
SG A:CYS67 3.5 1.0 1.0
ND1 A:HIS80 3.9 86.7 1.0
CB A:CYS67 4.0 1.0 1.0
C A:THR69 4.0 97.8 1.0
CB A:THR69 4.2 97.8 1.0
C A:CYS70 4.2 0.8 1.0
CG A:HIS80 4.2 86.7 1.0
CA A:CYS77 4.3 91.9 1.0
N A:GLY71 4.5 0.7 1.0
CA A:THR69 4.6 97.8 1.0
CG2 A:THR69 4.7 97.8 1.0
N A:THR69 4.9 97.8 1.0
O A:THR69 4.9 97.8 1.0

Zinc binding site 2 out of 8 in 6a5l

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:1.0
occ:1.00
 N A:CYS168 2.1 0.3 1.0
SG A:CYS107 2.7 0.9 1.0
CB A:ASN109 2.7 0.7 1.0
CA A:GLY167 2.8 0.4 1.0
C A:GLY167 2.8 0.4 1.0
SG A:CYS168 2.9 0.3 1.0
CA A:CYS168 3.2 0.3 1.0
CB A:CYS168 3.2 0.3 1.0
CA A:ASN109 3.6 0.7 1.0
N A:ASN109 3.7 0.7 1.0
N A:CYS110 3.7 0.4 1.0
CG A:ASN109 3.8 0.7 1.0
ND2 A:ASN109 3.9 0.7 1.0
O A:GLY167 4.0 0.4 1.0
C A:ASN109 4.1 0.7 1.0
N A:GLY167 4.1 0.4 1.0
O A:GLY166 4.2 0.9 1.0
C A:CYS168 4.2 0.3 1.0
N A:GLY169 4.2 0.7 1.0
SG A:CYS148 4.3 0.2 1.0
CB A:CYS107 4.3 0.9 1.0
CB A:CYS110 4.6 0.4 1.0
C A:GLY166 4.6 0.9 1.0
SG A:CYS110 4.6 0.4 1.0
CA A:CYS110 4.8 0.4 1.0
OD1 A:ASN109 4.8 0.7 1.0
NE2 A:GLN172 4.9 0.8 1.0
C A:MET108 4.9 0.5 1.0

Zinc binding site 3 out of 8 in 6a5l

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.6
occ:1.00
 SG B:CYS1166 2.3 83.4 1.0
SG B:CYS1182 2.3 96.3 1.0
SG B:CYS1163 2.4 81.6 1.0
CB B:CYS1166 2.8 83.4 1.0
CB B:CYS1163 3.1 81.6 1.0
SG B:CYS1185 3.2 91.9 1.0
CB B:CYS1185 3.2 91.9 1.0
N B:CYS1166 3.4 83.4 1.0
CB B:CYS1182 3.4 96.3 1.0
CA B:CYS1166 3.7 83.4 1.0
CA B:CYS1185 4.5 91.9 1.0
CA B:CYS1163 4.6 81.6 1.0
C B:CYS1166 4.6 83.4 1.0
N B:CYS1185 4.6 91.9 1.0
CB B:ASN1187 4.6 88.1 1.0
C B:ILE1165 4.6 81.9 1.0
N B:GLY1167 4.7 78.3 1.0
CA B:CYS1182 4.8 96.3 1.0
O B:CYS1163 4.9 81.6 1.0
O B:CYS1182 4.9 96.3 1.0
CB B:ILE1165 4.9 81.9 1.0
C B:CYS1163 4.9 81.6 1.0
N B:ILE1165 4.9 81.9 1.0

Zinc binding site 4 out of 8 in 6a5l

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.0
occ:1.00
 N C:CYS94 2.1 93.7 1.0
CB C:CYS94 2.5 93.7 1.0
SG C:CYS85 2.5 0.3 1.0
SG C:CYS94 2.5 93.7 1.0
CA C:CYS94 2.7 93.7 1.0
C C:GLU93 2.8 0.4 1.0
CB C:GLU93 2.8 0.4 1.0
CA C:GLU93 3.2 0.4 1.0
CB C:CYS85 3.6 0.3 1.0
SG C:CYS91 3.6 0.5 1.0
N C:GLU93 3.7 0.4 1.0
O C:GLU93 3.8 0.4 1.0
C C:CYS94 3.9 93.7 1.0
OE1 C:GLU93 4.0 0.4 1.0
SG C:CYS87 4.1 0.3 1.0
CG C:GLU93 4.2 0.4 1.0
O C:CYS94 4.5 93.7 1.0
N C:SER95 4.6 83.0 1.0
CD C:GLU93 4.6 0.4 1.0
O C:CYS91 4.7 0.5 1.0
C C:ASP92 4.9 97.3 1.0
CA C:CYS85 5.0 0.3 1.0
C C:CYS91 5.0 0.5 1.0

