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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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