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Zinc in PDB 8oeu: Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)

Enzymatic activity of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)

All present enzymatic activity of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4):
2.7.7.6;

Other elements in 8oeu:

The structure of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) (pdb code 8oeu). 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 the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4), PDB code: 8oeu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8oeu

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Zinc binding site 1 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:95.8
occ:1.00
 NE2 A:HIS84 2.0 75.8 1.0
SG A:CYS81 2.3 76.2 1.0
SG A:CYS74 2.3 88.8 1.0
SG A:CYS71 2.3 87.2 1.0
CD2 A:HIS84 2.7 75.8 1.0
CB A:CYS71 2.9 87.2 1.0
CE1 A:HIS84 3.2 75.8 1.0
CB A:CYS81 3.4 76.2 1.0
N A:CYS74 3.8 88.8 1.0
CB A:CYS74 3.8 88.8 1.0
CG A:HIS84 3.9 75.8 1.0
O A:CYS74 4.1 88.8 1.0
ND1 A:HIS84 4.2 75.8 1.0
CA A:CYS81 4.2 76.2 1.0
CA A:CYS74 4.3 88.8 1.0
CA A:CYS71 4.4 87.2 1.0
CB A:THR73 4.5 81.0 1.0
C A:CYS74 4.6 88.8 1.0
CA A:GLY63 4.7 83.8 1.0
N A:GLY83 4.7 71.8 1.0
O A:GLN62 4.7 77.1 1.0
CD A:PRO82 4.8 70.5 1.0
C A:THR73 4.8 81.0 1.0
C A:CYS81 4.8 76.2 1.0
N A:THR73 4.9 81.0 1.0
CA A:THR73 5.0 81.0 1.0
N A:PRO82 5.0 70.5 1.0
O A:ARG61 5.0 82.2 1.0
C A:CYS71 5.0 87.2 1.0
CA A:GLY83 5.0 71.8 1.0

Zinc binding site 2 out of 8 in 8oeu

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Zinc binding site 2 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:166.5
occ:1.00
 SG A:CYS114 2.3 133.4 1.0
SG A:CYS154 2.3 157.2 1.0
SG A:CYS111 2.3 133.1 1.0
SG A:CYS184 2.3 156.7 1.0
CB A:CYS184 3.0 156.7 1.0
CB A:CYS114 3.0 133.4 1.0
CB A:CYS111 3.0 133.1 1.0
N A:CYS114 3.4 133.4 1.0
CA A:CYS114 3.8 133.4 1.0
CB A:CYS154 3.8 157.2 1.0
N A:CYS184 3.9 156.7 1.0
CA A:CYS184 4.0 156.7 1.0
NE2 A:GLN188 4.1 146.1 1.0
CA A:CYS111 4.5 133.1 1.0
C A:GLY183 4.5 153.7 1.0
C A:PHE113 4.5 131.2 1.0
CB A:PHE113 4.6 131.2 1.0
C A:CYS114 4.6 133.4 1.0
N A:PHE113 4.8 131.2 1.0
N A:SER115 4.9 124.6 1.0
CA A:PHE113 4.9 131.2 1.0
CD2 A:PHE113 4.9 131.2 1.0
O A:CYS154 5.0 157.2 1.0

Zinc binding site 3 out of 8 in 8oeu

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Zinc binding site 3 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:99.0
occ:1.00
 SG B:CYS1199 2.3 73.2 1.0
SG B:CYS1214 2.3 82.3 1.0
SG B:CYS1196 2.3 76.2 1.0
SG B:CYS1217 2.3 85.7 1.0
CB B:CYS1196 2.8 76.2 1.0
CB B:CYS1217 3.2 85.7 1.0
CB B:CYS1199 3.4 73.2 1.0
CB B:CYS1214 3.6 82.3 1.0
N B:CYS1199 3.8 73.2 1.0
CA B:CYS1199 4.2 73.2 1.0
CA B:CYS1196 4.3 76.2 1.0
N B:CYS1217 4.5 85.7 1.0
CA B:CYS1217 4.5 85.7 1.0
CB B:LEU1198 4.7 77.5 1.0
ND2 B:ASN1219 4.7 81.3 1.0
O B:ARG1215 4.8 84.6 1.0
CB B:ASN1219 4.8 81.3 1.0
C B:LEU1198 4.9 77.5 1.0
C B:GLY1216 4.9 85.6 1.0
C B:CYS1196 4.9 76.2 1.0
CA B:CYS1214 5.0 82.3 1.0
O B:CYS1214 5.0 82.3 1.0
N B:GLY1200 5.0 69.0 1.0
C B:CYS1199 5.0 73.2 1.0

Zinc binding site 4 out of 8 in 8oeu

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Zinc binding site 4 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

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

b:88.5
occ:1.00
 SG C:CYS94 2.3 61.4 1.0
SG C:CYS88 2.3 69.5 1.0
SG C:CYS90 2.3 74.2 1.0
SG C:CYS97 2.3 55.3 1.0
CB C:CYS97 3.1 55.3 1.0
CB C:CYS88 3.2 69.5 1.0
CB C:CYS90 3.2 74.2 1.0
CB C:CYS94 3.4 61.4 1.0
N C:CYS94 3.6 61.4 1.0
N C:CYS97 3.9 55.3 1.0
CA C:CYS94 3.9 61.4 1.0
CA C:CYS97 4.1 55.3 1.0
O C:CYS94 4.1 61.4 1.0
C C:PHE93 4.2 60.6 1.0
N C:CYS90 4.3 74.2 1.0
C C:CYS94 4.3 61.4 1.0
CA C:CYS90 4.3 74.2 1.0
CA C:PHE93 4.5 60.6 1.0
C C:GLU96 4.6 59.6 1.0
CA C:CYS88 4.6 69.5 1.0
CB C:GLU96 4.8 59.6 1.0
N C:GLU96 4.9 59.6 1.0
C C:CYS97 5.0 55.3 1.0
C C:CYS88 5.0 69.5 1.0
O C:PHE93 5.0 60.6 1.0

Zinc binding site 5 out of 8 in 8oeu

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Zinc binding site 5 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:113.4
occ:1.00
 SG I:CYS89 2.3 95.7 1.0
SG I:CYS119 2.3 99.8 1.0
SG I:CYS86 2.3 89.5 1.0
SG I:CYS114 2.3 82.1 1.0
CB I:CYS114 3.0 82.1 1.0
CB I:CYS86 3.1 89.5 1.0
CB I:CYS119 3.5 99.8 1.0
CB I:CYS89 3.6 95.7 1.0
N I:CYS89 4.0 95.7 1.0
CB I:HIS121 4.2 86.1 1.0
CB I:HIS91 4.4 85.8 1.0
CA I:CYS89 4.4 95.7 1.0
CA I:CYS114 4.5 82.1 1.0
CA I:CYS86 4.6 89.5 1.0
N I:HIS121 4.6 86.1 1.0
CB I:LYS88 4.7 90.8 1.0
CA I:CYS119 4.8 99.8 1.0
N I:HIS91 4.8 85.8 1.0
C I:LYS88 4.9 90.8 1.0
CB I:ALA116 4.9 94.3 1.0
C I:CYS89 5.0 95.7 1.0

Zinc binding site 6 out of 8 in 8oeu

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Zinc binding site 6 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:165.0
occ:1.00
 SG I:CYS20 2.3 128.3 1.0
SG I:CYS39 2.3 138.2 1.0
SG I:CYS42 2.3 144.0 1.0
SG I:CYS17 2.3 130.8 1.0
CB I:CYS39 3.0 138.2 1.0
CB I:CYS17 3.2 130.8 1.0
CB I:CYS42 3.7 144.0 1.0
N I:CYS42 3.9 144.0 1.0
CB I:CYS20 4.0 128.3 1.0
N I:CYS20 4.3 128.3 1.0
CA I:CYS42 4.3 144.0 1.0
CB I:TYR44 4.3 135.7 1.0
CA I:CYS39 4.5 138.2 1.0
CA I:CYS20 4.7 128.3 1.0
CA I:CYS17 4.7 130.8 1.0
C I:CYS42 4.7 144.0 1.0
CB I:ASN41 4.7 134.8 1.0
C I:CYS39 4.9 138.2 1.0
C I:ASN41 4.9 134.8 1.0
CB I:GLU19 4.9 134.5 1.0
N I:TYR44 5.0 135.7 1.0
O I:CYS42 5.0 144.0 1.0

