Zinc in PDB 7ol0: Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)

Enzymatic activity of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)

All present enzymatic activity of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5):
2.7.7.6;

Other elements in 7ol0:

The structure of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) (pdb code 7ol0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5), PDB code: 7ol0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7ol0

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Zinc binding site 1 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:70.0
occ:1.00
NE2 A:HIS84 2.1 41.4 1.0
SG A:CYS74 2.3 51.6 1.0
SG A:CYS71 2.3 53.9 1.0
SG A:CYS81 2.3 47.3 1.0
CD2 A:HIS84 2.7 41.4 1.0
CB A:CYS71 2.9 53.9 1.0
CE1 A:HIS84 3.2 41.4 1.0
CB A:CYS81 3.5 47.3 1.0
N A:CYS74 3.8 51.6 1.0
CB A:CYS74 3.9 51.6 1.0
CG A:HIS84 4.0 41.4 1.0
ND1 A:HIS84 4.2 41.4 1.0
CA A:CYS81 4.2 47.3 1.0
CA A:CYS74 4.3 51.6 1.0
O A:CYS74 4.3 51.6 1.0
CA A:CYS71 4.4 53.9 1.0
CB A:THR73 4.5 46.5 1.0
CA A:GLY63 4.5 47.4 1.0
C A:CYS74 4.6 51.6 1.0
N A:GLY83 4.7 41.1 1.0
CD A:PRO82 4.7 42.9 1.0
N A:THR73 4.8 46.5 1.0
C A:THR73 4.8 46.5 1.0
C A:CYS81 4.9 47.3 1.0
N A:GLY63 4.9 47.4 1.0
CA A:THR73 4.9 46.5 1.0
CA A:GLY83 5.0 41.1 1.0
N A:PRO82 5.0 42.9 1.0

Zinc binding site 2 out of 8 in 7ol0

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Zinc binding site 2 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


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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 Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:116.6
occ:1.00
SG A:CYS111 2.3 72.6 1.0
SG A:CYS184 2.3 78.9 1.0
SG A:CYS114 2.3 75.6 1.0
SG A:CYS154 2.3 81.2 1.0
CB A:CYS154 3.1 81.2 1.0
CB A:CYS111 3.2 72.6 1.0
CB A:CYS114 3.7 75.6 1.0
CB A:CYS184 3.8 78.9 1.0
N A:CYS184 3.9 78.9 1.0
CA A:CYS184 4.2 78.9 1.0
O A:CYS184 4.2 78.9 1.0
N A:CYS114 4.2 75.6 1.0
C A:CYS184 4.3 78.9 1.0
NE2 A:GLN188 4.4 75.7 1.0
CA A:CYS114 4.6 75.6 1.0
CA A:CYS154 4.6 81.2 1.0
CA A:CYS111 4.6 72.6 1.0
C A:GLY183 4.9 68.1 1.0

Zinc binding site 3 out of 8 in 7ol0

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Zinc binding site 3 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:100.5
occ:1.00
SG B:CYS1199 2.3 49.1 1.0
SG B:CYS1214 2.3 64.8 1.0
SG B:CYS1196 2.3 50.7 1.0
SG B:CYS1217 2.3 65.7 1.0
CB B:CYS1196 2.9 50.7 1.0
CB B:CYS1199 3.1 49.1 1.0
CB B:CYS1217 3.2 65.7 1.0
CB B:CYS1214 3.5 64.8 1.0
N B:CYS1199 3.6 49.1 1.0
CA B:CYS1199 4.0 49.1 1.0
N B:CYS1217 4.3 65.7 1.0
CA B:CYS1196 4.4 50.7 1.0
CA B:CYS1217 4.4 65.7 1.0
OD1 B:ASN1219 4.5 64.1 1.0
CB B:LEU1198 4.7 48.8 1.0
N B:GLY1200 4.8 42.8 1.0
C B:CYS1199 4.8 49.1 1.0
C B:LEU1198 4.8 48.8 1.0
CA B:CYS1214 4.9 64.8 1.0
C B:CYS1196 4.9 50.7 1.0
O B:ARG1215 5.0 65.2 1.0
ND2 B:ASN1219 5.0 64.1 1.0

Zinc binding site 4 out of 8 in 7ol0

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Zinc binding site 4 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:88.7
occ:1.00
SG C:CYS94 2.3 35.5 1.0
SG C:CYS90 2.3 49.6 1.0
SG C:CYS88 2.3 45.6 1.0
SG C:CYS97 2.3 32.8 1.0
CB C:CYS88 3.1 45.6 1.0
CB C:CYS97 3.2 32.8 1.0
CB C:CYS90 3.4 49.6 1.0
CB C:CYS94 3.4 35.5 1.0
N C:CYS94 3.6 35.5 1.0
N C:CYS97 4.0 32.8 1.0
CA C:CYS94 4.0 35.5 1.0
O C:CYS94 4.2 35.5 1.0
CA C:CYS97 4.2 32.8 1.0
N C:CYS90 4.3 49.6 1.0
C C:CYS94 4.4 35.5 1.0
CA C:CYS90 4.4 49.6 1.0
CA C:CYS88 4.4 45.6 1.0
C C:PHE93 4.5 37.1 1.0
C C:GLU96 4.6 37.8 1.0
NZ Z:LYS718 4.7 54.4 1.0
C C:CYS88 4.7 45.6 1.0
CA C:PHE93 4.7 37.1 1.0
CB C:GLU96 4.8 37.8 1.0
N C:GLU96 4.9 37.8 1.0
N C:THR89 5.0 45.5 1.0

Zinc binding site 5 out of 8 in 7ol0

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Zinc binding site 5 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:85.2
occ:1.00
SG I:CYS119 2.3 54.6 1.0
SG I:CYS114 2.3 40.7 1.0
SG I:CYS89 2.3 57.6 1.0
SG I:CYS86 2.3 54.1 1.0
CB I:CYS114 3.1 40.7 1.0
CB I:CYS86 3.1 54.1 1.0
CB I:CYS119 3.4 54.6 1.0
CB I:CYS89 3.5 57.6 1.0
N I:CYS89 3.9 57.6 1.0
CA I:CYS89 4.2 57.6 1.0
CB I:HIS91 4.2 49.0 1.0
CB I:HIS121 4.4 43.7 1.0
CB I:ALA116 4.5 48.6 1.0
CA I:CYS114 4.5 40.7 1.0
CA I:CYS86 4.6 54.1 1.0
N I:HIS91 4.7 49.0 1.0
C I:CYS89 4.7 57.6 1.0
CB I:LYS88 4.7 54.7 1.0
CA I:CYS119 4.8 54.6 1.0
N I:GLY90 4.9 54.0 1.0
N I:HIS121 4.9 43.7 1.0

Zinc binding site 6 out of 8 in 7ol0

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Zinc binding site 6 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:95.8
occ:1.00
SG I:CYS20 2.3 61.5 1.0
SG I:CYS39 2.3 55.9 1.0
SG I:CYS17 2.3 57.5 1.0
SG I:CYS42 2.3 67.4 1.0
CB I:CYS42 2.9 67.4 1.0
CB I:CYS20 3.1 61.5 1.0
CB I:CYS17 3.3 57.5 1.0
CB I:CYS39 3.4 55.9 1.0
N I:CYS20 3.5 61.5 1.0
N I:CYS42 3.8 67.4 1.0
CA I:CYS20 3.8 61.5 1.0
CA I:CYS42 3.9 67.4 1.0
C I:CYS20 4.4 61.5 1.0
N I:ASN21 4.5 53.5 1.0
C I:ASN41 4.5 61.6 1.0
CA I:CYS17 4.7 57.5 1.0
C I:GLU19 4.7 63.4 1.0
CA I:CYS39 4.8 55.9 1.0
CB I:TYR44 4.8 57.6 1.0
N I:ASN22 4.9 51.4 1.0
CB I:ASN41 4.9 61.6 1.0
N I:GLU19 4.9 63.4 1.0
CB I:GLU19 4.9 63.4 1.0
OE1 I:GLU19 4.9 63.4 1.0
N I:ASN41 5.0 61.6 1.0

Zinc binding site 7 out of 8 in 7ol0

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Zinc binding site 7 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:43.0
occ:1.00
SG J:CYS45 2.3 20.5 1.0
SG J:CYS10 2.3 19.2 1.0
SG J:CYS44 2.3 22.2 1.0
SG J:CYS7 2.3 30.8 1.0
CB J:CYS7 3.1 30.8 1.0
N J:CYS45 3.3 20.5 1.0
CB J:CYS10 3.4 19.2 1.0
CB J:CYS44 3.5 22.2 1.0
CB J:CYS45 3.5 20.5 1.0
CA J:CYS45 3.7 20.5 1.0
C J:CYS44 3.7 22.2 1.0
N J:CYS10 3.8 19.2 1.0
CA J:CYS10 4.1 19.2 1.0
CA J:CYS44 4.2 22.2 1.0
O J:CYS44 4.2 22.2 1.0
NE J:ARG42 4.2 18.4 1.0
CA J:CYS7 4.6 30.8 1.0
CB J:THR9 4.6 23.9 1.0
CB J:LYS12 4.6 17.5 1.0
N J:GLY11 4.6 18.8 1.0
NH2 J:ARG42 4.7 18.4 1.0
C J:CYS10 4.8 19.2 1.0
N J:LYS12 4.8 17.5 1.0
N J:CYS44 4.8 22.2 1.0
C J:THR9 4.8 23.9 1.0
CB J:ARG42 4.9 18.4 1.0
CG2 J:THR9 4.9 23.9 1.0
N J:THR9 5.0 23.9 1.0
CZ J:ARG42 5.0 18.4 1.0
C J:CYS7 5.0 30.8 1.0

Zinc binding site 8 out of 8 in 7ol0

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Zinc binding site 8 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:86.5
occ:1.00
SG L:CYS22 2.3 46.4 1.0
SG L:CYS19 2.3 40.8 1.0
SG L:CYS36 2.3 49.3 1.0
SG L:CYS39 2.3 52.0 1.0
CB L:CYS19 3.0 40.8 1.0
CB L:CYS36 3.1 49.3 1.0
CB L:CYS22 3.4 46.4 1.0
CB L:CYS39 3.8 52.0 1.0
N L:CYS39 3.9 52.0 1.0
N L:CYS22 4.1 46.4 1.0
OG1 L:THR24 4.2 45.0 1.0
CA L:CYS22 4.3 46.4 1.0
CA L:CYS39 4.3 52.0 1.0
CA L:CYS19 4.5 40.8 1.0
CB L:TYR41 4.5 39.4 1.0
CA L:CYS36 4.5 49.3 1.0
CB L:GLU38 4.6 58.4 1.0
CG L:GLU21 4.7 48.6 1.0
N L:TYR41 4.7 39.4 1.0
N L:GLY40 4.7 46.6 1.0
C L:CYS39 4.8 52.0 1.0
C L:CYS22 4.9 46.4 1.0
C L:GLU38 5.0 58.4 1.0
N L:HIS23 5.0 43.8 1.0

Reference:

Y.Chen, S.M.Vos, C.Dienemann, M.Ninov, H.Urlaub, P.Cramer. Allosteric Transcription Stimulation By Rna Polymerase II Super Elongation Complex To Be Published.
Page generated: Sun Aug 22 09:53:12 2021

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