Zinc in PDB 5iya: Human Core-Pic in the Closed State

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

The structure of Human Core-Pic in the Closed State also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

Pages:

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

Binding sites:

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

Zinc binding site 1 out of 11 in the Human Core-Pic in the Closed 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 Closed 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 2.2 0.0 1.0 SG A:CYS74 2.4 0.0 1.0 SG A:CYS81 2.5 0.0 1.0 CB A:CYS74 2.8 0.0 1.0 CD2 A:HIS84 2.8 0.0 1.0 CE1 A:HIS84 3.2 0.0 1.0 CB A:CYS81 3.3 0.0 1.0 CB A:CYS71 3.5 0.0 1.0 CD A:PRO82 3.7 0.0 1.0 NE2 A:GLN72 3.7 0.0 1.0 CA A:CYS81 3.8 0.0 1.0 CG A:HIS84 4.1 0.0 1.0 O A:CYS71 4.1 0.0 1.0 ND1 A:HIS84 4.2 0.0 1.0 CA A:CYS74 4.3 0.0 1.0 CD A:GLN72 4.3 0.0 1.0 O A:GLN62 4.4 0.0 1.0 N A:PRO82 4.4 0.0 1.0 CG A:PRO82 4.5 0.0 1.0 C A:CYS81 4.5 0.0 1.0 OE1 A:GLN72 4.5 0.0 1.0 O A:ALA75 4.6 0.0 1.0 C A:CYS74 4.6 0.0 1.0 C A:CYS71 4.7 0.0 1.0 N A:GLY83 4.7 0.0 1.0 CA A:CYS71 4.7 0.0 1.0 O B:ALA1128 4.9 0.0 1.0 N A:ALA75 4.9 0.0 1.0 N A:CYS81 5.0 0.0 1.0

Zinc binding site 2 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:0.0 occ:1.00 CB A:CYS114 1.7 0.0 1.0 SG A:CYS114 2.3 0.0 1.0 SG A:CYS154 2.4 0.0 1.0 SG A:CYS111 2.4 0.0 1.0 SG A:CYS184 2.5 0.0 1.0 CB A:CYS184 3.0 0.0 1.0 CA A:CYS114 3.1 0.0 1.0 O A:CYS184 3.2 0.0 1.0 CB A:CYS111 3.4 0.0 1.0 N A:CYS114 3.7 0.0 1.0 CB A:CYS154 3.7 0.0 1.0 C A:CYS184 4.0 0.0 1.0 O A:GLY183 4.0 0.0 1.0 CA A:CYS184 4.1 0.0 1.0 O A:PHE112 4.1 0.0 1.0 C A:CYS114 4.2 0.0 1.0 CA A:CYS111 4.7 0.0 1.0 N A:SER115 4.7 0.0 1.0 O A:GLU155 4.8 0.0 1.0 O A:CYS114 4.8 0.0 1.0 C A:GLY183 4.9 0.0 1.0 C A:CYS111 4.9 0.0 1.0 N A:CYS184 4.9 0.0 1.0 O A:ARG186 5.0 0.0 1.0 C A:PHE113 5.0 0.0 1.0 CA A:CYS154 5.0 0.0 1.0

Zinc binding site 3 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:0.0 occ:1.00 SG B:CYS1122 2.3 0.0 1.0 SG B:CYS1140 2.3 0.0 1.0 SG B:CYS1137 2.4 0.0 1.0 CB B:CYS1119 2.5 0.0 1.0 SG B:CYS1119 2.5 0.0 1.0 CB B:CYS1140 3.0 0.0 1.0 CB B:CYS1137 3.7 0.0 1.0 CB B:CYS1122 3.9 0.0 1.0 CA B:CYS1119 4.0 0.0 1.0 N B:CYS1122 4.2 0.0 1.0 CA B:CYS1140 4.4 0.0 1.0 O B:CYS1122 4.4 0.0 1.0 CB B:LEU1121 4.5 0.0 1.0 O B:CYS1137 4.5 0.0 1.0 C B:CYS1119 4.6 0.0 1.0 N B:CYS1119 4.6 0.0 1.0 CA B:CYS1122 4.6 0.0 1.0 CD2 B:LEU1121 4.6 0.0 1.0 O B:ILE1124 4.7 0.0 1.0 N B:CYS1140 4.8 0.0 1.0 O B:CYS1119 4.8 0.0 1.0 C B:LEU1121 4.9 0.0 1.0 CA B:CYS1137 4.9 0.0 1.0 C B:CYS1122 5.0 0.0 1.0

