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Zinc in PDB 5iyd: Human Core-Pic in the Initial Transcribing State (No Iis)

Enzymatic activity of Human Core-Pic in the Initial Transcribing State (No Iis)

All present enzymatic activity of Human Core-Pic in the Initial Transcribing State (No Iis):
2.7.7.48; 2.7.7.6; 3.6.4.12;

Other elements in 5iyd:

The structure of Human Core-Pic in the Initial Transcribing State (No Iis) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Human Core-Pic in the Initial Transcribing State (No Iis) (pdb code 5iyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Human Core-Pic in the Initial Transcribing State (No Iis), PDB code: 5iyd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 5iyd

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Zinc binding site 1 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:0.0
occ:1.00
 CA A:CYS71 1.3 0.0 1.0
CB A:CYS71 1.5 0.0 1.0
SG A:CYS71 2.0 0.0 1.0
C A:CYS71 2.3 0.0 1.0
N A:CYS71 2.6 0.0 1.0
O A:ARG70 3.0 0.0 1.0
O A:GLN62 3.0 0.0 1.0
N A:GLN72 3.1 0.0 1.0
O A:CYS71 3.1 0.0 1.0
C A:ARG70 3.2 0.0 1.0
O A:ARG61 3.4 0.0 1.0
C A:GLN62 3.8 0.0 1.0
CA A:GLN72 4.5 0.0 1.0
CB A:VAL64 4.5 0.0 1.0
C A:GLY63 4.5 0.0 1.0
OD1 A:ASP59 4.5 0.0 1.0
CA A:GLY63 4.5 0.0 1.0
CG A:GLN72 4.5 0.0 1.0
C A:ARG61 4.5 0.0 1.0
N A:GLY63 4.6 0.0 1.0
CG1 A:VAL64 4.6 0.0 1.0
CA A:ARG70 4.7 0.0 1.0
CA A:GLN62 4.7 0.0 1.0
SG A:CYS81 4.7 0.0 1.0
O A:ALA75 4.7 0.0 1.0
N A:VAL64 4.7 0.0 1.0
O A:GLY63 4.8 0.0 1.0
CB A:GLN72 4.9 0.0 1.0

Zinc binding site 2 out of 11 in 5iyd

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Zinc binding site 2 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2004

b:0.0
occ:1.00
 SG A:CYS111 0.7 0.0 1.0
CB A:CYS111 1.9 0.0 1.0
CB A:CYS114 2.4 0.0 1.0
CA A:CYS111 3.0 0.0 1.0
C A:CYS111 3.0 0.0 1.0
O A:PHE112 3.1 0.0 1.0
O A:CYS111 3.3 0.0 1.0
CA A:CYS114 3.4 0.0 1.0
N A:CYS114 3.4 0.0 1.0
SG A:CYS154 3.5 0.0 1.0
N A:PHE112 3.7 0.0 1.0
CB A:CYS154 3.7 0.0 1.0
SG A:CYS114 3.7 0.0 1.0
OE1 A:GLN188 3.8 0.0 1.0
SG A:CYS184 3.8 0.0 1.0
C A:PHE112 3.9 0.0 1.0
C A:CYS114 4.1 0.0 1.0
N A:SER115 4.1 0.0 1.0
N A:CYS111 4.1 0.0 1.0
O A:LYS116 4.4 0.0 1.0
CA A:PHE112 4.4 0.0 1.0
CD A:GLN188 4.5 0.0 1.0
C A:PHE113 4.6 0.0 1.0
N A:LYS116 4.8 0.0 1.0
N A:PHE113 4.9 0.0 1.0
CB A:CYS184 4.9 0.0 1.0
O A:CYS114 5.0 0.0 1.0

