Atomistry » Zinc » PDB 6t6r-6tm5 » 6ted
Atomistry »
  Zinc »
    PDB 6t6r-6tm5 »
      6ted »

Zinc in PDB 6ted: Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1

Enzymatic activity of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1

All present enzymatic activity of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1:
2.7.7.6;

Other elements in 6ted:

The structure of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 (pdb code 6ted). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1, PDB code: 6ted:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 1 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:54.4
occ:1.00
 NE2 A:HIS84 1.9 29.6 1.0
SG A:CYS74 2.1 44.0 1.0
SG A:CYS71 2.3 48.6 1.0
CB A:CYS71 2.8 48.6 1.0
CD2 A:HIS84 2.9 29.6 1.0
CB A:CYS81 3.0 37.4 1.0
CE1 A:HIS84 3.0 29.6 1.0
SG A:CYS81 3.3 37.4 1.0
O A:PRO82 3.7 35.1 1.0
CB A:CYS74 3.7 44.0 1.0
N A:CYS74 3.9 44.0 1.0
CG A:HIS84 4.0 29.6 1.0
ND1 A:HIS84 4.1 29.6 1.0
CA A:CYS81 4.2 37.4 1.0
CA A:CYS71 4.3 48.6 1.0
O A:CYS74 4.3 44.0 1.0
CA A:GLY63 4.3 35.2 1.0
CA A:CYS74 4.3 44.0 1.0
N A:GLY63 4.7 35.2 1.0
C A:PRO82 4.7 35.1 1.0
C A:CYS74 4.8 44.0 1.0
C A:CYS81 4.8 37.4 1.0
CD A:PRO82 4.8 35.1 1.0
CB A:THR73 4.8 41.9 1.0
N A:PRO82 4.8 35.1 1.0

Zinc binding site 2 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 2 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:83.1
occ:1.00
 O A:ASN152 2.8 51.0 1.0
CA A:ARG186 3.3 58.8 1.0
N A:ARG186 3.6 58.8 1.0
SG A:CYS111 3.9 58.4 1.0
C A:ASN152 4.0 51.0 1.0
CB A:ARG186 4.0 58.8 1.0
CA A:GLY183 4.0 46.4 1.0
NE2 A:GLN188 4.0 54.3 1.0
C A:GLY183 4.1 46.4 1.0
CD2 A:LEU118 4.4 51.0 1.0
N A:CYS184 4.4 54.5 1.0
C A:ARG186 4.4 58.8 1.0
O A:GLY183 4.6 46.4 1.0
O A:CYS184 4.6 54.5 1.0
CD A:GLN188 4.6 54.3 1.0
N A:TYR187 4.6 61.5 1.0
CG A:GLN188 4.7 54.3 1.0
C A:CYS184 4.9 54.5 1.0
C A:GLY185 4.9 50.8 1.0
O A:GLY182 4.9 53.4 1.0

Zinc binding site 3 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 3 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:73.9
occ:1.00
 SG B:CYS1122 2.1 33.9 1.0
SG B:CYS1119 2.1 32.4 1.0
SG B:CYS1137 2.4 52.1 1.0
CB B:CYS1119 2.7 32.4 1.0
SG B:CYS1140 3.3 50.6 1.0
CB B:CYS1137 3.6 52.1 1.0
CB B:CYS1122 3.8 33.9 1.0
N B:CYS1122 4.0 33.9 1.0
CB B:CYS1140 4.0 50.6 1.0
CA B:CYS1119 4.2 32.4 1.0
CA B:CYS1122 4.4 33.9 1.0
C B:CYS1122 4.7 33.9 1.0
C B:CYS1119 4.8 32.4 1.0
O B:ILE1124 4.8 27.6 1.0
CB B:LEU1121 4.8 39.2 1.0
N B:LEU1121 4.8 39.2 1.0
N B:CYS1140 4.8 50.6 1.0
O B:CYS1122 4.9 33.9 1.0
C B:LEU1121 4.9 39.2 1.0
N B:CYS1119 4.9 32.4 1.0
CA B:CYS1137 5.0 52.1 1.0
CB B:ASN1142 5.0 47.3 1.0

