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Zinc in PDB 7ega: Tfiid-Based Intermediate Pic on Puma Promoter

Enzymatic activity of Tfiid-Based Intermediate Pic on Puma Promoter

All present enzymatic activity of Tfiid-Based Intermediate Pic on Puma Promoter:
2.3.1.48; 2.7.11.1; 2.7.7.6; 3.6.4.12;

Other elements in 7ega:

The structure of Tfiid-Based Intermediate Pic on Puma Promoter also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Tfiid-Based Intermediate Pic on Puma Promoter (pdb code 7ega). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Tfiid-Based Intermediate Pic on Puma Promoter, PDB code: 7ega:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7ega

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Zinc binding site 1 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn401

b:30.0
occ:1.00
 NE2 R:HIS18 2.0 0.0 1.0
CE1 R:HIS18 2.0 0.0 1.0
SG R:CYS34 2.1 0.0 1.0
SG R:CYS15 2.4 0.0 1.0
OE2 R:GLU36 3.0 0.0 1.0
SG R:CYS37 3.1 0.0 1.0
ND1 R:HIS18 3.2 0.0 1.0
CD2 R:HIS18 3.2 0.0 1.0
CB R:CYS15 3.4 0.0 1.0
CD R:GLU36 3.6 0.0 1.0
CB R:CYS34 3.6 0.0 1.0
OD1 R:ASP20 3.8 0.0 1.0
CG R:HIS18 3.8 0.0 1.0
CB R:ASP20 4.0 0.0 1.0
CA R:ASP20 4.0 0.0 1.0
CG R:ASP20 4.1 0.0 1.0
OE1 R:GLU36 4.2 0.0 1.0
CG R:GLU36 4.2 0.0 1.0
CB R:CYS37 4.3 0.0 1.0
OD1 R:ASN17 4.5 0.0 1.0
O R:CYS34 4.6 0.0 1.0
O R:HIS18 4.6 0.0 1.0
N R:ASP20 4.6 0.0 1.0
CA R:CYS15 4.8 0.0 1.0
CA R:CYS34 4.8 0.0 1.0
N R:CYS37 4.9 0.0 1.0
C R:CYS34 4.9 0.0 1.0
N R:CYS15 5.0 0.0 1.0

Zinc binding site 2 out of 10 in 7ega

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Zinc binding site 2 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn501

b:30.0
occ:1.00
 SG U:CYS132 2.1 0.0 1.0
SG U:CYS157 2.2 0.0 1.0
SG U:CYS129 2.2 0.0 1.0
SG U:CYS154 3.0 0.0 1.0
CB U:CYS129 3.0 0.0 1.0
CB U:CYS132 3.2 0.0 1.0
OG1 U:THR159 3.4 0.0 1.0
CB U:CYS154 3.6 0.0 1.0
N U:CYS132 3.6 0.0 1.0
CB U:CYS157 4.0 0.0 1.0
CA U:CYS132 4.0 0.0 1.0
O U:CYS157 4.3 0.0 1.0
CA U:CYS129 4.4 0.0 1.0
CB U:VAL131 4.4 0.0 1.0
CZ U:PHE156 4.5 0.0 1.0
O U:CYS129 4.5 0.0 1.0
CE1 U:PHE156 4.5 0.0 1.0
C U:CYS129 4.6 0.0 1.0
C U:VAL131 4.6 0.0 1.0
N U:VAL131 4.8 0.0 1.0
CB U:THR159 4.8 0.0 1.0
CA U:VAL131 4.8 0.0 1.0
CA U:CYS157 4.9 0.0 1.0
C U:CYS132 4.9 0.0 1.0
OG U:SER134 4.9 0.0 1.0
O U:THR159 4.9 0.0 1.0
C U:CYS157 4.9 0.0 1.0
N U:CYS157 4.9 0.0 1.0
CG1 U:VAL131 5.0 0.0 1.0

Zinc binding site 3 out of 10 in 7ega

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Zinc binding site 3 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2001

b:220.4
occ:1.00
 NE2 o:HIS84 2.1 210.6 1.0
CD2 o:HIS84 2.3 210.6 1.0
SG o:CYS71 2.4 215.1 1.0
SG o:CYS81 2.4 201.8 1.0
SG o:CYS74 3.1 208.6 1.0
CE1 o:HIS84 3.4 210.6 1.0
CA o:GLY63 3.4 218.4 1.0
CB o:CYS71 3.5 215.1 1.0
OG1 o:THR73 3.7 211.4 1.0
CG o:HIS84 3.7 210.6 1.0
N o:GLY63 3.7 218.4 1.0
ND1 o:HIS84 4.1 210.6 1.0
C o:GLY63 4.1 218.4 1.0
CB o:CYS81 4.2 201.8 1.0
O o:ARG61 4.3 223.1 1.0
O o:CYS74 4.4 208.6 1.0
C o:GLN62 4.5 219.1 1.0
O o:GLY63 4.5 218.4 1.0
N o:CYS74 4.5 208.6 1.0
CB o:CYS74 4.7 208.6 1.0
CA o:GLY83 4.8 205.4 1.0
N o:GLY83 4.8 205.4 1.0
C o:GLY83 4.8 205.4 1.0
O o:GLN62 4.9 219.1 1.0
N o:VAL64 4.9 215.2 1.0
CB o:HIS84 4.9 210.6 1.0
CA o:CYS71 4.9 215.1 1.0
CA o:CYS81 4.9 201.8 1.0
N o:HIS84 4.9 210.6 1.0
CB o:THR73 5.0 211.4 1.0

