Atomistry » Zinc » PDB 6gc8-6gml » 6gmh
Atomistry »
  Zinc »
    PDB 6gc8-6gml »
      6gmh »

Zinc in PDB 6gmh: Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6

Enzymatic activity of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6

All present enzymatic activity of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6:
2.7.7.6;

Other elements in 6gmh:

The structure of Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6 (pdb code 6gmh). 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 Activated Transcription Complex Pol II-Dsif-Paf-SPT6, PDB code: 6gmh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 1 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 NE2 A:HIS84 2.2 0.3 1.0
SG A:CYS74 2.5 0.8 1.0
CD2 A:HIS84 2.6 0.3 1.0
SG A:CYS71 2.6 0.2 1.0
CB A:CYS71 3.2 0.2 1.0
O A:PRO82 3.4 0.1 1.0
CE1 A:HIS84 3.5 0.3 1.0
CB A:CYS81 3.7 0.4 1.0
SG A:CYS81 3.7 0.4 1.0
OG1 A:THR73 3.7 0.6 1.0
CG A:HIS84 3.9 0.3 1.0
CB A:CYS74 4.1 0.8 1.0
CA A:GLY63 4.2 0.2 1.0
ND1 A:HIS84 4.3 0.3 1.0
N A:CYS74 4.3 0.8 1.0
O A:CYS74 4.6 0.8 1.0
N A:GLY63 4.6 0.2 1.0
C A:PRO82 4.6 0.1 1.0
CA A:CYS71 4.7 0.2 1.0
CA A:CYS74 4.7 0.8 1.0
C A:GLY63 4.9 0.2 1.0
CA A:CYS81 5.0 0.4 1.0

Zinc binding site 2 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 2 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.0
occ:1.00
 SG A:CYS114 2.6 0.5 1.0
SG A:CYS111 2.7 0.9 1.0
CE1 A:TYR187 3.1 0.0 1.0
CZ A:TYR187 3.4 0.0 1.0
CD1 A:TYR187 3.5 0.0 1.0
CD A:LYS116 3.6 0.2 1.0
CB A:CYS111 3.7 0.9 1.0
OH A:TYR187 3.8 0.0 1.0
SG A:CYS184 3.9 0.2 1.0
CE2 A:TYR187 4.0 0.0 1.0
CG A:TYR187 4.1 0.0 1.0
N A:CYS184 4.2 0.2 1.0
CB A:LYS116 4.2 0.2 1.0
CG A:LYS116 4.3 0.2 1.0
CB A:CYS114 4.3 0.5 1.0
CD2 A:TYR187 4.3 0.0 1.0
CE A:LYS116 4.4 0.2 1.0
NZ A:LYS116 4.4 0.2 1.0
O A:GLY182 4.5 0.7 1.0
CA A:GLY183 4.6 0.6 1.0
CB A:CYS184 4.8 0.2 1.0
O A:PHE112 4.8 0.2 1.0
C A:GLY183 5.0 0.6 1.0

Zinc binding site 3 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 3 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.7
occ:1.00
 SG B:CYS1122 2.5 0.5 1.0
SG B:CYS1137 2.5 0.2 1.0
SG B:CYS1119 2.5 0.1 1.0
CB B:CYS1140 2.5 0.2 1.0
CB B:CYS1119 2.9 0.1 1.0
SG B:CYS1140 3.2 0.2 1.0
CB B:CYS1137 3.4 0.2 1.0
CA B:CYS1140 3.9 0.2 1.0
CB B:CYS1122 4.0 0.5 1.0
O B:CYS1122 4.0 0.5 1.0
N B:CYS1122 4.0 0.5 1.0
N B:CYS1140 4.3 0.2 1.0
CA B:CYS1119 4.4 0.1 1.0
CA B:CYS1122 4.4 0.5 1.0
C B:CYS1122 4.6 0.5 1.0
CA B:CYS1137 4.8 0.2 1.0
ND2 B:ASN1142 4.8 0.3 1.0
C B:CYS1140 4.9 0.2 1.0
OD1 B:ASN1142 4.9 0.3 1.0
O B:CYS1137 4.9 0.2 1.0
O B:ARG1138 4.9 0.6 1.0
C B:CYS1137 5.0 0.2 1.0
CB B:LEU1121 5.0 0.8 1.0