Zinc binding site 4 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 4 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:66.5
occ:1.00
 SG C:CYS88 2.2 25.9 1.0
CB C:CYS94 2.3 27.9 1.0
SG C:CYS90 2.3 34.6 1.0
SG C:CYS97 2.6 17.3 1.0
CB C:CYS88 3.1 25.9 1.0
SG C:CYS94 3.3 27.9 1.0
CB C:CYS97 3.4 17.3 1.0
CB C:CYS90 3.4 34.6 1.0
CA C:CYS94 3.5 27.9 1.0
N C:CYS94 3.5 27.9 1.0
N C:CYS97 4.3 17.3 1.0
C C:PHE93 4.3 20.1 1.0
C C:CYS94 4.4 27.9 1.0
CA C:CYS97 4.4 17.3 1.0
CA C:CYS88 4.5 25.9 1.0
CA C:PHE93 4.5 20.1 1.0
CA C:CYS90 4.7 34.6 1.0
O C:CYS94 4.7 27.9 1.0
C C:GLU96 4.8 24.1 1.0
N C:CYS90 4.8 34.6 1.0
C C:CYS88 4.8 25.9 1.0
OE1 C:GLU96 4.9 24.1 1.0

Zinc binding site 5 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 5 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:71.3
occ:1.00
 SG I:CYS17 2.2 41.5 1.0
SG I:CYS20 2.3 41.3 1.0
CB I:CYS42 2.5 49.6 1.0
SG I:CYS39 2.8 44.8 1.0
CB I:CYS17 3.0 41.5 1.0
CB I:CYS39 3.1 44.8 1.0
CA I:CYS42 3.6 49.6 1.0
SG I:CYS42 3.6 49.6 1.0
N I:CYS42 3.7 49.6 1.0
N I:CYS20 3.9 41.3 1.0
CB I:CYS20 4.0 41.3 1.0
CB I:TYR44 4.3 45.6 1.0
C I:CYS42 4.4 49.6 1.0
CA I:CYS17 4.4 41.5 1.0
CA I:CYS20 4.5 41.3 1.0
CB I:GLU19 4.5 42.5 1.0
CA I:CYS39 4.6 44.8 1.0
N I:GLU19 4.6 42.5 1.0
CB I:ASN22 4.8 34.8 1.0
CD2 I:LEU24 4.8 35.4 1.0
C I:ASN41 4.8 51.8 1.0
O I:CYS42 4.9 49.6 1.0
N I:ASN22 4.9 34.8 1.0
C I:GLU19 4.9 42.5 1.0
CA I:GLU19 4.9 42.5 1.0

Zinc binding site 6 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 6 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:59.1
occ:1.00
 SG I:CYS114 2.1 26.2 1.0
SG I:CYS89 2.2 40.9 1.0
SG I:CYS119 2.2 35.0 1.0
SG I:CYS86 2.3 35.4 1.0
CB I:CYS114 2.6 26.2 1.0
CB I:CYS86 2.7 35.4 1.0
CB I:CYS119 3.5 35.0 1.0
CB I:CYS89 3.6 40.9 1.0
CA I:CYS114 4.0 26.2 1.0
N I:CYS89 4.1 40.9 1.0
CA I:CYS86 4.2 35.4 1.0
CB I:HIS91 4.3 35.2 1.0
CB I:HIS121 4.4 26.3 1.0
CA I:CYS89 4.4 40.9 1.0
N I:GLY90 4.5 37.3 1.0
N I:HIS91 4.6 35.2 1.0
N I:HIS121 4.7 26.3 1.0
C I:CYS114 4.8 26.2 1.0
CA I:CYS119 4.9 35.0 1.0
N I:CYS114 4.9 26.2 1.0
CB I:ALA116 4.9 33.7 1.0
N I:CYS86 5.0 35.4 1.0

Zinc binding site 7 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 7 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:23.8
occ:1.00
 SG J:CYS45 2.2 12.0 1.0
SG J:CYS7 2.2 0.2 1.0
CB J:CYS10 2.2 13.7 1.0
SG J:CYS44 2.2 12.8 1.0
SG J:CYS10 3.1 13.7 1.0
CB J:CYS7 3.1 0.2 1.0
N J:CYS45 3.4 12.0 1.0
CB J:CYS45 3.4 12.0 1.0
CA J:CYS10 3.4 13.7 1.0
N J:CYS10 3.5 13.7 1.0
CA J:CYS45 3.6 12.0 1.0
CB J:CYS44 3.7 12.8 1.0
C J:CYS44 3.8 12.8 1.0
CA J:CYS44 4.4 12.8 1.0
O J:CYS44 4.4 12.8 1.0
NE J:ARG42 4.4 4.0 1.0
N J:GLY11 4.4 15.1 1.0
C J:CYS10 4.4 13.7 1.0
CA J:CYS7 4.5 0.2 1.0
C J:THR9 4.6 10.6 1.0
CB J:LYS12 4.7 10.7 1.0
CB J:THR9 4.7 10.6 1.0
N J:LYS12 4.9 10.7 1.0
C J:CYS7 4.9 0.2 1.0