Zinc binding site 4 out of 10 in 7ega

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Zinc binding site 4 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2002

b:303.1
occ:1.00
 CB o:CYS114 1.9 287.1 1.0
SG o:CYS114 2.0 287.1 1.0
SG o:CYS154 2.6 287.9 1.0
SG o:CYS111 2.8 291.0 1.0
CB o:CYS154 3.2 287.9 1.0
CA o:CYS114 3.4 287.1 1.0
CB o:CYS184 3.4 285.0 1.0
CB o:CYS111 3.6 291.0 1.0
SG o:CYS184 3.7 285.0 1.0
O o:CYS114 3.8 287.1 1.0
C o:CYS114 4.0 287.1 1.0
N o:CYS114 4.2 287.1 1.0
O o:PHE112 4.5 289.8 1.0
CA o:CYS154 4.7 287.9 1.0
CA o:CYS184 4.9 285.0 1.0
C o:PHE113 5.0 290.2 1.0
CA o:CYS111 5.0 291.0 1.0

Zinc binding site 5 out of 10 in 7ega

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Zinc binding site 5 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
p:Zn1201

b:202.0
occ:1.00
 SG p:CYS1122 2.3 181.2 1.0
SG p:CYS1119 2.5 179.3 1.0
SG p:CYS1137 2.5 194.8 1.0
SG p:CYS1140 2.5 200.5 1.0
CB p:CYS1140 3.1 200.5 1.0
CB p:CYS1119 3.4 179.3 1.0
CB p:CYS1122 3.5 181.2 1.0
CD2 p:LEU1121 3.7 179.6 1.0
N p:CYS1122 3.9 181.2 1.0
CG p:LEU1121 3.9 179.6 1.0
CB p:CYS1137 4.0 194.8 1.0
CA p:CYS1122 4.2 181.2 1.0
CA p:CYS1140 4.4 200.5 1.0
N p:CYS1140 4.5 200.5 1.0
CB p:ASN1142 4.7 193.5 1.0
O p:ARG1138 4.7 201.5 1.0
CD1 p:LEU1121 4.7 179.6 1.0
O p:CYS1122 4.7 181.2 1.0
C p:CYS1122 4.8 181.2 1.0
CA p:CYS1119 4.8 179.3 1.0

Zinc binding site 6 out of 10 in 7ega

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Zinc binding site 6 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
q:Zn301

b:144.6
occ:1.00
 N q:CYS94 2.1 113.2 1.0
SG q:CYS90 2.3 126.5 1.0
SG q:CYS94 2.3 113.2 1.0
CB q:CYS94 2.4 113.2 1.0
SG q:CYS97 2.6 107.1 1.0
CA q:CYS94 2.7 113.2 1.0
C q:PHE93 2.7 113.5 1.0
O q:CYS94 3.2 113.2 1.0
C q:CYS94 3.3 113.2 1.0
CA q:PHE93 3.3 113.5 1.0
O q:PHE93 3.5 113.5 1.0
CB q:CYS90 3.6 126.5 1.0
N q:PHE93 4.0 113.5 1.0
O q:GLU91 4.2 127.2 1.0
CB q:CYS97 4.2 107.1 1.0
N q:CYS97 4.3 107.1 1.0
SG q:CYS88 4.4 121.9 1.0
N q:PRO95 4.5 108.8 1.0
CB q:PHE93 4.6 113.5 1.0
C q:GLU92 4.7 124.5 1.0
O q:GLU92 4.7 124.5 1.0
CA q:CYS97 4.7 107.1 1.0
N q:GLU96 4.8 111.6 1.0
CA q:CYS90 4.9 126.5 1.0
C q:CYS97 5.0 107.1 1.0

Zinc binding site 7 out of 10 in 7ega

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Zinc binding site 7 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Zn201

b:185.0
occ:1.00
 SG w:CYS39 2.4 170.9 1.0
SG w:CYS20 2.4 166.4 1.0
SG w:CYS17 2.4 165.5 1.0
SG w:CYS42 2.7 174.1 1.0
CB w:CYS17 2.8 165.5 1.0
CB w:CYS39 3.0 170.9 1.0
N w:CYS42 4.1 174.1 1.0
CB w:CYS20 4.1 166.4 1.0
CB w:CYS42 4.1 174.1 1.0
N w:CYS20 4.2 166.4 1.0
CA w:CYS17 4.2 165.5 1.0
CA w:CYS39 4.4 170.9 1.0
CA w:CYS42 4.5 174.1 1.0
OE2 w:GLU19 4.6 168.3 1.0
CA w:CYS20 4.6 166.4 1.0
CB w:ASN22 4.7 159.8 1.0
O w:CYS42 4.7 174.1 1.0
CB w:ASN41 4.7 171.6 1.0
C w:CYS42 4.8 174.1 1.0
N w:ASN22 4.8 159.8 1.0
CD2 w:LEU24 4.9 169.5 1.0
CB w:TYR44 4.9 172.3 1.0
C w:CYS20 4.9 166.4 1.0
N w:ASN21 4.9 161.1 1.0
N w:ASN41 5.0 171.6 1.0

