Zinc in PDB 8a40: Structure of Mammalian Pol II-Tfiis Elongation Complex

Enzymatic activity of Structure of Mammalian Pol II-Tfiis Elongation Complex

All present enzymatic activity of Structure of Mammalian Pol II-Tfiis Elongation Complex:
2.7.7.6;

Other elements in 8a40:

The structure of Structure of Mammalian Pol II-Tfiis Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Zinc atom in the Structure of Mammalian Pol II-Tfiis Elongation Complex (pdb code 8a40). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Structure of Mammalian Pol II-Tfiis Elongation Complex, PDB code: 8a40:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 8a40

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Zinc binding site 1 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:158.8
occ:1.00
 O A:GLY83 2.9 94.5 1.0
NE2 B:GLN1160 3.4 84.9 1.0
CB B:MET1125 3.7 98.5 1.0
SD B:MET1125 3.7 98.5 1.0
C A:GLY83 4.1 94.5 1.0
CG A:PRO82 4.1 94.0 1.0
CG B:MET1125 4.3 98.5 1.0
CB A:PRO82 4.5 94.0 1.0
CD B:GLN1160 4.6 84.9 1.0
CA A:HIS84 4.7 93.4 1.0
CA B:MET1125 4.8 98.5 1.0
N A:HIS84 4.9 93.4 1.0
C B:MET1125 4.9 98.5 1.0
CE B:MET1125 4.9 98.5 1.0
ND1 A:HIS84 5.0 93.4 1.0
C A:PRO82 5.0 94.0 1.0

Zinc binding site 2 out of 11 in 8a40

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Zinc binding site 2 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


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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 Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:175.9
occ:1.00
 N A:ASP120 3.2 160.7 1.0
CB A:ASP120 3.5 160.7 1.0
ND2 A:ASN123 3.5 162.8 1.0
CB A:ASN123 3.7 162.8 1.0
CG1 A:VAL119 3.8 151.5 1.0
CA A:ASP120 3.8 160.7 1.0
CG A:ASP120 3.9 160.7 1.0
CG A:ASN123 4.0 162.8 1.0
OD2 A:ASP120 4.0 160.7 1.0
O A:ASP120 4.0 160.7 1.0
C A:VAL119 4.1 151.5 1.0
CA A:VAL119 4.3 151.5 1.0
C A:ASP120 4.4 160.7 1.0
NZ A:LYS151 4.5 150.8 1.0
CA A:ASN123 4.6 162.8 1.0
N A:ASN123 4.6 162.8 1.0
OD1 A:ASP120 4.6 160.7 1.0
CB A:VAL119 4.7 151.5 1.0

Zinc binding site 3 out of 11 in 8a40

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Zinc binding site 3 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:120.5
occ:1.00
 NE2 A:HIS84 2.1 93.4 1.0
SG A:CYS74 2.3 105.5 1.0
SG A:CYS81 2.3 100.1 1.0
SG A:CYS71 2.3 107.7 1.0
CD2 A:HIS84 3.0 93.4 1.0
CE1 A:HIS84 3.1 93.4 1.0
OG1 A:THR73 3.2 102.0 1.0
CB A:CYS81 3.6 100.1 1.0
CB A:CYS74 3.9 105.5 1.0
CB A:CYS71 4.0 107.7 1.0
N A:CYS74 4.0 105.5 1.0
CG A:HIS84 4.2 93.4 1.0
ND1 A:HIS84 4.2 93.4 1.0
O A:CYS74 4.3 105.5 1.0
CA A:CYS74 4.4 105.5 1.0
CA A:CYS81 4.5 100.1 1.0
CB A:THR73 4.5 102.0 1.0
C A:CYS74 4.6 105.5 1.0
CG2 A:VAL64 4.7 106.5 1.0
C A:THR73 4.8 102.0 1.0
N A:GLY83 4.9 94.5 1.0

