Zinc in PDB 6a5t: Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome

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

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

Other elements in 6a5t:

The structure of Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome 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 (pdb code 6a5t). 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, PDB code: 6a5t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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
CB A:ASN109 2.7 0.7 1.0
SG A:CYS107 2.7 0.9 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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 3.4 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 6a5t

Go back to Zinc Binding Sites List in 6a5t
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-1) of the Nucleosome


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 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

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: Wed Dec 16 11:28:52 2020

Last articles

Zn in 8I9I
Zn in 8IJN
Zn in 8HIO
Zn in 8HHM
Zn in 8GRM
Zn in 8GRQ
Zn in 8G9F
Zn in 8GZG
Zn in 8GZH
Zn in 8G99
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy