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Zinc in PDB 5iyb: Human Core-Pic in the Open State

Enzymatic activity of Human Core-Pic in the Open State

All present enzymatic activity of Human Core-Pic in the Open State:
2.7.7.48; 2.7.7.6; 3.6.4.12;

Other elements in 5iyb:

The structure of Human Core-Pic in the Open State 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 Open State (pdb code 5iyb). 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 Open State, PDB code: 5iyb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 5iyb

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Zinc binding site 1 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.0
occ:1.00
 NE2 A:HIS84 2.0 0.0 1.0
SG A:CYS71 2.3 0.0 1.0
SG A:CYS74 2.5 0.0 1.0
SG A:CYS81 2.6 0.0 1.0
CB A:CYS74 2.8 0.0 1.0
CD2 A:HIS84 2.9 0.0 1.0
CE1 A:HIS84 3.1 0.0 1.0
CB A:CYS81 3.5 0.0 1.0
CB A:CYS71 3.6 0.0 1.0
OE1 A:GLN72 3.7 0.0 1.0
O A:CYS71 3.9 0.0 1.0
CG A:HIS84 4.1 0.0 1.0
ND1 A:HIS84 4.1 0.0 1.0
CA A:CYS81 4.2 0.0 1.0
CA A:CYS74 4.3 0.0 1.0
CD A:PRO82 4.6 0.0 1.0
C A:CYS71 4.7 0.0 1.0
O B:ALA1128 4.7 0.0 1.0
CA A:CYS71 4.8 0.0 1.0
C A:CYS74 4.8 0.0 1.0
CD A:GLN72 4.8 0.0 1.0
C A:CYS81 4.9 0.0 1.0
N A:GLY83 5.0 0.0 1.0
N A:PRO82 5.0 0.0 1.0

Zinc binding site 2 out of 11 in 5iyb

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Zinc binding site 2 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:0.0
occ:1.00
 CB A:CYS114 1.8 0.0 1.0
SG A:CYS114 2.4 0.0 1.0
SG A:CYS154 2.5 0.0 1.0
SG A:CYS111 2.5 0.0 1.0
SG A:CYS184 2.6 0.0 1.0
CB A:CYS184 3.0 0.0 1.0
CA A:CYS114 3.3 0.0 1.0
CB A:CYS154 3.5 0.0 1.0
O A:CYS184 3.7 0.0 1.0
N A:CYS114 3.8 0.0 1.0
CB A:CYS111 3.8 0.0 1.0
O A:GLY183 4.3 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 4.4 0.0 1.0
O A:PHE112 4.4 0.0 1.0
C A:GLY183 4.9 0.0 1.0
O A:CYS114 4.9 0.0 1.0
N A:SER115 4.9 0.0 1.0
N A:CYS184 5.0 0.0 1.0
CA A:CYS154 5.0 0.0 1.0

Zinc binding site 3 out of 11 in 5iyb

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Zinc binding site 3 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:0.0
occ:1.00
 SG B:CYS1122 2.4 0.0 1.0
SG B:CYS1137 2.5 0.0 1.0
SG B:CYS1140 2.5 0.0 1.0
SG B:CYS1119 2.7 0.0 1.0
CB B:CYS1119 3.1 0.0 1.0
CB B:CYS1140 3.4 0.0 1.0
CB B:CYS1122 3.6 0.0 1.0
N B:CYS1122 3.9 0.0 1.0
CB B:CYS1137 4.0 0.0 1.0
O B:CYS1122 4.1 0.0 1.0
CA B:CYS1122 4.2 0.0 1.0
N B:CYS1140 4.5 0.0 1.0
C B:CYS1122 4.6 0.0 1.0
CA B:CYS1140 4.6 0.0 1.0
O B:ARG1138 4.6 0.0 1.0
CA B:CYS1119 4.6 0.0 1.0
CB B:LEU1121 4.7 0.0 1.0
CD2 B:LEU1121 4.8 0.0 1.0
C B:LEU1121 5.0 0.0 1.0
CB B:ASN1142 5.0 0.0 1.0

Zinc binding site 4 out of 11 in 5iyb

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Zinc binding site 4 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.0
occ:1.00
 SG C:CYS90 2.3 0.0 1.0
SG C:CYS94 2.5 0.0 1.0
SG C:CYS97 2.5 0.0 1.0
SG C:CYS88 2.6 0.0 1.0
CB C:CYS88 3.0 0.0 1.0
CB C:CYS90 3.1 0.0 1.0
CB C:CYS97 3.4 0.0 1.0
CB C:CYS94 3.6 0.0 1.0
N C:CYS94 4.0 0.0 1.0
N C:CYS97 4.2 0.0 1.0
N C:CYS90 4.2 0.0 1.0
CA C:CYS90 4.2 0.0 1.0
CA C:CYS94 4.3 0.0 1.0
CA C:CYS88 4.4 0.0 1.0
CA C:CYS97 4.4 0.0 1.0
C C:PHE93 4.4 0.0 1.0
C C:CYS88 4.6 0.0 1.0
O C:CYS94 4.7 0.0 1.0
C C:GLU96 4.8 0.0 1.0
O C:CYS88 4.8 0.0 1.0
C C:CYS94 4.8 0.0 1.0
O C:PHE93 4.8 0.0 1.0
CB C:GLU96 4.9 0.0 1.0
C C:CYS90 5.0 0.0 1.0
CA C:PHE93 5.0 0.0 1.0

Zinc binding site 5 out of 11 in 5iyb

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Zinc binding site 5 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.0
occ:1.00
 SG I:CYS42 2.3 0.0 1.0
SG I:CYS20 2.3 0.0 1.0
SG I:CYS17 2.5 0.0 1.0
SG I:CYS39 2.5 0.0 1.0
CB I:CYS39 2.5 0.0 1.0
CB I:CYS17 3.4 0.0 1.0
CB I:CYS42 3.7 0.0 1.0
OD1 I:ASN41 3.7 0.0 1.0
CB I:CYS20 4.0 0.0 1.0
CA I:CYS39 4.0 0.0 1.0
N I:CYS20 4.2 0.0 1.0
OE1 I:GLU19 4.4 0.0 1.0
N I:CYS42 4.5 0.0 1.0
CA I:CYS20 4.6 0.0 1.0
CG I:ASN41 4.6 0.0 1.0
CA I:CYS42 4.7 0.0 1.0
N I:CYS39 4.8 0.0 1.0
CB I:TYR44 4.8 0.0 1.0
CA I:CYS17 4.8 0.0 1.0
C I:CYS39 4.8 0.0 1.0
CB I:GLU19 5.0 0.0 1.0

Zinc binding site 6 out of 11 in 5iyb

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Zinc binding site 6 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.0
occ:1.00
 SG I:CYS119 2.3 0.0 1.0
SG I:CYS89 2.4 0.0 1.0
SG I:CYS114 2.4 0.0 1.0
SG I:CYS86 2.5 0.0 1.0
CB I:CYS86 3.0 0.0 1.0
CB I:CYS119 3.0 0.0 1.0
CB I:CYS89 3.1 0.0 1.0
CB I:CYS114 3.2 0.0 1.0
N I:CYS89 3.6 0.0 1.0
CA I:CYS89 3.9 0.0 1.0
O I:CYS89 4.4 0.0 1.0
CA I:CYS86 4.5 0.0 1.0
CA I:CYS119 4.5 0.0 1.0
C I:CYS89 4.6 0.0 1.0
CA I:CYS114 4.7 0.0 1.0
CB I:LYS88 4.7 0.0 1.0
C I:LYS88 4.8 0.0 1.0
O I:HIS91 4.8 0.0 1.0
N I:CYS119 4.8 0.0 1.0
CB I:HIS121 5.0 0.0 1.0

Zinc binding site 7 out of 11 in 5iyb

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Zinc binding site 7 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.0
occ:1.00
 SG J:CYS10 2.2 0.0 1.0
SG J:CYS44 2.3 0.0 1.0
SG J:CYS45 2.4 0.0 1.0
SG J:CYS7 2.6 0.0 1.0
CB J:CYS10 3.1 0.0 1.0
CB J:CYS7 3.2 0.0 1.0
N J:CYS45 3.4 0.0 1.0
CB J:CYS44 3.6 0.0 1.0
CB J:CYS45 3.6 0.0 1.0
CA J:CYS45 3.7 0.0 1.0
C J:CYS44 3.8 0.0 1.0
N J:CYS10 3.8 0.0 1.0
CA J:CYS10 4.1 0.0 1.0
O J:CYS44 4.2 0.0 1.0
CA J:CYS44 4.3 0.0 1.0
CB J:THR9 4.4 0.0 1.0
O J:CYS7 4.5 0.0 1.0
CA J:CYS7 4.6 0.0 1.0
N J:GLY11 4.7 0.0 1.0
C J:THR9 4.8 0.0 1.0
C J:CYS7 4.8 0.0 1.0
CB J:LYS12 4.9 0.0 1.0
CA J:THR9 5.0 0.0 1.0
C J:CYS10 5.0 0.0 1.0
N J:THR9 5.0 0.0 1.0

Zinc binding site 8 out of 11 in 5iyb

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Zinc binding site 8 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 CB L:CYS39 2.1 0.0 1.0
SG L:CYS36 2.5 0.0 1.0
SG L:CYS19 2.5 0.0 1.0
SG L:CYS39 2.6 0.0 1.0
SG L:CYS22 2.6 0.0 1.0
CB L:CYS19 3.4 0.0 1.0
CA L:CYS39 3.4 0.0 1.0
CB L:CYS36 3.7 0.0 1.0
CB L:CYS22 3.7 0.0 1.0
N L:CYS39 3.8 0.0 1.0
O L:CYS39 3.8 0.0 1.0
C L:CYS39 3.9 0.0 1.0
O L:ARG37 4.3 0.0 1.0
OE1 L:GLU38 4.3 0.0 1.0
N L:CYS22 4.5 0.0 1.0
CA L:CYS22 4.6 0.0 1.0
OG1 L:THR24 4.7 0.0 1.0
O L:CYS36 4.7 0.0 1.0
CA L:CYS19 4.8 0.0 1.0
CA L:CYS36 4.9 0.0 1.0
C L:CYS36 4.9 0.0 1.0
N L:GLY40 5.0 0.0 1.0

Zinc binding site 9 out of 11 in 5iyb

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Zinc binding site 9 out of 11 in the Human Core-Pic in the Open State


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 Open State within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:0.0
occ:1.00
 CE1 M:HIS18 2.3 0.0 1.0
NE2 M:HIS18 2.4 0.0 1.0
SG M:CYS37 2.4 0.0 1.0
SG M:CYS34 2.5 0.0 1.0
SG M:CYS15 2.6 0.0 1.0
ND1 M:HIS18 3.3 0.0 1.0
CD2 M:LEU39 3.5 0.0 1.0
CB M:CYS34 3.5 0.0 1.0
CD2 M:HIS18 3.5 0.0 1.0
OD1 M:ASN17 3.6 0.0 1.0
CB M:CYS37 3.7 0.0 1.0
CG M:HIS18 4.0 0.0 1.0
N M:CYS37 4.2 0.0 1.0
CB M:CYS15 4.2 0.0 1.0
ND2 M:ASN17 4.2 0.0 1.0
CG M:ASN17 4.3 0.0 1.0
CB M:LEU39 4.4 0.0 1.0
CG M:LEU39 4.5 0.0 1.0
OE2 M:GLU36 4.5 0.0 1.0
CA M:CYS37 4.5 0.0 1.0
O M:HIS18 4.6 0.0 1.0
CD M:GLU36 4.6 0.0 1.0
CG M:GLU36 4.7 0.0 1.0
C M:GLU36 4.7 0.0 1.0
O M:CYS34 4.7 0.0 1.0
CA M:CYS34 4.8 0.0 1.0
C M:CYS34 4.8 0.0 1.0
N M:GLU36 5.0 0.0 1.0

Zinc binding site 10 out of 11 in 5iyb

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Zinc binding site 10 out of 11 in the Human Core-Pic in the Open State


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 Open State 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
SG Q:CYS132 2.8 0.0 1.0
CB Q:CYS154 2.9 0.0 1.0
O Q:CYS157 3.3 0.0 1.0
CB Q:CYS129 3.4 0.0 1.0
CB Q:CYS157 3.6 0.0 1.0
CB Q:CYS132 3.8 0.0 1.0
C Q:CYS157 3.9 0.0 1.0
N Q:CYS157 3.9 0.0 1.0
CA Q:CYS157 4.0 0.0 1.0
CE1 Q:PHE156 4.2 0.0 1.0
CA Q:CYS154 4.4 0.0 1.0
CZ Q:PHE156 4.4 0.0 1.0
N Q:CYS132 4.4 0.0 1.0
CD1 Q:PHE156 4.5 0.0 1.0
CA Q:CYS132 4.8 0.0 1.0
C Q:CYS154 4.9 0.0 1.0
N Q:HIS158 4.9 0.0 1.0
CE2 Q:PHE156 4.9 0.0 1.0
N Q:THR155 4.9 0.0 1.0
CA Q:CYS129 4.9 0.0 1.0
CB Q:VAL131 4.9 0.0 1.0
C Q:PHE156 5.0 0.0 1.0
CZ Q:PHE136 5.0 0.0 1.0
N Q:PHE156 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 18:28:10 2024

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