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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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