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Zinc in PDB 7eg9: Tfiid-Based Intermediate Pic on Scp Promoter

Enzymatic activity of Tfiid-Based Intermediate Pic on Scp Promoter

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

Other elements in 7eg9:

The structure of Tfiid-Based Intermediate Pic on Scp 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 Scp Promoter (pdb code 7eg9). 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 Scp Promoter, PDB code: 7eg9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7eg9

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Zinc binding site 1 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn401

b:30.0
occ:1.00
 OE2 R:GLU36 1.6 0.0 1.0
NE2 R:HIS18 2.2 0.0 1.0
SG R:CYS34 2.4 0.0 1.0
CD2 R:HIS18 2.5 0.0 1.0
CD R:GLU36 2.8 0.0 1.0
CE1 R:HIS18 3.5 0.0 1.0
CB R:CYS34 3.5 0.0 1.0
CG R:GLU36 3.7 0.0 1.0
O R:PRO19 3.7 0.0 1.0
OE1 R:GLU36 3.7 0.0 1.0
CG R:HIS18 3.8 0.0 1.0
O R:CYS34 3.9 0.0 1.0
CA R:ASP20 4.0 0.0 1.0
CB R:ASP20 4.2 0.0 1.0
ND1 R:HIS18 4.2 0.0 1.0
C R:PRO19 4.3 0.0 1.0
OD1 R:ASP20 4.4 0.0 1.0
CG R:ASP20 4.5 0.0 1.0
N R:ASP20 4.5 0.0 1.0
O R:HIS18 4.5 0.0 1.0
N R:CYS37 4.5 0.0 1.0
N R:GLY38 4.5 0.0 1.0
C R:CYS34 4.7 0.0 1.0
CB R:CYS37 4.7 0.0 1.0
CA R:CYS34 4.7 0.0 1.0
CB R:LEU39 4.8 0.0 1.0
C R:HIS18 4.9 0.0 1.0

Zinc binding site 2 out of 10 in 7eg9

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Zinc binding site 2 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn501

b:30.0
occ:1.00
 SG U:CYS157 1.6 0.0 1.0
SG U:CYS132 2.4 0.0 1.0
SG U:CYS154 2.6 0.0 1.0
CB U:CYS157 3.3 0.0 1.0
CE1 U:PHE156 3.4 0.0 1.0
CB U:CYS132 3.4 0.0 1.0
SG U:CYS129 3.4 0.0 1.0
CZ U:PHE156 3.4 0.0 1.0
CB U:CYS154 3.6 0.0 1.0
N U:CYS157 3.8 0.0 1.0
CD1 U:PHE156 3.9 0.0 1.0
O U:CYS157 3.9 0.0 1.0
CE2 U:PHE156 4.0 0.0 1.0
CA U:CYS157 4.0 0.0 1.0
CB U:CYS129 4.1 0.0 1.0
OG1 U:THR159 4.1 0.0 1.0
CG U:PHE156 4.4 0.0 1.0
C U:CYS157 4.4 0.0 1.0
CD2 U:PHE156 4.4 0.0 1.0
N U:CYS132 4.6 0.0 1.0
CA U:CYS132 4.6 0.0 1.0
OG U:SER134 4.7 0.0 1.0
C U:PHE156 4.8 0.0 1.0
N U:PHE156 4.8 0.0 1.0
N U:THR155 4.9 0.0 1.0
CA U:CYS154 5.0 0.0 1.0

Zinc binding site 3 out of 10 in 7eg9

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Zinc binding site 3 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2001

b:69.3
occ:1.00
 SG o:CYS81 2.0 40.5 1.0
SG o:CYS71 2.4 46.9 1.0
CB o:CYS71 3.0 46.9 1.0
NE2 o:HIS84 3.1 27.7 1.0
CD2 o:HIS84 3.2 27.7 1.0
CA o:GLY63 3.2 34.1 1.0
SG o:CYS74 3.6 45.6 1.0
CB o:CYS81 3.6 40.5 1.0
N o:GLY63 3.6 34.1 1.0
C o:GLY63 3.8 34.1 1.0
OG1 o:THR73 4.1 43.8 1.0
O o:CYS74 4.1 45.6 1.0
O o:GLY63 4.1 34.1 1.0
CE1 o:HIS84 4.5 27.7 1.0
CA o:CYS71 4.5 46.9 1.0
N o:VAL64 4.5 40.4 1.0
CG o:HIS84 4.5 27.7 1.0
C o:GLN62 4.6 29.1 1.0
CA o:CYS81 4.7 40.5 1.0
N o:CYS74 4.7 45.6 1.0
CG2 o:VAL64 4.8 40.4 1.0
O o:ARG61 4.9 39.8 1.0
N o:GLY83 5.0 31.7 1.0

Zinc binding site 4 out of 10 in 7eg9

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Zinc binding site 4 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2002

b:104.1
occ:1.00
 SG o:CYS114 2.3 63.4 1.0
CD o:LYS116 2.4 61.1 1.0
CG o:LYS116 2.8 61.1 1.0
NZ o:LYS116 2.8 61.1 1.0
CB o:CYS114 2.8 63.4 1.0
CE o:LYS116 3.0 61.1 1.0
SG o:CYS154 3.1 79.6 1.0
SG o:CYS111 3.5 62.2 1.0
CB o:CYS184 3.8 80.7 1.0
CB o:CYS111 4.0 62.2 1.0
CB o:LYS116 4.2 61.1 1.0
CA o:CYS114 4.2 63.4 1.0
CB o:CYS154 4.5 79.6 1.0
O o:GLY183 4.6 78.1 1.0
C o:CYS114 4.6 63.4 1.0
C o:GLY183 4.8 78.1 1.0
N o:CYS184 4.9 80.7 1.0
SG o:CYS184 4.9 80.7 1.0
N o:LYS116 5.0 61.1 1.0
N o:SER115 5.0 57.7 1.0
CA o:CYS184 5.0 80.7 1.0

Zinc binding site 5 out of 10 in 7eg9

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Zinc binding site 5 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp 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 7eg9

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Zinc binding site 6 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp 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 7eg9

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Zinc binding site 7 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp 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 7eg9

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Zinc binding site 8 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp 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 7eg9

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Zinc binding site 9 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp 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 7eg9

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Zinc binding site 10 out of 10 in the Tfiid-Based Intermediate Pic on Scp 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 Scp 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
CB z:GLU21 4.8 116.0 1.0
N z:ARG37 4.8 129.0 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 19:45:46 2024

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