Zinc binding site 5 out of 8 in 6a5l

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.4
occ:1.00
 CB I:ASN105 2.3 0.0 1.0
SG I:CYS75 2.5 0.3 1.0
SG I:CYS103 2.5 0.1 1.0
SG I:CYS78 2.6 0.4 1.0
N I:ASN105 3.3 0.0 1.0
CA I:ASN105 3.3 0.0 1.0
CG I:ASN105 3.4 0.0 1.0
CB I:CYS75 3.6 0.3 1.0
OD1 I:ASN105 3.6 0.0 1.0
N I:CYS106 3.7 0.4 1.0
CB I:CYS103 3.9 0.1 1.0
CB I:CYS78 3.9 0.4 1.0
C I:ASN105 4.0 0.0 1.0
N I:CYS78 4.2 0.4 1.0
C I:LEU104 4.4 0.5 1.0
OG I:SER80 4.4 0.5 1.0
ND2 I:ASN105 4.6 0.0 1.0
CA I:CYS78 4.6 0.4 1.0
SG I:CYS106 4.6 0.4 1.0
N I:LEU104 4.6 0.5 1.0
CB I:SER80 4.6 0.5 1.0
CB I:GLU77 4.9 0.8 1.0
CA I:CYS75 4.9 0.3 1.0
CA I:CYS106 5.0 0.4 1.0

Zinc binding site 6 out of 8 in 6a5l

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.3
occ:1.00
 CB I:CYS32 2.1 1.0 1.0
CB I:GLU9 2.1 0.4 1.0
SG I:CYS32 2.3 1.0 1.0
OE1 I:GLU9 2.5 0.4 1.0
N I:CYS10 3.2 0.1 1.0
CG I:GLU9 3.2 0.4 1.0
CA I:GLU9 3.2 0.4 1.0
C I:GLU9 3.2 0.4 1.0
CD I:GLU9 3.2 0.4 1.0
CA I:CYS32 3.7 1.0 1.0
CB I:CYS10 3.8 0.1 1.0
SG I:CYS7 3.9 0.7 1.0
O I:GLU9 3.9 0.4 1.0
N I:GLU9 4.0 0.4 1.0
CA I:CYS10 4.1 0.1 1.0
N I:CYS32 4.4 1.0 1.0
OE2 I:GLU9 4.5 0.4 1.0
N I:ASP33 4.5 0.3 1.0
C I:CYS32 4.5 1.0 1.0
CB I:TYR34 4.7 0.6 1.0
N I:TYR34 4.8 0.6 1.0
O I:ASN31 4.9 1.0 1.0

Zinc binding site 7 out of 8 in 6a5l

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:62.9
occ:1.00
 N J:CYS45 2.0 48.5 1.0
SG J:CYS7 2.1 48.7 1.0
SG J:CYS45 2.2 48.5 1.0
SG J:CYS44 2.2 45.3 1.0
CA J:CYS45 2.3 48.5 1.0
SG J:CYS10 2.6 47.5 1.0
CB J:CYS45 2.7 48.5 1.0
C J:CYS44 2.8 45.3 1.0
CB J:CYS7 2.9 48.7 1.0
CB J:CYS44 3.3 45.3 1.0
O J:CYS44 3.4 45.3 1.0
CA J:CYS44 3.6 45.3 1.0
CB J:CYS10 3.8 47.5 1.0
C J:CYS45 3.8 48.5 1.0
N J:CYS10 4.3 47.5 1.0
CA J:CYS7 4.4 48.7 1.0
N J:CYS44 4.4 45.3 1.0
O J:CYS45 4.6 48.5 1.0
N J:ARG46 4.6 51.5 1.0
CA J:CYS10 4.7 47.5 1.0
N J:GLY11 4.8 53.0 1.0
CG J:MET48 4.8 46.1 1.0
C J:CYS7 4.9 48.7 1.0

Zinc binding site 8 out of 8 in 6a5l

Go back to Zinc Binding Sites List in 6a5l
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna


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 Elongation Complex Stalled at Shl(-1) of the Nucleosome, with Foreign Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.5
occ:1.00
 SG L:CYS50 2.4 0.8 1.0
SG L:CYS53 2.5 0.5 1.0
SG L:CYS33 3.3 0.2 1.0
CB L:CYS50 3.3 0.8 1.0
SG L:CYS36 3.4 0.1 1.0
CB L:GLU52 3.5 0.9 1.0
CB L:CYS36 3.7 0.1 1.0
N L:CYS53 3.8 0.5 1.0
CB L:HIS55 3.9 0.5 1.0
CB L:CYS53 3.9 0.5 1.0
CG L:GLU52 4.1 0.9 1.0
N L:CYS36 4.2 0.1 1.0
CA L:GLU52 4.3 0.9 1.0
CB L:CYS33 4.4 0.2 1.0
CA L:CYS53 4.4 0.5 1.0
C L:GLU52 4.4 0.9 1.0
N L:GLU52 4.5 0.9 1.0
CA L:CYS36 4.6 0.1 1.0
CG L:HIS55 4.7 0.5 1.0
CB L:ALA35 4.8 0.8 1.0
CA L:CYS50 4.8 0.8 1.0
N L:HIS55 5.0 0.5 1.0
C L:CYS53 5.0 0.5 1.0
N L:ALA35 5.0 0.8 1.0

Reference:

T.Kujirai, H.Ehara, Y.Fujino, M.Shirouzu, S.I.Sekine, H.Kurumizaka. Structural Basis of the Nucleosome Transition During Rna Polymerase II Passage. Science V. 362 595 2018.
ISSN: ESSN 1095-9203
PubMed: 30287617
DOI: 10.1126/SCIENCE.AAU9904
Page generated: Mon Oct 28 17:15:59 2024

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