Zinc binding site 8 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 8 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:70.1
occ:1.00
 N L:TYR41 2.1 35.4 1.0
CA L:GLY40 2.3 41.8 1.0
N L:CYS36 2.5 42.1 1.0
C L:GLY40 2.5 41.8 1.0
N L:GLY40 3.0 41.8 1.0
O L:CYS36 3.0 42.1 1.0
NE L:ARG35 3.3 42.4 1.0
CA L:CYS36 3.3 42.1 1.0
C L:ARG35 3.4 42.4 1.0
CB L:CYS36 3.4 42.1 1.0
CB L:ARG35 3.5 42.4 1.0
CA L:TYR41 3.5 35.4 1.0
NH2 L:ARG35 3.5 42.4 1.0
C L:CYS36 3.5 42.1 1.0
O L:TYR41 3.5 35.4 1.0
CA L:ARG35 3.6 42.4 1.0
CZ L:ARG35 3.7 42.4 1.0
O L:GLY40 3.7 41.8 1.0
C L:TYR41 3.8 35.4 1.0
O L:GLU38 4.1 46.1 1.0
CG L:ARG35 4.2 42.4 1.0
C L:CYS39 4.2 45.7 1.0
CB L:TYR41 4.3 35.4 1.0
CD L:ARG35 4.3 42.4 1.0
O L:ARG35 4.4 42.4 1.0
O L:CYS39 4.8 45.7 1.0
C L:GLU38 4.8 46.1 1.0
N L:ARG37 4.8 48.1 1.0
N L:ARG42 4.9 24.2 1.0
NH1 L:ARG35 4.9 42.4 1.0

Zinc binding site 9 out of 9 in 6ted

Go back to Zinc Binding Sites List in 6ted
Zinc binding site 9 out of 9 in the Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Complete, Activated Transcription Complex Pol II-Dsif- Paf-SPT6 Uncovers Allosteric Elongation Activation By RTF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:93.2
occ:1.00
 N Y:CYS19 2.4 74.7 1.0
SG Y:CYS19 2.8 74.7 1.0
CB Y:CYS19 3.1 74.7 1.0
CB Y:LEU18 3.1 70.8 1.0
CA Y:CYS19 3.2 74.7 1.0
C Y:LEU18 3.4 70.8 1.0
CB Y:CYS16 3.5 76.1 1.0
CA Y:LEU18 3.5 70.8 1.0
N Y:LEU18 3.7 70.8 1.0
SG Y:CYS33 3.7 75.5 1.0
C Y:CYS19 4.0 74.7 1.0
N Y:SER20 4.0 72.7 1.0
SG Y:CYS16 4.2 76.1 1.0
CG Y:LEU18 4.4 70.8 1.0
O Y:LEU18 4.5 70.8 1.0
CD1 Y:LEU18 4.8 70.8 1.0
CA Y:CYS16 4.8 76.1 1.0
CB Y:CYS33 4.8 75.5 1.0
N Y:LEU17 4.9 75.0 1.0
N Y:LEU21 4.9 76.5 1.0
C Y:LEU17 4.9 75.0 1.0
O Y:CYS19 4.9 74.7 1.0
C Y:CYS16 4.9 76.1 1.0

Reference:

S.M.Vos, L.Farnung, A.Linden, H.Urlaub, P.Cramer. Structure of Complete Pol II-Dsif-Paf-SPT6 Transcription Complex Reveals RTF1 Allosteric Activation. Nat.Struct.Mol.Biol. V. 27 668 2020.
ISSN: ESSN 1545-9985
PubMed: 32541898
DOI: 10.1038/S41594-020-0437-1
Page generated: Tue Oct 29 07:58:24 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy