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Zinc in PDB 5iy9: Human Holo-Pic in the Initial Transcribing State (No Iis)

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

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

Other elements in 5iy9:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Holo-Pic in the Initial Transcribing State (No Iis) (pdb code 5iy9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Human Holo-Pic in the Initial Transcribing State (No Iis), PDB code: 5iy9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 5iy9

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Zinc binding site 1 out of 10 in the Human Holo-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 Holo-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
 NE2 A:HIS84 2.0 0.0 1.0
SG A:CYS71 2.2 0.0 1.0
SG A:CYS74 2.4 0.0 1.0
SG A:CYS81 2.5 0.0 1.0
CD2 A:HIS84 2.9 0.0 1.0
CE1 A:HIS84 3.0 0.0 1.0
CB A:CYS74 3.2 0.0 1.0
CB A:CYS71 3.4 0.0 1.0
CB A:CYS81 3.5 0.0 1.0
O A:CYS71 3.8 0.0 1.0
CG A:HIS84 4.1 0.0 1.0
CA A:CYS81 4.1 0.0 1.0
ND1 A:HIS84 4.1 0.0 1.0
O A:ALA75 4.3 0.0 1.0
CD A:PRO82 4.4 0.0 1.0
C A:CYS71 4.5 0.0 1.0
CA A:CYS71 4.5 0.0 1.0
CA A:CYS74 4.5 0.0 1.0
C A:CYS74 4.7 0.0 1.0
C A:CYS81 4.7 0.0 1.0
N A:PRO82 4.8 0.0 1.0
N A:GLY83 4.9 0.0 1.0
N A:ALA75 5.0 0.0 1.0

Zinc binding site 2 out of 10 in 5iy9

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Zinc binding site 2 out of 10 in the Human Holo-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 Holo-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
 CB A:CYS114 1.8 0.0 1.0
SG A:CYS154 2.1 0.0 1.0
SG A:CYS114 2.3 0.0 1.0
SG A:CYS184 2.5 0.0 1.0
SG A:CYS111 2.5 0.0 1.0
CB A:CYS184 2.9 0.0 1.0
CA A:CYS114 3.2 0.0 1.0
CB A:CYS154 3.3 0.0 1.0
CB A:CYS111 3.8 0.0 1.0
N A:CYS114 3.8 0.0 1.0
O A:CYS184 3.9 0.0 1.0
CA A:CYS184 4.3 0.0 1.0
C A:CYS114 4.3 0.0 1.0
C A:CYS184 4.5 0.0 1.0
O A:PHE112 4.5 0.0 1.0
O A:CYS154 4.5 0.0 1.0
CA A:CYS154 4.6 0.0 1.0
C A:CYS154 4.7 0.0 1.0
O A:GLY183 4.7 0.0 1.0
O A:CYS114 4.9 0.0 1.0
N A:SER115 5.0 0.0 1.0
O A:CYS111 5.0 0.0 1.0

Zinc binding site 3 out of 10 in 5iy9

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Zinc binding site 3 out of 10 in the Human Holo-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 Holo-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:CYS1122 2.3 0.0 1.0
SG B:CYS1140 2.5 0.0 1.0
SG B:CYS1119 2.5 0.0 1.0
SG B:CYS1137 2.7 0.0 1.0
CB B:CYS1119 3.0 0.0 1.0
CB B:CYS1140 3.4 0.0 1.0
CB B:CYS1122 3.8 0.0 1.0
N B:CYS1122 4.0 0.0 1.0
CB B:CYS1137 4.1 0.0 1.0
O B:CYS1122 4.1 0.0 1.0
CA B:CYS1122 4.3 0.0 1.0
CA B:CYS1119 4.5 0.0 1.0
CA B:CYS1140 4.6 0.0 1.0
N B:CYS1140 4.7 0.0 1.0
C B:CYS1122 4.7 0.0 1.0
O B:ARG1138 4.8 0.0 1.0
C B:LEU1121 4.9 0.0 1.0
CB B:LEU1121 4.9 0.0 1.0
O B:CYS1137 5.0 0.0 1.0
O B:ILE1124 5.0 0.0 1.0

Zinc binding site 4 out of 10 in 5iy9

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Zinc binding site 4 out of 10 in the Human Holo-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 Holo-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.0
occ:1.00
 SG C:CYS90 2.4 0.0 1.0
SG C:CYS88 2.5 0.0 1.0
SG C:CYS94 2.6 0.0 1.0
SG C:CYS97 2.6 0.0 1.0
CB C:CYS94 3.0 0.0 1.0
CB C:CYS97 3.3 0.0 1.0
CB C:CYS90 3.4 0.0 1.0
CB C:CYS88 3.5 0.0 1.0
N C:CYS94 3.8 0.0 1.0
CA C:CYS94 3.9 0.0 1.0
N C:CYS97 4.1 0.0 1.0
C C:PHE93 4.2 0.0 1.0
CA C:CYS97 4.3 0.0 1.0
N C:CYS90 4.4 0.0 1.0
CA C:CYS90 4.4 0.0 1.0
O C:PHE93 4.5 0.0 1.0
C C:CYS94 4.5 0.0 1.0
O C:CYS94 4.5 0.0 1.0
O C:GLU92 4.5 0.0 1.0
CA C:CYS88 4.7 0.0 1.0
O C:CYS88 4.8 0.0 1.0
C C:CYS88 4.8 0.0 1.0
C C:GLU96 4.9 0.0 1.0
CA C:PHE93 4.9 0.0 1.0

Zinc binding site 5 out of 10 in 5iy9

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Zinc binding site 5 out of 10 in the Human Holo-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 Holo-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
 SG I:CYS42 2.2 0.0 1.0
SG I:CYS20 2.3 0.0 1.0
SG I:CYS17 2.4 0.0 1.0
SG I:CYS39 2.5 0.0 1.0
CB I:CYS39 2.6 0.0 1.0
CB I:CYS17 3.1 0.0 1.0
OD1 I:ASN41 3.5 0.0 1.0
OE1 I:GLU19 3.7 0.0 1.0
CB I:CYS42 3.8 0.0 1.0
CB I:CYS20 3.8 0.0 1.0
CA I:CYS39 4.1 0.0 1.0
N I:CYS20 4.3 0.0 1.0
CG I:ASN41 4.4 0.0 1.0
CB I:TYR44 4.5 0.0 1.0
N I:CYS42 4.5 0.0 1.0
CA I:CYS17 4.6 0.0 1.0
CA I:CYS20 4.6 0.0 1.0
CA I:CYS42 4.7 0.0 1.0
C I:CYS39 4.8 0.0 1.0
N I:CYS39 4.8 0.0 1.0
ND2 I:ASN41 4.8 0.0 1.0
CD I:GLU19 4.8 0.0 1.0
CB I:GLU19 4.9 0.0 1.0
OD1 I:ASN22 4.9 0.0 1.0

Zinc binding site 6 out of 10 in 5iy9

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Zinc binding site 6 out of 10 in the Human Holo-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 Holo-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
 SG I:CYS86 2.1 0.0 1.0
SG I:CYS119 2.1 0.0 1.0
CB I:CYS86 2.2 0.0 1.0
SG I:CYS89 2.4 0.0 1.0
SG I:CYS114 2.4 0.0 1.0
CB I:CYS114 3.0 0.0 1.0
CB I:CYS119 3.3 0.0 1.0
CB I:CYS89 3.4 0.0 1.0
CA I:CYS86 3.7 0.0 1.0
N I:CYS89 4.0 0.0 1.0
CA I:CYS89 4.2 0.0 1.0
O I:PRO117 4.2 0.0 1.0
O I:ALA116 4.4 0.0 1.0
C I:CYS86 4.5 0.0 1.0
O I:CYS89 4.5 0.0 1.0
N I:CYS86 4.5 0.0 1.0
CA I:CYS114 4.5 0.0 1.0
CA I:CYS119 4.6 0.0 1.0
O I:CYS86 4.6 0.0 1.0
N I:GLY120 4.7 0.0 1.0
C I:CYS89 4.7 0.0 1.0
O I:HIS91 4.7 0.0 1.0
CB I:ALA116 4.8 0.0 1.0
N I:HIS121 4.9 0.0 1.0
N I:CYS119 4.9 0.0 1.0
CB I:HIS121 4.9 0.0 1.0
O I:HIS118 4.9 0.0 1.0

Zinc binding site 7 out of 10 in 5iy9

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Zinc binding site 7 out of 10 in the Human Holo-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 Holo-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
 SG J:CYS10 2.1 0.0 1.0
SG J:CYS45 2.5 0.0 1.0
SG J:CYS7 2.5 0.0 1.0
SG J:CYS44 2.7 0.0 1.0
CB J:CYS10 3.3 0.0 1.0
CB J:CYS7 3.3 0.0 1.0
N J:CYS45 3.4 0.0 1.0
N J:CYS10 3.5 0.0 1.0
CA J:CYS45 3.6 0.0 1.0
CB J:CYS45 3.6 0.0 1.0
C J:CYS44 3.8 0.0 1.0
CB J:CYS44 3.9 0.0 1.0
CA J:CYS10 4.0 0.0 1.0
O J:CYS44 4.3 0.0 1.0
N J:GLY11 4.3 0.0 1.0
CB J:THR9 4.3 0.0 1.0
CA J:CYS44 4.5 0.0 1.0
O J:CYS7 4.6 0.0 1.0
C J:THR9 4.6 0.0 1.0
C J:CYS10 4.6 0.0 1.0
CA J:CYS7 4.6 0.0 1.0
C J:CYS7 4.7 0.0 1.0
CA J:THR9 4.8 0.0 1.0
CB J:LYS12 4.8 0.0 1.0
N J:THR9 4.9 0.0 1.0
N J:LYS12 4.9 0.0 1.0
OG1 J:THR9 5.0 0.0 1.0

