Atomistry » Zinc » PDB 6a3n-6aem » 6a5p
Atomistry »
  Zinc »
    PDB 6a3n-6aem »
      6a5p »

Zinc in PDB 6a5p: Rna Polymerase II Elongation Complex Stalled at Shl(-5) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Stalled at Shl(-5) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Stalled at Shl(-5) of the Nucleosome:
2.7.7.6;

Other elements in 6a5p:

The structure of Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome (pdb code 6a5p). 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(-5) of the Nucleosome, PDB code: 6a5p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) 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
SG A:CYS70 2.4 0.8 1.0
SG A:CYS67 2.4 1.0 1.0
CB A:CYS70 2.5 0.8 1.0
SG A:CYS77 2.7 91.9 1.0
N A:CYS70 2.8 0.8 1.0
CE1 A:HIS80 2.9 86.7 1.0
CA A:CYS70 3.2 0.8 1.0
CD2 A:HIS80 3.2 86.7 1.0
CB A:CYS67 3.4 1.0 1.0
CB A:CYS77 3.9 91.9 1.0
C A:THR69 4.0 97.8 1.0
ND1 A:HIS80 4.1 86.7 1.0
C A:CYS70 4.1 0.8 1.0
CB A:THR69 4.2 97.8 1.0
CG A:HIS80 4.3 86.7 1.0
N A:GLY71 4.3 0.7 1.0
N A:THR69 4.4 97.8 1.0
CA A:THR69 4.4 97.8 1.0
CA A:GLY59 4.8 93.3 1.0
CA A:CYS67 4.8 1.0 1.0
CA A:CYS77 4.8 91.9 1.0
CG2 A:THR69 4.9 97.8 1.0
O A:LEU58 4.9 85.5 1.0

Zinc binding site 2 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:1.0
occ:1.00
 SG A:CYS148 2.5 0.2 1.0
SG A:CYS107 2.5 0.9 1.0
CB A:CYS148 3.1 0.2 1.0
N A:CYS168 3.3 0.3 1.0
CA A:GLY167 3.6 0.4 1.0
SG A:CYS168 3.7 0.3 1.0
CB A:CYS107 3.8 0.9 1.0
CB A:ASN109 3.9 0.7 1.0
C A:GLY167 4.0 0.4 1.0
O A:ASN170 4.0 0.3 1.0
NE2 A:GLN172 4.0 0.8 1.0
N A:GLY169 4.1 0.7 1.0
CA A:CYS168 4.4 0.3 1.0
N A:ASN109 4.4 0.7 1.0
CA A:CYS148 4.5 0.2 1.0
CB A:CYS168 4.6 0.3 1.0
N A:ASN170 4.6 0.3 1.0
SG A:CYS110 4.6 0.4 1.0
CA A:ASN109 4.7 0.7 1.0
C A:CYS168 4.7 0.3 1.0
CA A:CYS107 4.8 0.9 1.0
N A:CYS110 4.8 0.4 1.0
O A:CYS148 4.8 0.2 1.0
N A:MET108 4.8 0.5 1.0
C A:CYS148 4.9 0.2 1.0
N A:GLY167 4.9 0.4 1.0
C A:ASN170 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.6
occ:1.00
 SG B:CYS1185 2.5 91.9 1.0
SG B:CYS1163 2.5 81.6 1.0
SG B:CYS1166 2.5 83.4 1.0
SG B:CYS1182 2.5 96.3 1.0
CB B:CYS1185 3.2 91.9 1.0
N B:CYS1166 3.2 83.4 1.0
CB B:CYS1166 3.2 83.4 1.0
CB B:CYS1163 3.5 81.6 1.0
CB B:CYS1182 3.7 96.3 1.0
CA B:CYS1166 3.7 83.4 1.0
CB B:ILE1165 4.2 81.9 1.0
C B:ILE1165 4.3 81.9 1.0
CB B:ASN1187 4.4 88.1 1.0
ND2 B:ASN1187 4.4 88.1 1.0
N B:ILE1165 4.5 81.9 1.0
CA B:ILE1165 4.5 81.9 1.0
CA B:CYS1185 4.6 91.9 1.0
C B:CYS1166 4.6 83.4 1.0
CG2 B:ILE1165 4.7 81.9 1.0
N B:GLY1167 4.8 78.3 1.0
N B:CYS1185 4.8 91.9 1.0
O B:CYS1163 4.8 81.6 1.0
CA B:CYS1163 4.8 81.6 1.0
C B:CYS1163 4.9 81.6 1.0
CG B:ASN1187 5.0 88.1 1.0

Zinc binding site 4 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.0
occ:1.00
 OE1 C:GLU93 2.1 0.4 1.0
SG C:CYS91 2.5 0.5 1.0
CB C:GLU93 2.5 0.4 1.0
CD C:GLU93 2.7 0.4 1.0
CG C:GLU93 3.0 0.4 1.0
SG C:CYS85 3.1 0.3 1.0
SG C:CYS87 3.3 0.3 1.0
CB C:CYS87 3.4 0.3 1.0
CA C:GLU93 3.6 0.4 1.0
OE2 C:GLU93 3.7 0.4 1.0
N C:GLU93 3.8 0.4 1.0
N C:CYS94 3.9 93.7 1.0
SG C:CYS94 3.9 93.7 1.0
C C:GLU93 4.0 0.4 1.0
N C:CYS87 4.1 0.3 1.0
CB C:CYS91 4.3 0.5 1.0
CA C:CYS87 4.4 0.3 1.0
CB C:CYS94 4.5 93.7 1.0
CB C:CYS85 4.6 0.3 1.0
OG1 C:THR86 4.6 0.6 1.0
N C:THR86 4.6 0.6 1.0
C C:THR86 4.7 0.6 1.0
CA C:CYS94 4.8 93.7 1.0
C C:CYS91 4.9 0.5 1.0
N C:CYS91 5.0 0.5 1.0
CA C:CYS91 5.0 0.5 1.0
O C:GLU93 5.0 0.4 1.0