Zinc binding site 4 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.0 occ:1.00 SG C:CYS90 2.2 0.0 1.0 SG C:CYS94 2.2 0.0 1.0 SG C:CYS97 2.3 0.0 1.0 SG C:CYS88 2.4 0.0 1.0 CB C:CYS88 2.8 0.0 1.0 CB C:CYS90 3.1 0.0 1.0 CB C:CYS97 3.2 0.0 1.0 CB C:CYS94 3.5 0.0 1.0 N C:CYS94 3.7 0.0 1.0 O C:CYS88 3.9 0.0 1.0 N C:CYS97 4.0 0.0 1.0 CA C:CYS94 4.1 0.0 1.0 CA C:CYS88 4.1 0.0 1.0 CA C:CYS97 4.2 0.0 1.0 C C:CYS88 4.2 0.0 1.0 C C:PHE93 4.2 0.0 1.0 O C:CYS94 4.2 0.0 1.0 CA C:CYS90 4.3 0.0 1.0 N C:CYS90 4.4 0.0 1.0 C C:CYS94 4.5 0.0 1.0 C C:GLU96 4.5 0.0 1.0 CA C:SER85 4.6 0.0 1.0 CB C:GLU96 4.6 0.0 1.0 CA C:PHE93 4.7 0.0 1.0 OG C:SER85 4.8 0.0 1.0 O C:SER85 4.8 0.0 1.0 O C:PHE93 4.9 0.0 1.0 N C:GLU96 4.9 0.0 1.0 CA C:GLU96 4.9 0.0 1.0

Zinc binding site 5 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.0 occ:1.00 SG I:CYS42 2.1 0.0 1.0 SG I:CYS17 2.2 0.0 1.0 SG I:CYS20 2.3 0.0 1.0 SG I:CYS39 2.4 0.0 1.0 CB I:CYS39 2.6 0.0 1.0 CB I:CYS17 2.8 0.0 1.0 OD1 I:ASN41 3.2 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 4.0 0.0 1.0 CG I:ASN41 4.1 0.0 1.0 CA I:CYS39 4.1 0.0 1.0 CB I:GLU19 4.2 0.0 1.0 CA I:CYS17 4.3 0.0 1.0 ND2 I:ASN41 4.3 0.0 1.0 N I:CYS42 4.4 0.0 1.0 N I:CYS20 4.4 0.0 1.0 CB I:TYR44 4.4 0.0 1.0 CA I:CYS42 4.6 0.0 1.0 CB I:ASN22 4.7 0.0 1.0 CD I:GLU19 4.7 0.0 1.0 C I:CYS39 4.7 0.0 1.0 C I:CYS17 4.8 0.0 1.0 N I:GLU19 4.8 0.0 1.0 C I:GLU19 4.8 0.0 1.0 CA I:CYS20 4.8 0.0 1.0 OD1 I:ASN22 4.8 0.0 1.0 CA I:GLU19 4.8 0.0 1.0 N I:CYS39 4.9 0.0 1.0 CD2 I:LEU24 5.0 0.0 1.0

Zinc binding site 6 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:0.0 occ:1.00 SG I:CYS119 2.1 0.0 1.0 SG I:CYS86 2.3 0.0 1.0 CB I:CYS86 2.3 0.0 1.0 SG I:CYS89 2.3 0.0 1.0 SG I:CYS114 2.3 0.0 1.0 CB I:CYS114 2.5 0.0 1.0 CB I:CYS119 3.0 0.0 1.0 CA I:CYS86 3.7 0.0 1.0 CB I:CYS89 3.9 0.0 1.0 CA I:CYS114 4.0 0.0 1.0 O I:ALA116 4.1 0.0 1.0 CB I:ALA116 4.2 0.0 1.0 N I:CYS89 4.2 0.0 1.0 C I:CYS114 4.4 0.0 1.0 O I:CYS89 4.4 0.0 1.0 CA I:CYS119 4.5 0.0 1.0 N I:CYS86 4.5 0.0 1.0 CA I:CYS89 4.6 0.0 1.0 N I:ALA116 4.6 0.0 1.0 C I:CYS86 4.7 0.0 1.0 O I:CYS114 4.7 0.0 1.0 N I:CYS114 4.8 0.0 1.0 CA I:ALA116 4.8 0.0 1.0 O I:HIS91 4.8 0.0 1.0 C I:ALA116 4.8 0.0 1.0 N I:GLY120 4.8 0.0 1.0 C I:CYS89 5.0 0.0 1.0 N I:THR115 5.0 0.0 1.0

Zinc binding site 7 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:0.0 occ:1.00 SG J:CYS45 2.2 0.0 1.0 SG J:CYS10 2.3 0.0 1.0 SG J:CYS7 2.3 0.0 1.0 SG J:CYS44 2.4 0.0 1.0 CB J:CYS7 2.9 0.0 1.0 N J:CYS45 3.1 0.0 1.0 CB J:CYS45 3.3 0.0 1.0 CA J:CYS45 3.4 0.0 1.0 CB J:CYS10 3.6 0.0 1.0 C J:CYS44 3.6 0.0 1.0 CB J:CYS44 3.7 0.0 1.0 N J:CYS10 3.9 0.0 1.0 O J:CYS44 4.2 0.0 1.0 CB J:THR9 4.2 0.0 1.0 CA J:CYS44 4.2 0.0 1.0 CA J:CYS7 4.3 0.0 1.0 CA J:CYS10 4.3 0.0 1.0 O J:CYS7 4.6 0.0 1.0 C J:THR9 4.6 0.0 1.0 CB J:LYS12 4.6 0.0 1.0 C J:CYS7 4.7 0.0 1.0 CB J:ARG42 4.8 0.0 1.0 OG1 J:THR9 4.8 0.0 1.0 N J:GLY11 4.8 0.0 1.0 CA J:THR9 4.8 0.0 1.0 N J:THR9 4.8 0.0 1.0 C J:CYS45 4.9 0.0 1.0 N J:CYS44 4.9 0.0 1.0 N J:LYS12 5.0 0.0 1.0