Zinc binding site 3 out of 11 in 5iyd

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Zinc binding site 3 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2005

b:0.0
occ:1.00
 OE2 A:GLU613 4.2 0.0 1.0

Zinc binding site 4 out of 11 in 5iyd

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Zinc binding site 4 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:0.0
occ:1.00
 SG B:CYS1137 1.7 0.0 1.0
O B:ARG1138 2.1 0.0 1.0
C B:CYS1137 3.0 0.0 1.0
O B:ALA1126 3.1 0.0 1.0
CB B:CYS1137 3.1 0.0 1.0
C B:ARG1138 3.2 0.0 1.0
N B:ARG1138 3.2 0.0 1.0
O B:CYS1137 3.3 0.0 1.0
CA B:CYS1137 3.4 0.0 1.0
CA B:ARG1138 3.8 0.0 1.0
C B:ALA1126 4.2 0.0 1.0
N B:CYS1140 4.3 0.0 1.0
N B:GLY1139 4.3 0.0 1.0
CB B:ALA1126 4.3 0.0 1.0
CB B:ARG1138 4.6 0.0 1.0
SG B:CYS1140 4.7 0.0 1.0
CG A:MET34 4.7 0.0 1.0
CA B:GLY1139 4.7 0.0 1.0
CB B:CYS1140 4.8 0.0 1.0
CA B:ALA1126 4.8 0.0 1.0
N B:CYS1137 4.9 0.0 1.0
SG B:CYS1122 4.9 0.0 1.0
CB B:CYS1119 5.0 0.0 1.0

Zinc binding site 5 out of 11 in 5iyd

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Zinc binding site 5 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:

Zinc binding site 6 out of 11 in 5iyd

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Zinc binding site 6 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.0
occ:1.00
 CB I:CYS17 0.8 0.0 1.0
CA I:CYS17 0.9 0.0 1.0
C I:CYS17 1.8 0.0 1.0
N I:CYS17 1.9 0.0 1.0
SG I:CYS17 2.2 0.0 1.0
O I:CYS17 2.4 0.0 1.0
N I:GLN18 2.8 0.0 1.0
C I:PHE16 3.1 0.0 1.0
O I:ASN22 3.3 0.0 1.0
O I:PHE16 3.6 0.0 1.0
N I:ASN22 3.7 0.0 1.0
CD2 I:LEU24 3.9 0.0 1.0
N I:ASN21 4.0 0.0 1.0
CA I:GLN18 4.1 0.0 1.0
N I:GLU19 4.1 0.0 1.0
C I:ASN22 4.2 0.0 1.0
CA I:PHE16 4.4 0.0 1.0
SG I:CYS20 4.4 0.0 1.0
CA I:ASN21 4.4 0.0 1.0
N I:CYS20 4.4 0.0 1.0
CB I:CYS39 4.4 0.0 1.0
CA I:ASN22 4.5 0.0 1.0
CG I:LEU24 4.5 0.0 1.0
C I:GLN18 4.6 0.0 1.0
C I:ASN21 4.6 0.0 1.0
CB I:PHE16 4.7 0.0 1.0
SG I:CYS39 4.7 0.0 1.0
CD2 I:TYR44 4.8 0.0 1.0
C I:CYS20 4.9 0.0 1.0

Zinc binding site 7 out of 11 in 5iyd

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Zinc binding site 7 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.0
occ:1.00
 CB I:ALA116 1.5 0.0 1.0
CG I:HIS91 2.2 0.0 1.0
ND1 I:HIS91 2.2 0.0 1.0
CB I:HIS91 2.3 0.0 1.0
CA I:ALA116 3.0 0.0 1.0
CD2 I:HIS91 3.1 0.0 1.0
CE1 I:HIS91 3.1 0.0 1.0
NE2 I:HIS91 3.6 0.0 1.0
SG I:CYS89 3.7 0.0 1.0
N I:ALA116 3.7 0.0 1.0
CA I:HIS91 3.7 0.0 1.0
C I:ALA116 3.9 0.0 1.0
O I:LYS92 3.9 0.0 1.0
C I:HIS91 4.0 0.0 1.0
SG I:CYS114 4.2 0.0 1.0
O I:HIS91 4.2 0.0 1.0
N I:PRO117 4.4 0.0 1.0
O I:PRO117 4.4 0.0 1.0
N I:HIS91 4.5 0.0 1.0
N I:LYS92 4.6 0.0 1.0
CD I:PRO117 4.6 0.0 1.0
O I:ALA116 4.6 0.0 1.0
C I:THR115 5.0 0.0 1.0
CB I:CYS89 5.0 0.0 1.0