Zinc binding site 7 out of 8 in 8oeu

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Zinc binding site 7 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:41.0
occ:1.00
 SG J:CYS10 2.3 29.8 1.0
SG J:CYS45 2.3 33.6 1.0
SG J:CYS44 2.3 33.9 1.0
SG J:CYS7 2.3 27.2 1.0
CB J:CYS7 3.2 27.2 1.0
N J:CYS45 3.2 33.6 1.0
CB J:CYS10 3.4 29.8 1.0
CB J:CYS45 3.5 33.6 1.0
CB J:CYS44 3.6 33.9 1.0
CA J:CYS45 3.6 33.6 1.0
C J:CYS44 3.7 33.9 1.0
N J:CYS10 3.9 29.8 1.0
NE J:ARG42 4.0 35.0 1.0
O J:CYS44 4.1 33.9 1.0
CA J:CYS10 4.2 29.8 1.0
CA J:CYS44 4.2 33.9 1.0
NH2 J:ARG42 4.3 35.0 1.0
CB J:THR9 4.6 27.8 1.0
CA J:CYS7 4.6 27.2 1.0
CB J:LYS12 4.7 29.5 1.0
N J:GLY11 4.7 28.6 1.0
CZ J:ARG42 4.7 35.0 1.0
CB J:ARG42 4.8 35.0 1.0
N J:LYS12 4.9 29.5 1.0
C J:THR9 4.9 27.8 1.0
C J:CYS10 4.9 29.8 1.0
CG2 J:THR9 4.9 27.8 1.0
N J:CYS44 4.9 33.9 1.0

Zinc binding site 8 out of 8 in 8oeu

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Zinc binding site 8 out of 8 in the Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the Mammalian Pol II-SPT6 Complex (Composite Structure, Structure 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:122.5
occ:1.00
 SG L:CYS22 2.3 87.9 1.0
SG L:CYS36 2.3 93.2 1.0
SG L:CYS19 2.3 84.8 1.0
SG L:CYS39 2.3 96.0 1.0
CB L:CYS36 3.0 93.2 1.0
CB L:CYS19 3.2 84.8 1.0
CB L:CYS22 3.6 87.9 1.0
CB L:CYS39 3.7 96.0 1.0
OG1 L:THR24 3.8 87.6 1.0
N L:CYS22 4.0 87.9 1.0
N L:CYS39 4.0 96.0 1.0
OE1 L:GLU38 4.2 96.7 1.0
CB L:TYR41 4.3 80.9 1.0
CA L:CYS39 4.3 96.0 1.0
CA L:CYS22 4.4 87.9 1.0
CA L:CYS36 4.5 93.2 1.0
N L:TYR41 4.6 80.9 1.0
CA L:CYS19 4.6 84.8 1.0
C L:CYS39 4.8 96.0 1.0
CB L:GLU38 4.8 96.7 1.0
N L:GLY40 4.8 93.5 1.0
ND2 L:ASN26 4.8 88.5 1.0
CB L:GLU21 4.9 84.0 1.0
C L:CYS22 5.0 87.9 1.0
C L:GLU38 5.0 96.7 1.0

Reference:

Y.Chen, G.Kokic, C.Dienemann, O.Dybkov, H.Urlaub, P.Cramer. Structure of Transcribing Rna Polymerase II-Elongin Complex Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-01138-W
Page generated: Thu Oct 31 08:44:15 2024

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