Zinc binding site 8 out of 10 in 7ega

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Zinc binding site 8 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
w:Zn202

b:168.0
occ:1.00
 SG w:CYS89 2.3 141.3 1.0
SG w:CYS119 2.3 136.9 1.0
SG w:CYS86 2.3 138.7 1.0
SG w:CYS114 2.4 129.6 1.0
CB w:CYS86 2.8 138.7 1.0
CB w:CYS114 3.0 129.6 1.0
CB w:CYS119 3.4 136.9 1.0
CB w:CYS89 3.6 141.3 1.0
N w:CYS89 4.3 141.3 1.0
CA w:CYS86 4.3 138.7 1.0
CB w:HIS121 4.4 132.1 1.0
CB w:HIS91 4.5 137.1 1.0
CA w:CYS114 4.5 129.6 1.0
CA w:CYS89 4.5 141.3 1.0
CB w:ALA116 4.6 136.1 1.0
CA w:CYS119 4.8 136.9 1.0
N w:HIS91 4.8 137.1 1.0
C w:CYS86 4.9 138.7 1.0
N w:HIS121 5.0 132.1 1.0

Zinc binding site 9 out of 10 in 7ega

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Zinc binding site 9 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
x:Zn101

b:95.7
occ:1.00
 SG x:CYS45 2.3 74.9 1.0
SG x:CYS44 2.4 74.5 1.0
SG x:CYS7 2.5 65.1 1.0
CB x:CYS10 2.5 73.6 1.0
SG x:CYS10 2.5 73.6 1.0
N x:CYS10 3.2 73.6 1.0
CA x:CYS10 3.4 73.6 1.0
CB x:CYS7 3.5 65.1 1.0
CB x:CYS45 3.8 74.9 1.0
N x:CYS45 3.9 74.9 1.0
CA x:CYS45 4.0 74.9 1.0
CB x:CYS44 4.1 74.5 1.0
C x:CYS44 4.1 74.5 1.0
O x:CYS44 4.3 74.5 1.0
C x:THR9 4.4 65.5 1.0
N x:GLY11 4.4 66.3 1.0
C x:CYS10 4.5 73.6 1.0
CB x:THR9 4.6 65.5 1.0
NE x:ARG42 4.6 77.0 1.0
CA x:CYS44 4.7 74.5 1.0
N x:THR9 4.8 65.5 1.0
CA x:THR9 4.8 65.5 1.0
CA x:CYS7 4.9 65.1 1.0
CB x:LYS12 4.9 67.2 1.0
N x:LYS12 4.9 67.2 1.0

Zinc binding site 10 out of 10 in 7ega

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Zinc binding site 10 out of 10 in the Tfiid-Based Intermediate Pic on Puma Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Tfiid-Based Intermediate Pic on Puma Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
z:Zn101

b:140.6
occ:1.00
 SG z:CYS22 2.3 114.7 1.0
SG z:CYS36 2.3 121.3 1.0
SG z:CYS19 2.3 111.2 1.0
CB z:CYS39 2.5 125.0 1.0
CB z:CYS36 3.0 121.3 1.0
SG z:CYS39 3.1 125.0 1.0
CB z:CYS19 3.2 111.2 1.0
CB z:CYS22 3.7 114.7 1.0
CA z:CYS39 3.8 125.0 1.0
N z:CYS22 4.0 114.7 1.0
CB z:TYR41 4.2 106.7 1.0
N z:CYS39 4.2 125.0 1.0
O z:ARG37 4.3 129.0 1.0
C z:CYS39 4.4 125.0 1.0
CA z:CYS22 4.5 114.7 1.0
CA z:CYS36 4.5 121.3 1.0
CA z:CYS19 4.6 111.2 1.0
OG1 z:THR24 4.7 118.6 1.0
N z:GLY40 4.7 118.0 1.0
N z:ARG37 4.8 129.0 1.0
CB z:GLU21 4.8 116.0 1.0
N z:GLU21 4.9 116.0 1.0
N z:TYR41 5.0 106.7 1.0

Reference:

X.Chen, Y.Qi, Z.Wu, X.Wang, J.Li, D.Zhao, H.Hou, Y.Li, Z.Yu, W.Liu, M.Wang, Y.Ren, Z.Li, H.Yang, Y.Xu. Structural Insights Into Preinitiation Complex Assembly on Core Promoters. Science 2021.
ISSN: ESSN 1095-9203
PubMed: 33795473
DOI: 10.1126/SCIENCE.ABA8490
Page generated: Tue Oct 29 19:46:52 2024

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