Zinc binding site 4 out of 11 in 8a40

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Zinc binding site 4 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:176.2
occ:1.00
 CB A:CYS114 1.8 146.4 1.0
SG A:CYS114 2.3 146.4 1.0
SG A:CYS111 2.3 144.3 1.0
SG A:CYS184 2.3 161.6 1.0
CB A:CYS184 2.4 161.6 1.0
CA A:CYS114 3.2 146.4 1.0
CB A:CYS111 3.3 144.3 1.0
N A:CYS114 3.8 146.4 1.0
O A:PHE112 3.8 144.2 1.0
CA A:CYS184 3.9 161.6 1.0
SG A:CYS154 4.0 159.6 1.0
O A:CYS184 4.0 161.6 1.0
C A:CYS114 4.2 146.4 1.0
O A:GLY183 4.4 162.4 1.0
C A:CYS184 4.4 161.6 1.0
C A:PHE113 4.5 145.5 1.0
CA A:CYS111 4.6 144.3 1.0
N A:CYS184 4.6 161.6 1.0
C A:CYS111 4.7 144.3 1.0
CB A:CYS154 4.7 159.6 1.0
O A:PHE113 4.7 145.5 1.0
O A:CYS111 4.8 144.3 1.0
N A:SER115 4.8 138.9 1.0
C A:GLY183 4.8 162.4 1.0
NE2 A:GLN188 4.8 148.0 1.0
C A:PHE112 4.9 144.2 1.0
O A:CYS114 4.9 146.4 1.0

Zinc binding site 5 out of 11 in 8a40

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Zinc binding site 5 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2007

b:164.7
occ:1.00
 O I:SER51 2.1 133.3 1.0
N A:TYR1177 2.3 129.0 1.0
CB A:TYR1177 2.6 129.0 1.0
C I:SER51 2.8 133.3 1.0
C A:TYR1176 2.8 119.8 1.0
CA A:TYR1177 3.0 129.0 1.0
CA A:TYR1176 3.3 119.8 1.0
CA I:CYS52 3.3 126.7 1.0
N I:CYS52 3.3 126.7 1.0
O A:TYR1176 3.6 119.8 1.0
OG I:SER51 3.7 133.3 1.0
CA I:SER51 3.8 133.3 1.0
CD2 I:LEU35 3.9 128.3 1.0
C A:TYR1177 4.0 129.0 1.0
C I:CYS52 4.1 126.7 1.0
CG A:TYR1177 4.1 129.0 1.0
O A:TYR1177 4.2 129.0 1.0
CB A:TYR1176 4.2 119.8 1.0
O A:ILE1175 4.2 114.9 1.0
N I:ILE53 4.2 117.5 1.0
CB I:SER51 4.4 133.3 1.0
N A:TYR1176 4.4 119.8 1.0
CB I:CYS52 4.5 126.7 1.0
CG1 I:ILE53 4.5 117.5 1.0
CZ3 A:TRP1210 4.6 123.9 1.0
C A:ILE1175 4.7 114.9 1.0
CD2 A:TYR1177 4.8 129.0 1.0
CD1 I:ILE53 5.0 117.5 1.0
O I:CYS52 5.0 126.7 1.0

Zinc binding site 6 out of 11 in 8a40

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Zinc binding site 6 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:160.7
occ:1.00
 O B:ASN1120 2.1 106.8 1.0
O B:LEU1121 2.1 109.3 1.0
C B:LEU1121 2.7 109.3 1.0
CE B:MET1172 2.8 95.4 1.0
CA B:LEU1121 2.9 109.3 1.0
C B:ASN1120 3.1 106.8 1.0
N B:LEU1121 3.4 109.3 1.0
N B:CYS1122 3.9 104.4 1.0
CB B:LEU1121 4.2 109.3 1.0
SD B:MET1172 4.3 95.4 1.0
CA B:ASN1120 4.4 106.8 1.0
CA B:CYS1122 4.6 104.4 1.0
CD2 B:LEU1121 4.7 109.3 1.0
C B:CYS1122 4.9 104.4 1.0
O B:CYS1122 5.0 104.4 1.0

Zinc binding site 7 out of 11 in 8a40

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Zinc binding site 7 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:141.4
occ:1.00
 SG B:CYS1122 2.3 104.4 1.0
SG B:CYS1137 2.3 109.0 1.0
SG B:CYS1119 2.3 105.4 1.0
SG B:CYS1140 2.3 114.0 1.0
CB B:CYS1119 2.9 105.4 1.0
CB B:CYS1140 3.0 114.0 1.0
N B:CYS1122 3.6 104.4 1.0
CB B:CYS1122 3.6 104.4 1.0
CB B:CYS1137 3.8 109.0 1.0
CA B:CYS1122 4.1 104.4 1.0
CB B:LEU1121 4.3 109.3 1.0
CA B:CYS1140 4.3 114.0 1.0
O B:CYS1122 4.4 104.4 1.0
CA B:CYS1119 4.4 105.4 1.0
N B:CYS1140 4.4 114.0 1.0
C B:CYS1122 4.6 104.4 1.0
C B:LEU1121 4.7 109.3 1.0
N B:LEU1121 4.7 109.3 1.0
CB B:ASN1142 4.8 111.1 1.0
CA B:LEU1121 4.8 109.3 1.0
ND2 B:ASN1142 5.0 111.1 1.0

Zinc binding site 8 out of 11 in 8a40

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Zinc binding site 8 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:

Zinc binding site 9 out of 11 in 8a40

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Zinc binding site 9 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:151.4
occ:1.00
 SG I:CYS42 2.3 129.1 1.0
SG I:CYS20 2.3 123.5 1.0
SG I:CYS39 2.3 127.8 1.0
SG I:CYS17 2.3 122.7 1.0
CB I:CYS39 2.9 127.8 1.0
CB I:CYS17 3.1 122.7 1.0
CB I:CYS42 3.8 129.1 1.0
CB I:CYS20 4.0 123.5 1.0
N I:CYS20 4.0 123.5 1.0
N I:CYS42 4.3 129.1 1.0
CA I:CYS39 4.4 127.8 1.0
CB I:GLU19 4.5 124.7 1.0
CA I:CYS20 4.5 123.5 1.0
CA I:CYS42 4.6 129.1 1.0
CA I:CYS17 4.6 122.7 1.0
CB I:TYR44 4.7 120.7 1.0
ND2 I:ASN22 4.8 120.9 1.0
C I:ASN41 4.8 127.0 1.0
CB I:ASN22 4.9 120.9 1.0
N I:GLU19 5.0 124.7 1.0
C I:GLU19 5.0 124.7 1.0

Zinc binding site 10 out of 11 in 8a40

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Zinc binding site 10 out of 11 in the Structure of Mammalian Pol II-Tfiis Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Mammalian Pol II-Tfiis Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:134.5
occ:1.00
 SG I:CYS89 2.3 110.5 1.0
SG I:CYS114 2.3 99.2 1.0
SG I:CYS86 2.3 105.9 1.0
SG I:CYS119 2.3 106.6 1.0
CB I:CYS86 2.9 105.9 1.0
CB I:CYS114 3.0 99.2 1.0
CB I:CYS119 3.6 106.6 1.0
CB I:CYS89 3.9 110.5 1.0
N I:CYS89 4.2 110.5 1.0
CB I:ALA116 4.3 102.2 1.0
CB I:HIS91 4.4 102.1 1.0
CA I:CYS86 4.4 105.9 1.0
CA I:CYS114 4.5 99.2 1.0
CA I:CYS89 4.6 110.5 1.0
N I:HIS91 4.7 102.1 1.0
CB I:HIS121 4.7 96.4 1.0
N I:GLY120 4.9 99.9 1.0
N I:GLY90 4.9 104.9 1.0
CA I:CYS119 5.0 106.6 1.0

Reference:

L.Farnung, M.Ochmann, G.Garg, S.M.Vos, P.Cramer. Structure of A Backtracked Hexasomal Intermediate of Nucleosome Transcription. Mol.Cell V. 82 3126 2022.
ISSN: ISSN 1097-2765
PubMed: 35858621
DOI: 10.1016/J.MOLCEL.2022.06.027
Page generated: Wed Oct 30 17:31:37 2024

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