Atomistry » Zinc » PDB 7ecc-7eqz » 7edx
Atomistry »
  Zinc »
    PDB 7ecc-7eqz »
      7edx »

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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Go back to Zinc Binding Sites List in 7edx
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy