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Zinc in PDB 6gml: Structure of Paused Transcription Complex Pol II-Dsif-Nelf

Enzymatic activity of Structure of Paused Transcription Complex Pol II-Dsif-Nelf

All present enzymatic activity of Structure of Paused Transcription Complex Pol II-Dsif-Nelf:
2.7.7.6;

Other elements in 6gml:

The structure of Structure of Paused Transcription Complex Pol II-Dsif-Nelf also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 9 in 6gml

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Zinc binding site 1 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Paused Transcription Complex Pol II-Dsif-Nelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:73.4
occ:1.00
 CB A:CYS114 2.5 60.6 1.0
SG A:CYS114 2.6 60.6 1.0
SG A:CYS111 2.6 52.1 1.0
N A:GLY183 3.6 54.3 1.0
CB A:CYS111 3.7 52.1 1.0
CA A:CYS114 3.8 60.6 1.0
N A:CYS114 3.9 60.6 1.0
CG A:LYS116 4.1 54.4 1.0
CE2 A:TYR187 4.1 59.8 1.0
CD2 A:TYR187 4.1 59.8 1.0
CA A:GLY183 4.1 54.3 1.0
CB A:LYS116 4.3 54.4 1.0
C A:CYS114 4.6 60.6 1.0
C A:GLY182 4.7 53.8 1.0
C A:GLY183 4.7 54.3 1.0
CA A:GLY182 4.8 53.8 1.0
SG A:CYS184 4.8 56.0 1.0
N A:LYS116 4.9 54.4 1.0
N A:SER115 5.0 54.1 1.0

Zinc binding site 2 out of 9 in 6gml

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Zinc binding site 2 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Paused Transcription Complex Pol II-Dsif-Nelf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:68.5
occ:1.00
 NE2 A:HIS84 2.2 32.7 1.0
SG A:CYS71 2.4 41.2 1.0
SG A:CYS81 2.4 35.8 1.0
SG A:CYS74 2.5 35.3 1.0
CD2 A:HIS84 2.6 32.7 1.0
CB A:CYS71 2.9 41.2 1.0
CE1 A:HIS84 3.5 32.7 1.0
CG A:HIS84 3.9 32.7 1.0
N A:CYS74 3.9 35.3 1.0
CB A:CYS81 3.9 35.8 1.0
CB A:CYS74 3.9 35.3 1.0
CA A:GLY63 4.1 38.7 1.0
ND1 A:HIS84 4.3 32.7 1.0
CA A:CYS71 4.4 41.2 1.0
CA A:CYS74 4.4 35.3 1.0
CB A:THR73 4.5 38.3 1.0
O A:GLN62 4.6 37.1 1.0
CA A:CYS81 4.6 35.8 1.0
O A:CYS74 4.7 35.3 1.0
C A:CYS74 4.7 35.3 1.0
N A:GLY83 4.7 32.7 1.0
N A:GLY63 4.7 38.7 1.0
C A:GLY63 4.9 38.7 1.0
O A:ARG61 4.9 39.9 1.0
C A:GLN62 4.9 37.1 1.0
N A:THR73 4.9 38.3 1.0
C A:THR73 5.0 38.3 1.0
CD A:PRO82 5.0 30.6 1.0
CG2 A:VAL64 5.0 39.4 1.0

Zinc binding site 3 out of 9 in 6gml

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Zinc binding site 3 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Paused Transcription Complex Pol II-Dsif-Nelf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:58.5
occ:1.00
 SG B:CYS1119 2.5 32.2 1.0
SG B:CYS1122 2.5 36.0 1.0
SG B:CYS1137 2.5 48.8 1.0
CB B:CYS1140 2.6 47.0 1.0
SG B:CYS1140 3.2 47.0 1.0
CB B:CYS1137 3.2 48.8 1.0
CB B:CYS1119 3.9 32.2 1.0
CB B:CYS1122 4.0 36.0 1.0
N B:CYS1122 4.1 36.0 1.0
CA B:CYS1140 4.1 47.0 1.0
O B:CYS1122 4.3 36.0 1.0
N B:CYS1140 4.4 47.0 1.0
ND2 B:ASN1142 4.5 49.2 1.0
CA B:CYS1122 4.5 36.0 1.0
CA B:CYS1137 4.7 48.8 1.0
CB B:LEU1121 4.7 36.2 1.0
OD1 B:ASN1142 4.8 49.2 1.0
O B:CYS1137 4.8 48.8 1.0
CG B:ASN1142 4.8 49.2 1.0
C B:CYS1122 4.9 36.0 1.0
C B:CYS1140 5.0 47.0 1.0
CD1 B:ILE1124 5.0 29.4 1.0

Zinc binding site 4 out of 9 in 6gml

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Zinc binding site 4 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Paused Transcription Complex Pol II-Dsif-Nelf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:67.0
occ:1.00
 SG C:CYS88 2.4 27.2 1.0
SG C:CYS97 2.4 16.6 1.0
SG C:CYS90 2.5 37.8 1.0
SG C:CYS94 2.5 23.1 1.0
CB C:CYS88 2.6 27.2 1.0
CB C:CYS97 3.2 16.6 1.0
CB C:CYS90 3.3 37.8 1.0
CB C:CYS94 3.8 23.1 1.0
CA C:CYS88 4.1 27.2 1.0
N C:CYS97 4.1 16.6 1.0
NZ Z:LYS718 4.2 17.1 1.0
N C:CYS94 4.2 23.1 1.0
N C:CYS90 4.3 37.8 1.0
CA C:CYS97 4.3 16.6 1.0
CA C:CYS90 4.4 37.8 1.0
C C:CYS88 4.5 27.2 1.0
CA C:CYS94 4.6 23.1 1.0
C C:PHE93 4.6 26.0 1.0
O C:SER85 4.7 17.4 1.0
CA C:PHE93 4.8 26.0 1.0
N C:CYS88 4.9 27.2 1.0
C C:GLU96 4.9 20.3 1.0
O C:CYS88 4.9 27.2 1.0
N C:THR89 4.9 33.4 1.0
O C:CYS94 5.0 23.1 1.0

Zinc binding site 5 out of 9 in 6gml

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Zinc binding site 5 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Paused Transcription Complex Pol II-Dsif-Nelf within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn200

b:66.8
occ:1.00
 SG I:CYS20 2.5 42.0 1.0
SG I:CYS17 2.5 39.9 1.0
SG I:CYS42 2.5 43.2 1.0
SG I:CYS39 2.6 39.0 1.0
CB I:CYS39 2.7 39.0 1.0
CB I:CYS17 2.9 39.9 1.0
CB I:CYS42 3.9 43.2 1.0
CB I:CYS20 4.1 42.0 1.0
N I:CYS42 4.2 43.2 1.0
CA I:CYS39 4.2 39.0 1.0
CA I:CYS17 4.3 39.9 1.0
N I:CYS20 4.3 42.0 1.0
CA I:CYS42 4.5 43.2 1.0
CD2 I:LEU24 4.7 37.9 1.0
CB I:TYR44 4.7 39.4 1.0
CA I:CYS20 4.7 42.0 1.0
N I:ASN22 4.7 39.4 1.0
N I:ASN21 4.8 37.0 1.0
CB I:ASN22 4.8 39.4 1.0
C I:CYS42 4.9 43.2 1.0
N I:CYS39 4.9 39.0 1.0

Zinc binding site 6 out of 9 in 6gml

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Zinc binding site 6 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Paused Transcription Complex Pol II-Dsif-Nelf within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:58.9
occ:1.00
 SG I:CYS89 2.5 31.6 1.0
SG I:CYS86 2.5 32.1 1.0
SG I:CYS119 2.7 38.6 1.0
SG I:CYS114 3.2 26.9 1.0
CB I:CYS114 3.2 26.9 1.0
CB I:CYS119 3.3 38.6 1.0
CB I:HIS121 3.5 26.1 1.0
CB I:CYS86 3.5 32.1 1.0
CB I:CYS89 3.7 31.6 1.0
N I:HIS121 3.9 26.1 1.0
N I:CYS89 4.0 31.6 1.0
CA I:HIS121 4.3 26.1 1.0
CA I:CYS89 4.5 31.6 1.0
CA I:CYS119 4.5 38.6 1.0
CG I:HIS121 4.6 26.1 1.0
N I:GLY120 4.6 29.4 1.0
CB I:LYS88 4.6 28.1 1.0
C I:CYS119 4.6 38.6 1.0
CA I:CYS114 4.7 26.9 1.0
O I:HIS121 4.8 26.1 1.0
CA I:CYS86 4.9 32.1 1.0
CD2 I:HIS121 5.0 26.1 1.0
C I:HIS121 5.0 26.1 1.0

Zinc binding site 7 out of 9 in 6gml

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Zinc binding site 7 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

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

b:48.9
occ:1.00
 SG J:CYS45 2.4 21.6 1.0
SG J:CYS10 2.4 23.6 1.0
SG J:CYS7 2.5 28.0 1.0
CB J:CYS10 2.5 23.6 1.0
SG J:CYS44 2.7 23.7 1.0
N J:CYS10 3.3 23.6 1.0
CB J:CYS7 3.4 28.0 1.0
CA J:CYS10 3.5 23.6 1.0
N J:CYS45 3.7 21.6 1.0
CB J:CYS45 3.8 21.6 1.0
C J:CYS44 4.0 23.7 1.0
CA J:CYS45 4.0 21.6 1.0
CB J:CYS44 4.1 23.7 1.0
NE J:ARG42 4.2 17.0 1.0
O J:CYS44 4.3 23.7 1.0
C J:THR9 4.4 28.0 1.0
CB J:LYS12 4.5 22.4 1.0
C J:CYS10 4.6 23.6 1.0
CB J:THR9 4.6 28.0 1.0
N J:GLY11 4.6 28.9 1.0
CA J:CYS44 4.6 23.7 1.0
NH2 J:ARG42 4.6 17.0 1.0
CA J:CYS7 4.8 28.0 1.0
N J:THR9 4.8 28.0 1.0
CA J:THR9 4.9 28.0 1.0
N J:LYS12 4.9 22.4 1.0
CZ J:ARG42 4.9 17.0 1.0
CB J:ARG42 4.9 17.0 1.0

Zinc binding site 8 out of 9 in 6gml

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Zinc binding site 8 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

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

b:66.3
occ:1.00
 SG L:CYS36 2.5 38.0 1.0
CB L:CYS22 2.5 35.7 1.0
CG2 L:THR24 2.6 34.0 1.0
SG L:CYS22 2.6 35.7 1.0
CG L:GLU38 2.8 40.0 1.0
CB L:GLU38 2.9 40.0 1.0
CB L:CYS19 3.6 35.8 1.0
SG L:CYS19 3.9 35.8 1.0
N L:GLU38 3.9 40.0 1.0
CB L:THR24 4.0 34.0 1.0
CA L:CYS22 4.0 35.7 1.0
CA L:GLU38 4.0 40.0 1.0
CB L:CYS36 4.1 38.0 1.0
CD L:GLU38 4.2 40.0 1.0
C L:CYS22 4.6 35.7 1.0
N L:THR24 4.6 34.0 1.0
N L:CYS39 4.7 37.4 1.0
O L:CYS19 4.8 35.8 1.0
CA L:THR24 4.8 34.0 1.0
N L:CYS22 4.8 35.7 1.0
C L:GLU38 4.9 40.0 1.0
O L:CYS22 4.9 35.7 1.0
OE2 L:GLU38 4.9 40.0 1.0
OG1 L:THR24 4.9 34.0 1.0
OE1 L:GLU38 5.0 40.0 1.0

Zinc binding site 9 out of 9 in 6gml

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Zinc binding site 9 out of 9 in the Structure of Paused Transcription Complex Pol II-Dsif-Nelf


Mono view


Stereo pair view

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

b:0.3
occ:1.00
 SG Y:CYS16 2.5 81.2 1.0
SG Y:CYS33 2.5 73.7 1.0
SG Y:CYS19 2.5 84.5 1.0
CB Y:CYS16 3.4 81.2 1.0
N Y:CYS19 3.7 84.5 1.0
CB Y:CYS19 3.7 84.5 1.0
CB Y:CYS33 3.9 73.7 1.0
CB Y:LEU18 4.0 79.2 1.0
CD1 Y:LEU40 4.2 85.1 1.0
CA Y:CYS19 4.2 84.5 1.0
C Y:LEU18 4.6 79.2 1.0
N Y:LEU18 4.6 79.2 1.0
CA Y:LEU18 4.6 79.2 1.0
CD2 Y:LEU18 4.6 79.2 1.0
CG Y:LEU18 4.7 79.2 1.0
CB Y:LEU21 4.7 77.5 1.0
N Y:CYS36 4.8 80.7 1.0
CA Y:CYS16 4.8 81.2 1.0
C Y:CYS19 4.8 84.5 1.0
CB Y:CYS36 4.9 80.7 1.0
N Y:SER20 5.0 78.2 1.0

Reference:

S.M.Vos, L.Farnung, H.Urlaub, P.Cramer. Structure of Paused Transcription Complex Pol II-Dsif-Nelf. Nature V. 560 601 2018.
ISSN: ESSN 1476-4687
PubMed: 30135580
DOI: 10.1038/S41586-018-0442-2
Page generated: Mon Oct 28 21:54:39 2024

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