Zinc binding site 8 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.0 occ:1.00 CB L:CYS39 2.2 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 SG L:CYS22 2.5 0.0 1.0 CB L:CYS19 2.9 0.0 1.0 CB L:CYS22 3.1 0.0 1.0 O L:CYS39 3.3 0.0 1.0 CA L:CYS39 3.4 0.0 1.0 CB L:CYS36 3.6 0.0 1.0 C L:CYS39 3.7 0.0 1.0 N L:CYS22 3.8 0.0 1.0 O L:ARG37 4.0 0.0 1.0 N L:CYS39 4.0 0.0 1.0 CA L:CYS22 4.1 0.0 1.0 CA L:CYS19 4.4 0.0 1.0 O L:TYR41 4.4 0.0 1.0 OG1 L:THR24 4.8 0.0 1.0 N L:TYR41 4.8 0.0 1.0 CA L:CYS36 4.8 0.0 1.0 N L:GLY40 4.9 0.0 1.0 C L:CYS36 4.9 0.0 1.0 C L:GLU21 4.9 0.0 1.0 C L:CYS19 5.0 0.0 1.0 C L:CYS22 5.0 0.0 1.0

Zinc binding site 9 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn401 b:0.0 occ:1.00 CE1 M:HIS18 1.9 0.0 1.0 SG M:CYS34 2.2 0.0 1.0 NE2 M:HIS18 2.3 0.0 1.0 SG M:CYS37 2.4 0.0 1.0 SG M:CYS15 2.5 0.0 1.0 CD2 M:LEU39 2.7 0.0 1.0 ND1 M:HIS18 3.1 0.0 1.0 OE2 M:GLU36 3.4 0.0 1.0 CB M:CYS15 3.5 0.0 1.0 CD2 M:HIS18 3.6 0.0 1.0 CB M:CYS37 3.6 0.0 1.0 CB M:CYS34 3.6 0.0 1.0 CD M:GLU36 3.8 0.0 1.0 CG M:HIS18 4.0 0.0 1.0 CG M:LEU39 4.0 0.0 1.0 CD1 M:LEU39 4.1 0.0 1.0 OD1 M:ASN17 4.2 0.0 1.0 O M:CYS34 4.2 0.0 1.0 CG M:GLU36 4.3 0.0 1.0 OE1 M:GLU36 4.3 0.0 1.0 OD1 M:ASP20 4.4 0.0 1.0 N M:CYS37 4.4 0.0 1.0 CA M:CYS37 4.6 0.0 1.0 CB M:ASP20 4.7 0.0 1.0 C M:CYS34 4.7 0.0 1.0 CA M:ASP20 4.7 0.0 1.0 CA M:CYS34 4.8 0.0 1.0 CG M:ASP20 4.8 0.0 1.0 N M:GLY38 4.9 0.0 1.0 CA M:CYS15 5.0 0.0 1.0 O M:HIS18 5.0 0.0 1.0

Zinc binding site 10 out of 11 in the Human Core-Pic in the Closed 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 Closed State within 5.0Å range: probe atom residue distance (Å) B Occ Q:Zn501 b:0.0 occ:1.00 SG Q:CYS154 2.0 0.0 1.0 SG Q:CYS157 2.1 0.0 1.0 SG Q:CYS129 2.5 0.0 1.0 CB Q:CYS154 2.6 0.0 1.0 SG Q:CYS132 2.8 0.0 1.0 CB Q:CYS129 3.1 0.0 1.0 O Q:CYS157 3.5 0.0 1.0 OG1 Q:THR159 3.5 0.0 1.0 CB Q:CYS157 3.8 0.0 1.0 CA Q:CYS154 4.0 0.0 1.0 CB Q:CYS132 4.1 0.0 1.0 C Q:CYS157 4.2 0.0 1.0 N Q:CYS157 4.2 0.0 1.0 CA Q:CYS157 4.3 0.0 1.0 O Q:THR159 4.5 0.0 1.0 C Q:CYS154 4.5 0.0 1.0 CZ Q:PHE156 4.5 0.0 1.0 N Q:THR155 4.5 0.0 1.0 CE1 Q:PHE156 4.6 0.0 1.0 CA Q:CYS129 4.6 0.0 1.0 N Q:CYS132 4.8 0.0 1.0 CE2 Q:PHE156 4.9 0.0 1.0 CB Q:THR159 4.9 0.0 1.0 N Q:CYS154 4.9 0.0 1.0 CD1 Q:PHE156 5.0 0.0 1.0

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