Zinc binding site 4 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 4 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.4
occ:1.00
 SG C:CYS90 2.4 0.0 1.0
SG C:CYS88 2.4 0.1 1.0
SG C:CYS94 2.4 91.8 1.0
SG C:CYS97 2.5 92.7 1.0
CB C:CYS97 2.5 92.7 1.0
CB C:CYS88 2.9 0.1 1.0
N C:CYS97 3.6 92.7 1.0
CA C:CYS97 3.6 92.7 1.0
CB C:CYS90 3.7 0.0 1.0
CB C:CYS94 3.8 91.8 1.0
N C:CYS94 4.1 91.8 1.0
C C:GLU96 4.3 92.2 1.0
CA C:CYS88 4.3 0.1 1.0
CA C:CYS94 4.4 91.8 1.0
O C:CYS94 4.5 91.8 1.0
N C:CYS90 4.6 0.0 1.0
CA C:CYS90 4.7 0.0 1.0
C C:CYS94 4.7 91.8 1.0
C C:CYS97 4.7 92.7 1.0
C C:CYS88 4.8 0.1 1.0
CB C:GLU96 4.9 92.2 1.0
O C:GLU96 4.9 92.2 1.0
CA C:GLU96 5.0 92.2 1.0

Zinc binding site 5 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 5 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.5
occ:1.00
 SG I:CYS17 2.4 0.9 1.0
SG I:CYS39 2.4 0.9 1.0
SG I:CYS20 2.4 0.9 1.0
SG I:CYS42 2.5 0.1 1.0
CB I:CYS39 2.6 0.9 1.0
CB I:CYS17 3.1 0.9 1.0
CB I:CYS42 3.8 0.1 1.0
N I:CYS42 3.8 0.1 1.0
CB I:CYS20 4.0 0.9 1.0
CA I:CYS39 4.1 0.9 1.0
N I:CYS20 4.2 0.9 1.0
O I:CYS42 4.2 0.1 1.0
CA I:CYS42 4.2 0.1 1.0
C I:CYS42 4.5 0.1 1.0
CA I:CYS17 4.5 0.9 1.0
CA I:CYS20 4.6 0.9 1.0
CB I:ASN41 4.8 0.8 1.0
CB I:TYR44 4.8 0.5 1.0
C I:CYS39 4.9 0.9 1.0
N I:CYS39 4.9 0.9 1.0
CB I:GLU19 4.9 0.6 1.0
C I:ASN41 4.9 0.8 1.0
CB I:ASN22 4.9 0.4 1.0
N I:ASN41 4.9 0.8 1.0
OD1 I:ASN22 5.0 0.4 1.0

Zinc binding site 6 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 6 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.7
occ:1.00
 SG I:CYS114 2.4 0.0 1.0
SG I:CYS89 2.4 0.4 1.0
SG I:CYS119 2.4 0.7 1.0
SG I:CYS86 2.4 0.2 1.0
CB I:CYS86 2.8 0.2 1.0
CB I:CYS119 3.4 0.7 1.0
CB I:CYS114 3.4 0.0 1.0
CB I:CYS89 3.8 0.4 1.0
CB I:HIS91 4.0 0.7 1.0
N I:CYS89 4.0 0.4 1.0
N I:HIS91 4.2 0.7 1.0
CA I:CYS86 4.3 0.2 1.0
CA I:CYS89 4.4 0.4 1.0
N I:GLY90 4.6 0.3 1.0
O I:THR115 4.6 0.1 1.0
C I:CYS89 4.7 0.4 1.0
CA I:HIS91 4.7 0.7 1.0
CA I:CYS119 4.8 0.7 1.0
CA I:CYS114 4.9 0.0 1.0
CB I:HIS121 5.0 0.3 1.0
O I:HIS91 5.0 0.7 1.0

Zinc binding site 7 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 7 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:96.0
occ:1.00
 SG J:CYS45 2.4 71.3 1.0
SG J:CYS44 2.4 71.2 1.0
SG J:CYS7 2.4 66.2 1.0
CB J:CYS10 2.5 70.5 1.0
N J:CYS45 3.0 71.3 1.0
CB J:CYS7 3.1 66.2 1.0
C J:CYS44 3.2 71.2 1.0
CA J:CYS45 3.3 71.3 1.0
CB J:CYS44 3.3 71.2 1.0
CB J:CYS45 3.4 71.3 1.0
N J:CYS10 3.4 70.5 1.0
CA J:CYS10 3.6 70.5 1.0
O J:CYS44 3.7 71.2 1.0
SG J:CYS10 3.7 70.5 1.0
CA J:CYS44 3.9 71.2 1.0
CA J:CYS7 4.6 66.2 1.0
C J:CYS10 4.6 70.5 1.0
C J:THR9 4.6 66.8 1.0
N J:GLY11 4.7 68.9 1.0
N J:CYS44 4.7 71.2 1.0
CB J:THR9 4.7 66.8 1.0
NE J:ARG42 4.8 70.3 1.0
C J:CYS45 4.8 71.3 1.0
CB J:LYS12 4.9 67.0 1.0

Zinc binding site 8 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 8 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.3
occ:1.00
 O L:GLU38 2.5 0.3 1.0
SG L:CYS22 2.5 0.5 1.0
SG L:CYS39 2.5 0.6 1.0
SG L:CYS19 2.6 0.5 1.0
SG L:CYS36 2.6 0.9 1.0
CB L:CYS36 2.9 0.9 1.0
CB L:CYS19 3.5 0.5 1.0
C L:GLU38 3.6 0.3 1.0
CB L:CYS22 3.7 0.5 1.0
CB L:CYS39 3.9 0.6 1.0
CB L:TYR41 4.0 0.9 1.0
N L:CYS22 4.2 0.5 1.0
N L:TYR41 4.3 0.9 1.0
CA L:CYS36 4.3 0.9 1.0
CG L:GLU38 4.3 0.3 1.0
N L:CYS39 4.4 0.6 1.0
CA L:CYS39 4.5 0.6 1.0
CA L:CYS22 4.5 0.5 1.0
N L:GLY40 4.6 0.9 1.0
C L:CYS39 4.6 0.6 1.0
CA L:GLU38 4.7 0.3 1.0
C L:CYS36 4.7 0.9 1.0
N L:GLU38 4.7 0.3 1.0
CA L:TYR41 4.8 0.9 1.0
O L:CYS36 4.9 0.9 1.0
CA L:CYS19 4.9 0.5 1.0
CB L:GLU21 5.0 0.0 1.0

Zinc binding site 9 out of 9 in 6gmh

Go back to Zinc Binding Sites List in 6gmh
Zinc binding site 9 out of 9 in the Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 SG Y:CYS33 2.6 0.7 1.0
SG Y:CYS19 2.6 0.8 1.0
SG Y:CYS36 2.7 0.2 1.0
SG Y:CYS16 2.7 0.0 1.0
CB Y:CYS36 2.7 0.2 1.0
CB Y:CYS19 3.4 0.8 1.0
CB Y:CYS16 3.7 0.0 1.0
CB Y:CYS33 3.8 0.7 1.0
N Y:CYS19 3.8 0.8 1.0
N Y:CYS36 3.9 0.2 1.0
CA Y:CYS36 3.9 0.2 1.0
CD1 Y:LEU40 4.1 0.2 1.0
CA Y:CYS19 4.2 0.8 1.0
CB Y:LEU18 4.2 0.8 1.0
CB Y:ASN35 4.4 0.3 1.0
C Y:LEU18 4.6 0.8 1.0
C Y:ASN35 4.7 0.3 1.0
CG Y:LEU18 4.7 0.8 1.0
C Y:CYS36 4.7 0.2 1.0
CD2 Y:LEU18 4.8 0.8 1.0
CA Y:LEU18 4.8 0.8 1.0
N Y:LEU18 4.9 0.8 1.0
CA Y:ASN35 5.0 0.3 1.0

Reference:

S.M.Vos, L.Farnung, M.Boehning, C.Wigge, A.Linden, H.Urlaub, P.Cramer. Structure of Activated Transcription Complex Pol II-Dsif-Paf-SPT6. Nature V. 560 607 2018.
ISSN: ISSN 0028-0836
PubMed: 30135578
DOI: 10.1038/S41586-018-0440-4
Page generated: Mon Oct 28 21:54:40 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