Zinc binding site 8 out of 10 in 5iy9

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Zinc binding site 8 out of 10 in the Human Holo-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 Holo-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
 CB L:CYS39 1.8 0.0 1.0
SG L:CYS22 2.3 0.0 1.0
SG L:CYS19 2.3 0.0 1.0
SG L:CYS36 2.4 0.0 1.0
SG L:CYS39 2.5 0.0 1.0
CA L:CYS39 3.2 0.0 1.0
CB L:CYS22 3.3 0.0 1.0
CB L:CYS19 3.3 0.0 1.0
CB L:CYS36 3.4 0.0 1.0
N L:CYS39 3.7 0.0 1.0
O L:CYS39 3.7 0.0 1.0
C L:CYS39 3.7 0.0 1.0
OE1 L:GLU38 4.0 0.0 1.0
N L:CYS22 4.1 0.0 1.0
O L:ARG37 4.1 0.0 1.0
CA L:CYS22 4.2 0.0 1.0
OG1 L:THR24 4.2 0.0 1.0
CA L:CYS19 4.7 0.0 1.0
CA L:CYS36 4.8 0.0 1.0
N L:GLY40 4.8 0.0 1.0
C L:CYS22 4.9 0.0 1.0
N L:HIS23 4.9 0.0 1.0
C L:CYS36 4.9 0.0 1.0
N L:GLY20 4.9 0.0 1.0
C L:GLU38 4.9 0.0 1.0

Zinc binding site 9 out of 10 in 5iy9

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Zinc binding site 9 out of 10 in the Human Holo-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 Holo-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
 SG M:CYS37 2.3 0.0 1.0
NE2 M:HIS18 2.3 0.0 1.0
CD2 M:LEU39 2.4 0.0 1.0
CE1 M:HIS18 2.5 0.0 1.0
SG M:CYS34 2.5 0.0 1.0
SG M:CYS15 2.5 0.0 1.0
CB M:CYS34 3.4 0.0 1.0
CD2 M:HIS18 3.4 0.0 1.0
ND1 M:HIS18 3.5 0.0 1.0
CB M:CYS37 3.7 0.0 1.0
OD1 M:ASN17 3.7 0.0 1.0
CB M:CYS15 3.9 0.0 1.0
CG M:LEU39 3.9 0.0 1.0
OE2 M:GLU36 4.0 0.0 1.0
CG M:HIS18 4.0 0.0 1.0
CD M:GLU36 4.2 0.0 1.0
N M:CYS37 4.3 0.0 1.0
O M:CYS34 4.3 0.0 1.0
ND2 M:ASN17 4.4 0.0 1.0
CG M:GLU36 4.4 0.0 1.0
CG M:ASN17 4.5 0.0 1.0
CD1 M:LEU39 4.5 0.0 1.0
CA M:CYS37 4.6 0.0 1.0
CA M:CYS34 4.6 0.0 1.0
C M:CYS34 4.6 0.0 1.0
OE1 M:GLU36 4.7 0.0 1.0
O M:HIS18 4.7 0.0 1.0
CB M:LEU39 4.9 0.0 1.0
C M:GLU36 4.9 0.0 1.0

Zinc binding site 10 out of 10 in 5iy9

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Zinc binding site 10 out of 10 in the Human Holo-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 Holo-Pic in the Initial Transcribing State (No Iis) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn501

b:0.0
occ:1.00
 SG Q:CYS154 2.1 0.0 1.0
SG Q:CYS157 2.1 0.0 1.0
SG Q:CYS129 2.6 0.0 1.0
CB Q:CYS154 2.7 0.0 1.0
SG Q:CYS132 2.8 0.0 1.0
CB Q:CYS129 3.5 0.0 1.0
CB Q:CYS132 3.6 0.0 1.0
CB Q:CYS157 3.7 0.0 1.0
CA Q:CYS154 4.2 0.0 1.0
N Q:CYS157 4.2 0.0 1.0
N Q:CYS132 4.2 0.0 1.0
CA Q:CYS157 4.3 0.0 1.0
N Q:HIS158 4.3 0.0 1.0
C Q:CYS157 4.3 0.0 1.0
N Q:THR159 4.4 0.0 1.0
CA Q:CYS132 4.6 0.0 1.0
OG1 Q:THR159 4.6 0.0 1.0
CB Q:THR159 4.7 0.0 1.0
C Q:CYS154 4.8 0.0 1.0
CB Q:VAL131 4.8 0.0 1.0
CZ Q:PHE156 4.8 0.0 1.0
N Q:THR155 4.9 0.0 1.0
CE2 Q:PHE156 4.9 0.0 1.0
CA Q:CYS129 4.9 0.0 1.0
O Q:THR159 4.9 0.0 1.0
O Q:CYS157 4.9 0.0 1.0
CA Q:HIS158 5.0 0.0 1.0
CZ Q:PHE136 5.0 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 18:27:01 2024

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