Zinc binding site 8 out of 11 in 5iyd

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Zinc binding site 8 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.0
occ:1.00
 CA J:VAL14 1.1 0.0 1.0
N J:VAL14 1.1 0.0 1.0
CB J:VAL14 1.5 0.0 1.0
CG1 J:VAL14 1.9 0.0 1.0
C J:VAL14 2.0 0.0 1.0
C J:ILE13 2.3 0.0 1.0
N J:GLY15 2.4 0.0 1.0
CG2 J:VAL14 2.9 0.0 1.0
O J:ILE13 3.0 0.0 1.0
O J:VAL14 3.1 0.0 1.0
CA J:ILE13 3.3 0.0 1.0
N J:ARG6 3.5 0.0 1.0
O J:LYS12 3.7 0.0 1.0
CA J:GLY15 3.9 0.0 1.0
CA J:ARG6 4.0 0.0 1.0
OD1 J:ASN16 4.1 0.0 1.0
CG2 J:ILE13 4.2 0.0 1.0
N J:ILE13 4.3 0.0 1.0
CB J:ILE13 4.3 0.0 1.0
N J:CYS7 4.3 0.0 1.0
C J:VAL5 4.4 0.0 1.0
C J:LYS12 4.4 0.0 1.0
O J:PRO4 4.5 0.0 1.0
C J:ARG6 4.6 0.0 1.0
CA J:VAL5 4.7 0.0 1.0
N J:ASN16 4.8 0.0 1.0
C J:GLY15 4.8 0.0 1.0

Zinc binding site 9 out of 11 in 5iyd

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Zinc binding site 9 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 O L:GLU38 1.3 0.0 1.0
C L:GLU38 1.7 0.0 1.0
CA L:GLU38 2.1 0.0 1.0
N L:GLU38 2.8 0.0 1.0
N L:CYS39 2.8 0.0 1.0
NZ M:LYS226 3.0 0.0 1.0
CB L:GLU38 3.5 0.0 1.0
CA L:CYS39 3.7 0.0 1.0
C L:ARG37 3.8 0.0 1.0
CE M:LYS226 4.0 0.0 1.0
CG L:GLU38 4.1 0.0 1.0
C L:CYS39 4.1 0.0 1.0
O L:ARG37 4.3 0.0 1.0
N L:GLY40 4.5 0.0 1.0
CD L:GLU38 4.5 0.0 1.0
O L:CYS39 4.6 0.0 1.0
OE2 L:GLU38 4.8 0.0 1.0
O L:CYS36 4.8 0.0 1.0
CA L:ARG37 4.8 0.0 1.0

Zinc binding site 10 out of 11 in 5iyd

Go back to Zinc Binding Sites List in 5iyd
Zinc binding site 10 out of 11 in the Human Core-Pic in the Initial Transcribing State (No Iis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human Core-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:0.0
occ:1.00
 N M:ALA21 1.0 0.0 1.0
CA M:ALA21 1.2 0.0 1.0
CB M:ALA21 1.7 0.0 1.0
C M:ASP20 1.9 0.0 1.0
O M:ASP20 2.4 0.0 1.0
C M:ALA21 2.7 0.0 1.0
CA M:ASP20 3.2 0.0 1.0
N M:ILE22 3.3 0.0 1.0
O M:ALA21 3.6 0.0 1.0
O M:PRO19 3.6 0.0 1.0
OE2 M:GLU36 3.9 0.0 1.0
CG M:ASP20 4.0 0.0 1.0
CB M:ASP20 4.1 0.0 1.0
N M:ASP20 4.1 0.0 1.0
OD2 M:ASP20 4.1 0.0 1.0
C M:PRO19 4.3 0.0 1.0
OD1 M:ASP20 4.4 0.0 1.0
CA M:ILE22 4.7 0.0 1.0
CD M:GLU36 4.9 0.0 1.0

Reference:

Y.He, C.Yan, J.Fang, C.Inouye, R.Tjian, I.Ivanov, E.Nogales. Near-Atomic Resolution Visualization of Human Transcription Promoter Opening. Nature V. 533 359 2016.
ISSN: ESSN 1476-4687
PubMed: 27193682
DOI: 10.1038/NATURE17970
Page generated: Sun Oct 27 18:32:55 2024

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