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Zinc in PDB 7edx: P53-Bound Tfiid-Based Core Pic on HDM2 Promoter

Enzymatic activity of P53-Bound Tfiid-Based Core Pic on HDM2 Promoter

All present enzymatic activity of P53-Bound Tfiid-Based Core Pic on HDM2 Promoter:
2.3.1.48; 2.7.11.1; 2.7.7.6; 3.6.4.12;

Other elements in 7edx:

The structure of P53-Bound Tfiid-Based Core Pic on HDM2 Promoter also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter (pdb code 7edx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter, PDB code: 7edx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7edx

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Zinc binding site 1 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P53-Bound Tfiid-Based Core Pic on HDM2 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn401

b:30.0
occ:1.00
 SG R:CYS34 2.1 0.0 1.0
NE2 R:HIS18 2.2 0.0 1.0
CD2 R:HIS18 2.5 0.0 1.0
OE2 R:GLU36 3.0 0.0 1.0
SG R:CYS37 3.1 0.0 1.0
CE1 R:HIS18 3.5 0.0 1.0
CD R:GLU36 3.6 0.0 1.0
CB R:CYS34 3.6 0.0 1.0
O R:PRO19 3.7 0.0 1.0
CG R:HIS18 3.8 0.0 1.0
CA R:ASP20 4.0 0.0 1.0
OE1 R:GLU36 4.2 0.0 1.0
CB R:ASP20 4.2 0.0 1.0
CG R:GLU36 4.2 0.0 1.0
ND1 R:HIS18 4.2 0.0 1.0
CB R:CYS37 4.3 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
O R:CYS34 4.6 0.0 1.0
CA R:CYS34 4.8 0.0 1.0
N R:CYS37 4.9 0.0 1.0
C R:HIS18 4.9 0.0 1.0
C R:CYS34 4.9 0.0 1.0

Zinc binding site 2 out of 9 in 7edx

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Zinc binding site 2 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P53-Bound Tfiid-Based Core Pic on HDM2 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2001

b:220.4
occ:1.00
 NE2 o:HIS84 1.9 210.6 1.0
SG o:CYS74 2.5 208.6 1.0
CD2 o:HIS84 2.5 210.6 1.0
SG o:CYS71 2.5 215.1 1.0
SG o:CYS81 2.5 201.8 1.0
CE1 o:HIS84 3.1 210.6 1.0
OG1 o:THR73 3.4 211.4 1.0
CB o:CYS71 3.5 215.1 1.0
CG o:HIS84 3.8 210.6 1.0
CA o:GLY63 4.0 218.4 1.0
O o:CYS74 4.0 208.6 1.0
N o:CYS74 4.0 208.6 1.0
ND1 o:HIS84 4.0 210.6 1.0
CB o:CYS74 4.1 208.6 1.0
CB o:CYS81 4.1 201.8 1.0
N o:GLY63 4.3 218.4 1.0
CA o:CYS74 4.5 208.6 1.0
O o:ARG61 4.6 223.1 1.0
C o:GLY63 4.6 218.4 1.0
C o:CYS74 4.7 208.6 1.0
CB o:THR73 4.7 211.4 1.0
CA o:CYS81 4.8 201.8 1.0
CA o:CYS71 4.9 215.1 1.0
N o:THR73 4.9 211.4 1.0
C o:THR73 4.9 211.4 1.0
O o:GLY63 5.0 218.4 1.0
N o:GLY83 5.0 205.4 1.0

Zinc binding site 3 out of 9 in 7edx

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Zinc binding site 3 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of P53-Bound Tfiid-Based Core Pic on HDM2 Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Zn2002

b:303.1
occ:1.00
 CB o:CYS114 2.4 287.1 1.0
SG o:CYS184 2.7 285.0 1.0
SG o:CYS111 2.7 291.0 1.0
SG o:CYS114 2.9 287.1 1.0
SG o:CYS154 2.9 287.9 1.0
CB o:CYS154 2.9 287.9 1.0
CB o:CYS184 3.0 285.0 1.0
CA o:CYS114 3.9 287.1 1.0
CB o:CYS111 4.0 291.0 1.0
O o:PHE112 4.2 289.8 1.0
N o:CYS114 4.4 287.1 1.0
CA o:CYS154 4.5 287.9 1.0
CA o:CYS184 4.5 285.0 1.0
CE1 o:PHE113 4.7 290.2 1.0
O o:CYS114 4.7 287.1 1.0
NE2 o:GLN188 4.7 295.1 1.0
C o:CYS114 4.8 287.1 1.0
CD1 o:PHE113 4.8 290.2 1.0
O o:PHE113 4.8 290.2 1.0
C o:PHE113 4.9 290.2 1.0

Zinc binding site 4 out of 9 in 7edx

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Zinc binding site 4 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of P53-Bound Tfiid-Based Core Pic on HDM2 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 5 out of 9 in 7edx

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Zinc binding site 5 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of P53-Bound Tfiid-Based Core Pic on HDM2 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 6 out of 9 in 7edx

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Zinc binding site 6 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of P53-Bound Tfiid-Based Core Pic on HDM2 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:CYS17 2.4 165.5 1.0
SG w:CYS20 2.4 166.4 1.0
SG w:CYS42 2.4 174.1 1.0
CB w:CYS17 2.8 165.5 1.0
CB w:CYS39 3.0 170.9 1.0
CB w:CYS42 3.7 174.1 1.0
N w:CYS42 4.0 174.1 1.0
CB w:CYS20 4.1 166.4 1.0
N w:CYS20 4.2 166.4 1.0
CA w:CYS17 4.2 165.5 1.0
CA w:CYS42 4.4 174.1 1.0
CA w:CYS39 4.4 170.9 1.0
OE2 w:GLU19 4.6 168.3 1.0
CA w:CYS20 4.6 166.4 1.0
O w:CYS42 4.7 174.1 1.0
CB w:ASN22 4.7 159.8 1.0
C w:CYS42 4.7 174.1 1.0
CB w:ASN41 4.8 171.6 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

Zinc binding site 7 out of 9 in 7edx

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Zinc binding site 7 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of P53-Bound Tfiid-Based Core Pic on HDM2 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 8 out of 9 in 7edx

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Zinc binding site 8 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of P53-Bound Tfiid-Based Core Pic on HDM2 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 9 out of 9 in 7edx

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Zinc binding site 9 out of 9 in the P53-Bound Tfiid-Based Core Pic on HDM2 Promoter


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of P53-Bound Tfiid-Based Core Pic on HDM2 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 19:40:28 2024

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