Zinc binding site 5 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.4
occ:1.00
 SG I:CYS75 2.5 0.3 1.0
SG I:CYS78 2.5 0.4 1.0
SG I:CYS103 3.1 0.1 1.0
SG I:CYS106 3.1 0.4 1.0
CB I:ASN105 3.3 0.0 1.0
CB I:GLU77 3.4 0.8 1.0
CB I:CYS78 3.4 0.4 1.0
CB I:CYS75 3.5 0.3 1.0
N I:CYS78 3.6 0.4 1.0
N I:CYS106 3.7 0.4 1.0
CB I:CYS106 3.7 0.4 1.0
CG I:GLU77 3.9 0.8 1.0
CA I:CYS78 4.1 0.4 1.0
CG I:ASN105 4.1 0.0 1.0
CB I:CYS103 4.2 0.1 1.0
OD1 I:ASN105 4.3 0.0 1.0
CA I:GLU77 4.3 0.8 1.0
CA I:ASN105 4.3 0.0 1.0
CA I:CYS106 4.3 0.4 1.0
C I:GLU77 4.4 0.8 1.0
C I:ASN105 4.4 0.0 1.0
N I:GLU77 4.5 0.8 1.0
N I:ASN105 4.6 0.0 1.0
CA I:CYS75 4.9 0.3 1.0

Zinc binding site 6 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.3
occ:1.00
 O I:GLU9 2.3 0.4 1.0
C I:GLU9 2.4 0.4 1.0
N I:CYS10 2.5 0.1 1.0
CB I:CYS10 2.6 0.1 1.0
CA I:CYS10 2.7 0.1 1.0
CB I:GLU9 3.2 0.4 1.0
CB I:CYS32 3.2 1.0 1.0
CA I:GLU9 3.4 0.4 1.0
SG I:CYS10 3.6 0.1 1.0
SG I:CYS32 3.8 1.0 1.0
C I:CYS10 4.2 0.1 1.0
N I:GLU9 4.5 0.4 1.0
SG I:CYS7 4.5 0.7 1.0
CA I:CYS32 4.5 1.0 1.0
CG I:GLU9 4.7 0.4 1.0
OE1 I:GLU9 4.7 0.4 1.0
O I:ASN31 4.8 1.0 1.0
N I:CYS32 4.9 1.0 1.0
N I:ASN11 5.0 0.8 1.0
O I:CYS10 5.0 0.1 1.0

Zinc binding site 7 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) 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 2.1 48.5 1.0
C J:CYS44 2.3 45.3 1.0
SG J:CYS7 2.4 48.7 1.0
SG J:CYS45 2.4 48.5 1.0
SG J:CYS44 2.4 45.3 1.0
CB J:CYS7 2.5 48.7 1.0
CA J:CYS45 2.6 48.5 1.0
CB J:CYS44 2.9 45.3 1.0
O J:CYS44 2.9 45.3 1.0
CB J:CYS45 3.0 48.5 1.0
CA J:CYS44 3.1 45.3 1.0
SG J:CYS10 3.5 47.5 1.0
CA J:CYS7 3.8 48.7 1.0
C J:CYS45 4.1 48.5 1.0
N J:CYS44 4.1 45.3 1.0
N J:CYS10 4.3 47.5 1.0
CB J:CYS10 4.3 47.5 1.0
CG J:MET48 4.5 46.1 1.0
NH2 J:ARG42 4.6 44.8 1.0
N J:ARG46 4.6 51.5 1.0
N J:CYS7 4.7 48.7 1.0
C J:CYS7 4.8 48.7 1.0
CB J:MET48 4.8 46.1 1.0
CA J:CYS10 4.9 47.5 1.0
N J:GLY11 4.9 53.0 1.0
N J:PHE8 4.9 37.5 1.0

Zinc binding site 8 out of 8 in 6a5p

Go back to Zinc Binding Sites List in 6a5p
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-5) 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(-5) of the Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.5
occ:1.00
 N L:CYS36 2.3 0.1 1.0
SG L:CYS50 2.4 0.8 1.0
SG L:CYS36 2.4 0.1 1.0
SG L:CYS33 2.5 0.2 1.0
CB L:CYS36 2.6 0.1 1.0
CA L:CYS36 3.0 0.1 1.0
CB L:ALA35 3.1 0.8 1.0
C L:ALA35 3.2 0.8 1.0
CA L:ALA35 3.4 0.8 1.0
CB L:CYS50 3.5 0.8 1.0
N L:ALA35 3.6 0.8 1.0
CB L:CYS33 3.8 0.2 1.0
C L:CYS36 4.0 0.1 1.0
O L:ALA35 4.3 0.8 1.0
SG L:CYS53 4.3 0.5 1.0
N L:ALA37 4.4 0.2 1.0
CA L:CYS50 4.6 0.8 1.0
CB L:GLU52 4.7 0.9 1.0
CG L:GLU52 4.8 0.9 1.0
O L:CYS36 4.8 0.1 1.0
CB L:HIS55 4.9 0.5 1.0
C L:GLY34 4.9 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: Mon Oct 28 17:19:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy