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Zinc in PDB 8of0: Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1

Enzymatic activity of Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1

All present enzymatic activity of Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1:
2.7.7.6;

Other elements in 8of0:

The structure of Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1 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, Structure 1 (pdb code 8of0). 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, Structure 1, PDB code: 8of0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8of0

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Zinc binding site 1 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:90.7
occ:1.00
 NE2 A:HIS84 2.1 50.5 1.0
SG A:CYS74 2.3 65.5 1.0
SG A:CYS81 2.3 52.1 1.0
SG A:CYS71 2.3 65.5 1.0
CD2 A:HIS84 2.8 50.5 1.0
CB A:CYS71 2.9 65.5 1.0
CE1 A:HIS84 3.2 50.5 1.0
CB A:CYS81 3.5 52.1 1.0
CB A:CYS74 3.7 65.5 1.0
N A:CYS74 3.8 65.5 1.0
CG A:HIS84 4.0 50.5 1.0
ND1 A:HIS84 4.2 50.5 1.0
CA A:CYS81 4.2 52.1 1.0
CA A:CYS74 4.2 65.5 1.0
CA A:GLY63 4.4 60.0 1.0
O A:CYS74 4.4 65.5 1.0
CA A:CYS71 4.4 65.5 1.0
N A:GLY83 4.5 45.8 1.0
CD A:PRO82 4.5 43.8 1.0
CB A:THR73 4.6 62.5 1.0
C A:CYS74 4.6 65.5 1.0
C A:CYS81 4.7 52.1 1.0
N A:PRO82 4.8 43.8 1.0
CA A:GLY83 4.9 45.8 1.0
C A:THR73 4.9 62.5 1.0
N A:GLY63 5.0 60.0 1.0

Zinc binding site 2 out of 8 in 8of0

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Zinc binding site 2 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:176.9
occ:1.00
 SG A:CYS111 2.3 104.5 1.0
SG A:CYS114 2.3 107.4 1.0
SG A:CYS184 2.3 119.4 1.0
SG A:CYS154 2.3 121.6 1.0
CB A:CYS114 2.8 107.4 1.0
CB A:CYS111 3.0 104.5 1.0
CB A:CYS184 3.1 119.4 1.0
N A:CYS114 3.3 107.4 1.0
CA A:CYS114 3.6 107.4 1.0
N A:CYS184 3.7 119.4 1.0
NE2 A:GLN188 3.8 116.9 1.0
CB A:CYS154 3.8 121.6 1.0
CA A:CYS184 4.0 119.4 1.0
C A:CYS114 4.4 107.4 1.0
CA A:CYS111 4.5 104.5 1.0
N A:SER115 4.5 98.4 1.0
C A:PHE113 4.5 106.7 1.0
N A:PHE113 4.7 106.7 1.0
C A:GLY183 4.8 109.8 1.0
CB A:PHE113 4.8 106.7 1.0
CD A:GLN188 4.9 116.9 1.0
CA A:PHE113 4.9 106.7 1.0
O A:CYS154 5.0 121.6 1.0

Zinc binding site 3 out of 8 in 8of0

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Zinc binding site 3 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2000

b:105.7
occ:1.00
 SG B:CYS1199 2.3 60.0 1.0
SG B:CYS1196 2.3 58.3 1.0
SG B:CYS1214 2.3 79.1 1.0
SG B:CYS1217 2.3 85.6 1.0
CB B:CYS1196 2.8 58.3 1.0
CB B:CYS1199 3.1 60.0 1.0
CB B:CYS1217 3.2 85.6 1.0
N B:CYS1199 3.7 60.0 1.0
CB B:CYS1214 3.8 79.1 1.0
CA B:CYS1199 4.0 60.0 1.0
CA B:CYS1196 4.3 58.3 1.0
N B:CYS1217 4.4 85.6 1.0
CA B:CYS1217 4.4 85.6 1.0
O B:ARG1215 4.7 80.1 1.0
CB B:LEU1198 4.7 60.4 1.0
C B:CYS1199 4.8 60.0 1.0
C B:LEU1198 4.8 60.4 1.0
N B:GLY1200 4.8 54.2 1.0
C B:CYS1196 4.9 58.3 1.0
CB B:ASN1219 4.9 78.2 1.0
O B:CYS1214 4.9 79.1 1.0
N B:LEU1198 5.0 60.4 1.0

Zinc binding site 4 out of 8 in 8of0

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


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:109.7
occ:1.00
 SG C:CYS94 2.3 49.4 1.0
SG C:CYS88 2.3 58.9 1.0
SG C:CYS90 2.3 73.1 1.0
SG C:CYS97 2.3 43.5 1.0
CB C:CYS94 3.1 49.4 1.0
CB C:CYS97 3.1 43.5 1.0
N C:CYS94 3.2 49.4 1.0
CB C:CYS88 3.4 58.9 1.0
CB C:CYS90 3.6 73.1 1.0
CA C:CYS94 3.6 49.4 1.0
N C:CYS97 4.0 43.5 1.0
O C:CYS94 4.1 49.4 1.0
CA C:CYS97 4.2 43.5 1.0
C C:CYS94 4.2 49.4 1.0
N C:CYS90 4.2 73.1 1.0
C C:PHE93 4.4 47.2 1.0
CA C:CYS90 4.5 73.1 1.0
N C:PHE93 4.6 47.2 1.0
CA C:PHE93 4.6 47.2 1.0
N C:THR89 4.8 68.4 1.0
CA C:CYS88 4.8 58.9 1.0
C C:GLU96 4.8 45.9 1.0
N C:GLU96 5.0 45.9 1.0

Zinc binding site 5 out of 8 in 8of0

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Zinc binding site 5 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:142.2
occ:1.00
 SG I:CYS119 2.3 70.7 1.0
SG I:CYS114 2.3 66.4 1.0
SG I:CYS86 2.3 75.7 1.0
SG I:CYS89 2.3 82.0 1.0
CB I:CYS86 2.8 75.7 1.0
CB I:CYS114 3.1 66.4 1.0
CB I:CYS119 3.4 70.7 1.0
CB I:CYS89 3.5 82.0 1.0
N I:CYS89 3.8 82.0 1.0
CA I:CYS89 4.1 82.0 1.0
CA I:CYS86 4.3 75.7 1.0
N I:GLY90 4.4 79.3 1.0
CB I:HIS91 4.4 78.9 1.0
N I:HIS91 4.5 78.9 1.0
C I:CYS89 4.5 82.0 1.0
CB I:HIS121 4.6 65.6 1.0
CA I:CYS114 4.6 66.4 1.0
CA I:CYS119 4.8 70.7 1.0
CB I:LYS88 4.8 78.7 1.0
C I:LYS88 4.9 78.7 1.0

Zinc binding site 6 out of 8 in 8of0

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Zinc binding site 6 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:158.9
occ:1.00
 SG I:CYS20 2.3 105.1 1.0
SG I:CYS39 2.3 108.5 1.0
SG I:CYS42 2.3 114.5 1.0
SG I:CYS17 2.3 103.3 1.0
CB I:CYS39 3.2 108.5 1.0
CB I:CYS17 3.3 103.3 1.0
CB I:CYS20 3.5 105.1 1.0
N I:CYS20 3.8 105.1 1.0
CB I:CYS42 3.8 114.5 1.0
N I:CYS42 3.9 114.5 1.0
CA I:CYS20 4.1 105.1 1.0
CA I:CYS42 4.4 114.5 1.0
CB I:TYR44 4.4 103.7 1.0
CB I:ASN41 4.6 111.4 1.0
CA I:CYS39 4.7 108.5 1.0
C I:CYS20 4.7 105.1 1.0
CA I:CYS17 4.7 103.3 1.0
CB I:GLU19 4.8 102.8 1.0
C I:ASN41 4.8 111.4 1.0
N I:ASN41 4.8 111.4 1.0
C I:CYS42 4.9 114.5 1.0
C I:GLU19 4.9 102.8 1.0
CB I:ASN22 4.9 97.1 1.0
N I:GLU19 5.0 102.8 1.0

Zinc binding site 7 out of 8 in 8of0

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Zinc binding site 7 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:42.0
occ:1.00
 SG J:CYS10 2.3 29.3 1.0
SG J:CYS44 2.3 29.1 1.0
SG J:CYS7 2.3 42.7 1.0
SG J:CYS45 2.3 27.3 1.0
CB J:CYS7 3.1 42.7 1.0
N J:CYS45 3.4 27.3 1.0
CB J:CYS44 3.5 29.1 1.0
CB J:CYS10 3.6 29.3 1.0
C J:CYS44 3.6 29.1 1.0
CB J:CYS45 3.7 27.3 1.0
CA J:CYS45 3.8 27.3 1.0
N J:CYS10 4.0 29.3 1.0
O J:CYS44 4.0 29.1 1.0
CA J:CYS44 4.2 29.1 1.0
NE J:ARG42 4.3 28.9 1.0
CA J:CYS10 4.3 29.3 1.0
CA J:CYS7 4.5 42.7 1.0
NH2 J:ARG42 4.5 28.9 1.0
CB J:LYS12 4.6 27.1 1.0
CB J:THR9 4.7 34.0 1.0
N J:GLY11 4.7 28.8 1.0
N J:LYS12 4.8 27.1 1.0
CZ J:ARG42 4.9 28.9 1.0
N J:CYS44 4.9 29.1 1.0
CB J:ARG42 5.0 28.9 1.0
C J:THR9 5.0 34.0 1.0
C J:CYS7 5.0 42.7 1.0

Zinc binding site 8 out of 8 in 8of0

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Zinc binding site 8 out of 8 in the Structure of the Mammalian Pol II-SPT6-Elongin Complex, Structure 1


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, Structure 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:140.1
occ:1.00
 SG L:CYS22 2.3 73.1 1.0
SG L:CYS19 2.3 67.8 1.0
SG L:CYS36 2.3 76.1 1.0
SG L:CYS39 2.3 82.4 1.0
CB L:CYS19 3.0 67.8 1.0
CB L:CYS22 3.1 73.1 1.0
CB L:CYS36 3.1 76.1 1.0
CB L:CYS39 3.7 82.4 1.0
N L:CYS39 3.9 82.4 1.0
N L:CYS22 3.9 73.1 1.0
CA L:CYS22 4.1 73.1 1.0
CA L:CYS39 4.2 82.4 1.0
CB L:TYR41 4.3 66.2 1.0
CA L:CYS19 4.5 67.8 1.0
CB L:GLU38 4.6 86.5 1.0
CA L:CYS36 4.6 76.1 1.0
C L:CYS39 4.6 82.4 1.0
N L:TYR41 4.7 66.2 1.0
CG L:GLU21 4.7 71.3 1.0
OG1 L:THR24 4.7 72.6 1.0
C L:CYS22 4.8 73.1 1.0
C L:GLU38 4.8 86.5 1.0
N L:GLY40 4.8 73.0 1.0
N L:GLU38 5.0 86.5 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 08:44:55 2024

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