Atomistry » Zinc » PDB 6a57-6agg » 6a5o
Atomistry »
  Zinc »
    PDB 6a57-6agg »
      6a5o »

Zinc in PDB 6a5o: Rna Polymerase II Elongation Complex Stalled at Shl(-6) of the Nucleosome

Enzymatic activity of Rna Polymerase II Elongation Complex Stalled at Shl(-6) of the Nucleosome

All present enzymatic activity of Rna Polymerase II Elongation Complex Stalled at Shl(-6) of the Nucleosome:
2.7.7.6;

Other elements in 6a5o:

The structure of Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) of the Nucleosome (pdb code 6a5o). 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(-6) of the Nucleosome, PDB code: 6a5o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 3.1 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 6a5o

Go back to Zinc Binding Sites List in 6a5o
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Stalled at Shl(-6) 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(-6) 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 17:18:16 2024

Last articles

Al in 1E2E
Al in 1BR1
Al in 1E1R
Al in 1BS1
Al in 1AGR
Al in 1A6E
Ag in 9KHW
Ag in 9GDM
Ag in 8DYK
Ag in 8GY1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy