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Zinc in PDB 7okx: Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)

Enzymatic activity of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)

All present enzymatic activity of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure):
2.7.7.6;

Other elements in 7okx:

The structure of Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure) 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)-ELL2-EAF1 (Composite Structure) (pdb code 7okx). 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)-ELL2-EAF1 (Composite Structure), PDB code: 7okx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7okx

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Zinc binding site 1 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:86.0
occ:1.00
 NE2 A:HIS84 2.1 39.9 1.0
SG A:CYS81 2.3 45.8 1.0
SG A:CYS74 2.3 50.4 1.0
SG A:CYS71 2.3 54.0 1.0
CD2 A:HIS84 2.6 39.9 1.0
CB A:CYS71 3.0 54.0 1.0
CE1 A:HIS84 3.3 39.9 1.0
CB A:CYS81 3.6 45.8 1.0
CG A:HIS84 3.9 39.9 1.0
CB A:CYS74 3.9 50.4 1.0
N A:CYS74 3.9 50.4 1.0
ND1 A:HIS84 4.1 39.9 1.0
CA A:CYS81 4.3 45.8 1.0
CA A:GLY63 4.3 47.3 1.0
CA A:CYS74 4.4 50.4 1.0
CA A:CYS71 4.5 54.0 1.0
CB A:THR73 4.5 47.1 1.0
O A:CYS74 4.7 50.4 1.0
N A:GLY83 4.7 38.1 1.0
CD A:PRO82 4.7 37.9 1.0
N A:GLY63 4.7 47.3 1.0
C A:CYS74 4.8 50.4 1.0
C A:CYS81 4.9 45.8 1.0
CA A:GLY83 5.0 38.1 1.0
C A:GLY63 5.0 47.3 1.0
N A:THR73 5.0 47.1 1.0
C A:THR73 5.0 47.1 1.0
N A:PRO82 5.0 37.9 1.0

Zinc binding site 2 out of 8 in 7okx

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Zinc binding site 2 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:124.6
occ:1.00
 CB A:CYS184 2.1 79.7 1.0
SG A:CYS114 2.3 69.9 1.0
SG A:CYS111 2.3 65.6 1.0
SG A:CYS154 2.3 76.8 1.0
SG A:CYS184 2.3 79.7 1.0
CB A:CYS111 3.1 65.6 1.0
CB A:CYS154 3.2 76.8 1.0
CB A:CYS114 3.5 69.9 1.0
CA A:CYS184 3.6 79.7 1.0
N A:CYS114 4.0 69.9 1.0
N A:CYS184 4.2 79.7 1.0
CA A:CYS114 4.3 69.9 1.0
C A:CYS184 4.3 79.7 1.0
NE2 A:GLN188 4.4 72.2 1.0
N A:GLY185 4.4 74.2 1.0
CA A:CYS111 4.5 65.6 1.0
CA A:CYS154 4.7 76.8 1.0
C A:CYS114 4.9 69.9 1.0
N A:ARG186 4.9 75.4 1.0

Zinc binding site 3 out of 8 in 7okx

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Zinc binding site 3 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:108.5
occ:1.00
 SG B:CYS1199 2.3 49.7 1.0
SG B:CYS1214 2.3 52.7 1.0
SG B:CYS1196 2.3 45.4 1.0
SG B:CYS1217 2.3 64.8 1.0
CB B:CYS1196 2.9 45.4 1.0
CB B:CYS1217 3.0 64.8 1.0
CB B:CYS1199 3.0 49.7 1.0
CB B:CYS1214 3.4 52.7 1.0
N B:CYS1199 3.5 49.7 1.0
CA B:CYS1199 3.8 49.7 1.0
CA B:CYS1217 4.2 64.8 1.0
N B:CYS1217 4.3 64.8 1.0
OD1 B:ASN1219 4.4 55.0 1.0
CA B:CYS1196 4.4 45.4 1.0
C B:CYS1199 4.6 49.7 1.0
CB B:LEU1198 4.6 46.0 1.0
C B:LEU1198 4.7 46.0 1.0
N B:GLY1200 4.8 42.6 1.0
CA B:CYS1214 4.8 52.7 1.0
O B:CYS1214 4.9 52.7 1.0
N B:LEU1198 5.0 46.0 1.0
CA B:LEU1198 5.0 46.0 1.0

Zinc binding site 4 out of 8 in 7okx

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Zinc binding site 4 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


Mono view


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:104.9
occ:1.00
 SG C:CYS94 2.3 41.6 1.0
SG C:CYS90 2.3 55.4 1.0
SG C:CYS88 2.3 49.6 1.0
SG C:CYS97 2.3 37.0 1.0
CB C:CYS97 3.2 37.0 1.0
CB C:CYS90 3.2 55.4 1.0
CB C:CYS88 3.2 49.6 1.0
CB C:CYS94 3.7 41.6 1.0
N C:CYS94 3.8 41.6 1.0
N C:CYS97 3.9 37.0 1.0
CA C:CYS97 4.2 37.0 1.0
NZ Z:LYS718 4.2 52.4 1.0
N C:CYS90 4.2 55.4 1.0
CA C:CYS94 4.2 41.6 1.0
CA C:CYS90 4.3 55.4 1.0
C C:PHE93 4.4 38.4 1.0
O C:CYS94 4.4 41.6 1.0
CA C:CYS88 4.6 49.6 1.0
CA C:PHE93 4.6 38.4 1.0
C C:GLU96 4.6 40.2 1.0
C C:CYS94 4.6 41.6 1.0
CB C:GLU96 4.7 40.2 1.0
C C:CYS88 4.9 49.6 1.0

Zinc binding site 5 out of 8 in 7okx

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Zinc binding site 5 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:126.8
occ:1.00
 SG I:CYS119 2.3 64.0 1.0
SG I:CYS89 2.3 69.0 1.0
SG I:CYS86 2.3 62.4 1.0
SG I:CYS114 2.3 51.3 1.0
CB I:CYS86 3.1 62.4 1.0
CB I:CYS114 3.1 51.3 1.0
CB I:CYS119 3.4 64.0 1.0
CB I:CYS89 3.6 69.0 1.0
N I:CYS89 3.9 69.0 1.0
CB I:HIS91 4.2 61.3 1.0
CA I:CYS89 4.3 69.0 1.0
CB I:HIS121 4.4 54.4 1.0
CA I:CYS86 4.6 62.4 1.0
CB I:ALA116 4.6 57.2 1.0
CA I:CYS114 4.6 51.3 1.0
N I:HIS91 4.6 61.3 1.0
CB I:LYS88 4.8 63.6 1.0
C I:CYS89 4.8 69.0 1.0
CA I:CYS119 4.8 64.0 1.0
N I:GLY90 4.8 62.6 1.0
N I:HIS121 4.9 54.4 1.0

Zinc binding site 6 out of 8 in 7okx

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Zinc binding site 6 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:78.9
occ:1.00
 CB I:CYS20 1.9 34.2 1.0
CB I:CYS42 2.2 49.8 1.0
SG I:CYS39 2.3 45.5 1.0
SG I:CYS17 2.4 35.1 1.0
SG I:CYS42 2.4 49.8 1.0
SG I:CYS20 2.4 34.2 1.0
CB I:CYS39 3.3 45.5 1.0
CA I:CYS20 3.3 34.2 1.0
CB I:CYS17 3.4 35.1 1.0
CA I:CYS42 3.7 49.8 1.0
N I:CYS20 3.8 34.2 1.0
C I:CYS20 4.1 34.2 1.0
N I:CYS42 4.2 49.8 1.0
OD1 I:ASN41 4.3 45.7 1.0
N I:ASN21 4.3 30.1 1.0
C I:CYS42 4.6 49.8 1.0
C I:GLU19 4.7 35.0 1.0
N I:ASP43 4.7 50.3 1.0
CA I:CYS39 4.7 45.5 1.0
CB I:TYR44 4.8 47.0 1.0
N I:ASN22 4.8 32.4 1.0
O I:CYS20 4.8 34.2 1.0
CA I:CYS17 4.9 35.1 1.0
N I:TYR44 4.9 47.0 1.0

Zinc binding site 7 out of 8 in 7okx

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Zinc binding site 7 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:57.4
occ:1.00
 SG J:CYS10 2.3 15.2 1.0
SG J:CYS45 2.3 21.8 1.0
SG J:CYS44 2.3 20.3 1.0
SG J:CYS7 2.3 15.2 1.0
CB J:CYS7 3.2 15.2 1.0
N J:CYS45 3.3 21.8 1.0
CB J:CYS10 3.4 15.2 1.0
CB J:CYS45 3.6 21.8 1.0
CB J:CYS44 3.6 20.3 1.0
CA J:CYS45 3.6 21.8 1.0
C J:CYS44 3.6 20.3 1.0
N J:CYS10 3.9 15.2 1.0
O J:CYS44 4.1 20.3 1.0
CA J:CYS44 4.2 20.3 1.0
NE J:ARG42 4.2 23.2 1.0
CA J:CYS10 4.3 15.2 1.0
NH2 J:ARG42 4.5 23.2 1.0
CB J:LYS12 4.6 15.4 1.0
CB J:THR9 4.6 14.6 1.0
CA J:CYS7 4.7 15.2 1.0
N J:GLY11 4.8 16.1 1.0
N J:LYS12 4.8 15.4 1.0
CB J:ARG42 4.9 23.2 1.0
CZ J:ARG42 4.9 23.2 1.0
N J:CYS44 4.9 20.3 1.0
C J:CYS10 4.9 15.2 1.0
C J:THR9 4.9 14.6 1.0

Zinc binding site 8 out of 8 in 7okx

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Zinc binding site 8 out of 8 in the Structure of Active Transcription Elongation Complex Pol II-Dsif (SPT5-KOW5)-ELL2-EAF1 (Composite Structure)


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)-ELL2-EAF1 (Composite Structure) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:98.8
occ:1.00
 SG L:CYS22 2.3 53.1 1.0
SG L:CYS36 2.3 57.0 1.0
SG L:CYS19 2.3 49.5 1.0
SG L:CYS39 2.3 56.2 1.0
CB L:CYS36 3.1 57.0 1.0
CB L:CYS19 3.1 49.5 1.0
CB L:CYS22 3.3 53.1 1.0
CB L:CYS39 3.8 56.2 1.0
N L:CYS22 4.0 53.1 1.0
N L:CYS39 4.0 56.2 1.0
OG1 L:THR24 4.2 52.0 1.0
CA L:CYS22 4.2 53.1 1.0
CA L:CYS39 4.4 56.2 1.0
CB L:TYR41 4.4 43.0 1.0
CA L:CYS36 4.5 57.0 1.0
CA L:CYS19 4.6 49.5 1.0
N L:TYR41 4.7 43.0 1.0
CG L:GLU21 4.7 52.0 1.0
N L:GLY40 4.8 48.8 1.0
C L:CYS22 4.9 53.1 1.0
C L:CYS39 4.9 56.2 1.0
CB L:GLU38 4.9 59.6 1.0
O L:TYR41 4.9 43.0 1.0
N L:HIS23 5.0 51.0 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: Wed Oct 30 08:34:20 2024

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