Zinc in PDB 8oev: Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)

Enzymatic activity of Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)

All present enzymatic activity of Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3):
2.7.7.6;

Other elements in 8oev:

The structure of Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) 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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) (pdb code 8oev). 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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3), PDB code: 8oev:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8oev

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Zinc binding site 1 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:69.9
occ:1.00
 NE2 A:HIS84 2.1 40.4 1.0
SG A:CYS74 2.3 53.4 1.0
SG A:CYS81 2.3 43.1 1.0
SG A:CYS71 2.3 55.6 1.0
CD2 A:HIS84 2.6 40.4 1.0
CB A:CYS71 2.9 55.6 1.0
CE1 A:HIS84 3.2 40.4 1.0
CB A:CYS81 3.6 43.1 1.0
CG A:HIS84 3.9 40.4 1.0
CB A:CYS74 3.9 53.4 1.0
N A:CYS74 3.9 53.4 1.0
ND1 A:HIS84 4.1 40.4 1.0
O A:CYS74 4.2 53.4 1.0
CA A:CYS81 4.3 43.1 1.0
CA A:CYS74 4.4 53.4 1.0
CA A:CYS71 4.4 55.6 1.0
CA A:GLY63 4.5 48.1 1.0
CB A:THR73 4.6 50.2 1.0
N A:GLY83 4.6 37.5 1.0
CD A:PRO82 4.7 37.6 1.0
C A:CYS74 4.7 53.4 1.0
O A:GLN62 4.7 42.7 1.0
C A:CYS81 4.9 43.1 1.0
C A:THR73 4.9 50.2 1.0
N A:THR73 4.9 50.2 1.0
CA A:GLY83 4.9 37.5 1.0
N A:PRO82 4.9 37.6 1.0

Zinc binding site 2 out of 8 in 8oev

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Zinc binding site 2 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:122.3
occ:1.00
 CB A:CYS184 2.2 87.2 1.0
SG A:CYS111 2.3 79.4 1.0
SG A:CYS114 2.3 79.0 1.0
SG A:CYS154 2.3 89.8 1.0
SG A:CYS184 2.3 87.2 1.0
CB A:CYS111 3.1 79.4 1.0
CB A:CYS114 3.4 79.0 1.0
N A:CYS114 3.7 79.0 1.0
CA A:CYS184 3.7 87.2 1.0
CB A:CYS154 4.1 89.8 1.0
NE2 A:GLN188 4.1 84.3 1.0
CA A:CYS114 4.1 79.0 1.0
N A:CYS184 4.3 87.2 1.0
C A:CYS184 4.5 87.2 1.0
CA A:CYS111 4.6 79.4 1.0
CB A:PHE113 4.7 78.7 1.0
C A:PHE113 4.8 78.7 1.0
C A:CYS114 4.9 79.0 1.0
N A:PHE113 4.9 78.7 1.0
CD2 A:PHE113 5.0 78.7 1.0

Zinc binding site 3 out of 8 in 8oev

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


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:97.5
occ:1.00
 SG B:CYS1199 2.3 50.8 1.0
SG B:CYS1196 2.3 51.1 1.0
SG B:CYS1214 2.3 61.3 1.0
SG B:CYS1217 2.3 68.3 1.0
CB B:CYS1196 2.7 51.1 1.0
CB B:CYS1217 3.1 68.3 1.0
CB B:CYS1199 3.2 50.8 1.0
CB B:CYS1214 3.7 61.3 1.0
N B:CYS1199 3.8 50.8 1.0
CA B:CYS1199 4.1 50.8 1.0
CA B:CYS1196 4.2 51.1 1.0
CA B:CYS1217 4.4 68.3 1.0
N B:CYS1217 4.4 68.3 1.0
CB B:LEU1198 4.7 52.6 1.0
O B:ARG1215 4.8 60.0 1.0
ND2 B:ASN1219 4.8 64.8 1.0
C B:LEU1198 4.8 52.6 1.0
CB B:ASN1219 4.9 64.8 1.0
C B:CYS1199 4.9 50.8 1.0
C B:GLY1216 4.9 63.1 1.0
C B:CYS1196 4.9 51.1 1.0
N B:GLY1200 5.0 44.0 1.0

Zinc binding site 4 out of 8 in 8oev

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


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:85.0
occ:1.00
 SG C:CYS94 2.3 33.2 1.0
SG C:CYS88 2.3 42.4 1.0
SG C:CYS90 2.3 53.5 1.0
SG C:CYS97 2.3 29.0 1.0
CB C:CYS97 3.2 29.0 1.0
CB C:CYS90 3.2 53.5 1.0
CB C:CYS88 3.2 42.4 1.0
CB C:CYS94 3.5 33.2 1.0
N C:CYS94 3.7 33.2 1.0
N C:CYS97 4.0 29.0 1.0
CA C:CYS94 4.1 33.2 1.0
N C:CYS90 4.2 53.5 1.0
CA C:CYS97 4.2 29.0 1.0
CA C:CYS90 4.3 53.5 1.0
C C:PHE93 4.3 34.3 1.0
O C:CYS94 4.3 33.2 1.0
C C:CYS94 4.5 33.2 1.0
CA C:CYS88 4.6 42.4 1.0
CA C:PHE93 4.6 34.3 1.0
C C:GLU96 4.7 31.0 1.0
C C:CYS88 4.8 42.4 1.0
CB C:GLU96 5.0 31.0 1.0
C C:CYS97 5.0 29.0 1.0
N C:THR89 5.0 51.1 1.0

Zinc binding site 5 out of 8 in 8oev

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Zinc binding site 5 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:89.6
occ:1.00
 SG I:CYS119 2.3 54.0 1.0
SG I:CYS89 2.3 61.1 1.0
SG I:CYS86 2.3 59.2 1.0
SG I:CYS114 2.3 49.3 1.0
CB I:CYS86 3.0 59.2 1.0
CB I:CYS114 3.1 49.3 1.0
CB I:CYS119 3.4 54.0 1.0
CB I:CYS89 3.4 61.1 1.0
N I:CYS89 4.0 61.1 1.0
CA I:CYS89 4.2 61.1 1.0
CB I:HIS91 4.3 53.2 1.0
CB I:HIS121 4.4 53.0 1.0
CA I:CYS86 4.5 59.2 1.0
CA I:CYS114 4.6 49.3 1.0
CB I:ALA116 4.7 46.2 1.0
N I:HIS91 4.7 53.2 1.0
C I:CYS89 4.7 61.1 1.0
N I:GLY90 4.8 59.0 1.0
CA I:CYS119 4.8 54.0 1.0
N I:HIS121 4.8 53.0 1.0
CB I:LYS88 4.9 59.5 1.0
C I:LYS88 4.9 59.5 1.0

Zinc binding site 6 out of 8 in 8oev

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Zinc binding site 6 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:115.1
occ:1.00
 SG I:CYS39 2.3 89.8 1.0
SG I:CYS42 2.3 94.5 1.0
SG I:CYS20 2.3 82.0 1.0
SG I:CYS17 2.3 81.2 1.0
CB I:CYS17 3.2 81.2 1.0
CB I:CYS39 3.3 89.8 1.0
CB I:CYS42 3.6 94.5 1.0
N I:CYS20 3.8 82.0 1.0
CB I:CYS20 3.9 82.0 1.0
N I:CYS42 3.9 94.5 1.0
CB I:GLU19 4.3 87.8 1.0
CA I:CYS42 4.3 94.5 1.0
CB I:TYR44 4.3 87.2 1.0
CA I:CYS20 4.3 82.0 1.0
N I:GLU19 4.6 87.8 1.0
C I:GLU19 4.7 87.8 1.0
CA I:CYS17 4.7 81.2 1.0
CA I:CYS39 4.7 89.8 1.0
CA I:GLU19 4.8 87.8 1.0
C I:CYS42 4.8 94.5 1.0
CG I:GLU19 4.8 87.8 1.0
CB I:ASN22 4.8 74.0 1.0
C I:CYS20 4.9 82.0 1.0
N I:ASN22 4.9 74.0 1.0
N I:ASN21 4.9 75.5 1.0
CB I:ASN41 4.9 88.9 1.0
N I:TYR44 5.0 87.2 1.0

Zinc binding site 7 out of 8 in 8oev

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Zinc binding site 7 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3)


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:31.5
occ:1.00
 SG J:CYS45 2.3 16.5 1.0
SG J:CYS10 2.3 14.2 1.0
SG J:CYS44 2.3 15.1 1.0
SG J:CYS7 2.3 10.8 1.0
N J:CYS45 3.2 16.5 1.0
CB J:CYS7 3.2 10.8 1.0
CB J:CYS10 3.5 14.2 1.0
CB J:CYS45 3.5 16.5 1.0
CB J:CYS44 3.6 15.1 1.0
CA J:CYS45 3.6 16.5 1.0
C J:CYS44 3.6 15.1 1.0
N J:CYS10 3.9 14.2 1.0
NE J:ARG42 4.1 14.6 1.0
O J:CYS44 4.1 15.1 1.0
CA J:CYS44 4.2 15.1 1.0
CA J:CYS10 4.3 14.2 1.0
NH2 J:ARG42 4.5 14.6 1.0
CB J:LYS12 4.6 13.8 1.0
CA J:CYS7 4.6 10.8 1.0
CB J:THR9 4.7 14.5 1.0
CZ J:ARG42 4.8 14.6 1.0
CB J:ARG42 4.8 14.6 1.0
N J:GLY11 4.8 13.5 1.0
N J:LYS12 4.9 13.8 1.0
N J:CYS44 4.9 15.1 1.0
C J:CYS10 4.9 14.2 1.0
C J:THR9 5.0 14.5 1.0
CD J:ARG42 5.0 14.6 1.0

Zinc binding site 8 out of 8 in 8oev

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


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-Elongin Complex, Lacking Eloa Latch (Composite Structure, Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:118.8
occ:1.00
 SG L:CYS22 2.3 61.2 1.0
SG L:CYS19 2.3 54.1 1.0
SG L:CYS36 2.3 63.5 1.0
SG L:CYS39 2.3 64.3 1.0
CB L:CYS19 3.0 54.1 1.0
CB L:CYS36 3.1 63.5 1.0
CB L:CYS22 3.2 61.2 1.0
CB L:CYS39 3.8 64.3 1.0
N L:CYS22 3.9 61.2 1.0
N L:CYS39 4.0 64.3 1.0
CA L:CYS22 4.1 61.2 1.0
OG1 L:THR24 4.2 59.0 1.0
CB L:TYR41 4.4 49.9 1.0
CA L:CYS39 4.4 64.3 1.0
CA L:CYS19 4.5 54.1 1.0
CB L:GLU38 4.6 68.7 1.0
CA L:CYS36 4.6 63.5 1.0
C L:CYS22 4.8 61.2 1.0
N L:TYR41 4.8 49.9 1.0
OE1 L:GLU38 4.9 68.7 1.0
C L:CYS39 4.9 64.3 1.0
ND2 L:ASN26 5.0 61.0 1.0
N L:GLY40 5.0 57.4 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 08:44:12 2024

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