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Zinc in PDB 6o9l: Human Holo-Pic in the Closed State

Enzymatic activity of Human Holo-Pic in the Closed State

All present enzymatic activity of Human Holo-Pic in the Closed State:
2.3.1.48; 2.7.11.22; 2.7.11.23; 2.7.7.48; 2.7.7.6; 3.6.4.12;

Other elements in 6o9l:

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

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Human Holo-Pic in the Closed State (pdb code 6o9l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Human Holo-Pic in the Closed State, PDB code: 6o9l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 6o9l

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Zinc binding site 1 out of 17 in the Human Holo-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 Holo-Pic in the Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.0
occ:1.00
 SG A:CYS81 2.5 0.0 1.0
NE2 A:HIS84 2.6 0.0 1.0
NE2 A:GLN72 2.7 0.0 1.0
CB A:CYS74 2.8 0.0 1.0
SG A:CYS74 2.9 0.0 1.0
CD2 A:HIS84 3.1 0.0 1.0
CE1 A:HIS84 3.7 0.0 1.0
O B:ALA1128 3.8 0.0 1.0
CD A:GLN72 3.9 0.0 1.0
O A:GLN62 3.9 0.0 1.0
CB A:CYS81 4.0 0.0 1.0
CG A:HIS84 4.3 0.0 1.0
CA A:CYS74 4.3 0.0 1.0
CG A:GLN72 4.4 0.0 1.0
ND1 A:HIS84 4.6 0.0 1.0
SG A:CYS71 4.7 0.0 1.0
CA A:CYS81 4.9 0.0 1.0
N A:CYS74 4.9 0.0 1.0
OE1 A:GLN72 4.9 0.0 1.0
C B:ALA1128 4.9 0.0 1.0

Zinc binding site 2 out of 17 in 6o9l

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Zinc binding site 2 out of 17 in the Human Holo-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 Holo-Pic in the Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2003

b:0.0
occ:1.00
 O A:CYS184 2.6 0.0 1.0
CB A:CYS114 2.7 0.0 1.0
SG A:CYS111 3.0 0.0 1.0
SG A:CYS114 3.1 0.0 1.0
SG A:CYS154 3.2 0.0 1.0
SG A:CYS184 3.3 0.0 1.0
CB A:CYS184 3.6 0.0 1.0
C A:CYS184 3.7 0.0 1.0
CB A:CYS111 3.8 0.0 1.0
CA A:CYS114 4.0 0.0 1.0
N A:ARG186 4.1 0.0 1.0
O A:GLY183 4.1 0.0 1.0
CB A:CYS154 4.3 0.0 1.0
CA A:CYS184 4.3 0.0 1.0
O A:PHE112 4.3 0.0 1.0
N A:CYS114 4.4 0.0 1.0
CB A:ARG186 4.4 0.0 1.0
O A:ARG186 4.4 0.0 1.0
N A:GLY185 4.7 0.0 1.0
CA A:ARG186 4.7 0.0 1.0

Zinc binding site 3 out of 17 in 6o9l

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Zinc binding site 3 out of 17 in the Human Holo-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 Holo-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 2.6 0.0 1.0
SG B:CYS1119 2.8 0.0 1.0
CB B:CYS1119 3.3 0.0 1.0
CB B:CYS1140 3.8 0.0 1.0
SG B:CYS1137 3.8 0.0 1.0
N B:CYS1140 3.9 0.0 1.0
SG B:CYS1140 4.0 0.0 1.0
CB B:CYS1122 4.2 0.0 1.0
CA B:CYS1140 4.4 0.0 1.0
N B:CYS1122 4.4 0.0 1.0
CB B:ASN1142 4.5 0.0 1.0
ND2 B:ASN1142 4.6 0.0 1.0
O B:CYS1122 4.7 0.0 1.0
CA B:CYS1122 4.8 0.0 1.0
CA B:CYS1119 4.8 0.0 1.0
C B:GLY1139 4.8 0.0 1.0
O B:CYS1137 4.8 0.0 1.0
CB B:CYS1137 4.8 0.0 1.0
CA B:GLY1139 4.9 0.0 1.0
C B:CYS1122 5.0 0.0 1.0

Zinc binding site 4 out of 17 in 6o9l

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Zinc binding site 4 out of 17 in the Human Holo-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 Holo-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:CYS94 2.6 0.0 1.0
SG C:CYS88 2.7 0.0 1.0
CB C:CYS88 2.8 0.0 1.0
SG C:CYS97 3.1 0.0 1.0
SG C:CYS90 3.2 0.0 1.0
CB C:CYS94 4.0 0.0 1.0
CB C:CYS97 4.1 0.0 1.0
CA C:SER85 4.2 0.0 1.0
CA C:CYS88 4.3 0.0 1.0
O C:TYR84 4.3 0.0 1.0
CB C:CYS90 4.5 0.0 1.0
N C:CYS94 4.6 0.0 1.0
O C:SER85 4.7 0.0 1.0
O C:GLU92 4.7 0.0 1.0
OG C:SER85 4.8 0.0 1.0
CB C:SER85 4.8 0.0 1.0
CA C:CYS94 4.9 0.0 1.0
C C:CYS88 4.9 0.0 1.0
C C:TYR84 4.9 0.0 1.0
N C:SER85 4.9 0.0 1.0
O C:GLN83 4.9 0.0 1.0
N C:CYS88 4.9 0.0 1.0
C C:SER85 5.0 0.0 1.0

Zinc binding site 5 out of 17 in 6o9l

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Zinc binding site 5 out of 17 in the Human Holo-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 Holo-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:CYS20 2.6 0.0 1.0
SG I:CYS42 2.7 0.0 1.0
CB I:CYS39 2.8 0.0 1.0
CD2 I:LEU24 3.4 0.0 1.0
OD1 I:ASN41 3.6 0.0 1.0
SG I:CYS39 3.8 0.0 1.0
CA I:CYS39 4.1 0.0 1.0
CB I:CYS20 4.2 0.0 1.0
SG I:CYS17 4.2 0.0 1.0
N I:CYS39 4.3 0.0 1.0
CB I:CYS17 4.3 0.0 1.0
CB I:CYS42 4.4 0.0 1.0
CB I:TYR44 4.6 0.0 1.0
CG I:ASN41 4.6 0.0 1.0
CB I:ASN22 4.7 0.0 1.0
CG I:LEU24 4.7 0.0 1.0
O I:ASN22 4.8 0.0 1.0
N I:CYS42 4.9 0.0 1.0
ND2 I:ASN41 4.9 0.0 1.0

Zinc binding site 6 out of 17 in 6o9l

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Zinc binding site 6 out of 17 in the Human Holo-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 Holo-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:CYS114 2.6 0.0 1.0
CB I:CYS114 2.8 0.0 1.0
CB I:CYS119 3.7 0.0 1.0
SG I:CYS86 3.9 0.0 1.0
SG I:CYS89 4.1 0.0 1.0
CA I:CYS114 4.2 0.0 1.0
SG I:CYS119 4.4 0.0 1.0
CB I:ALA116 4.5 0.0 1.0
O I:ALA116 4.6 0.0 1.0
CH2 I:TRP123 4.7 0.0 1.0
N I:ALA116 4.7 0.0 1.0
C I:CYS114 4.7 0.0 1.0
CB I:CYS86 4.8 0.0 1.0
N I:THR115 4.9 0.0 1.0
N I:CYS114 4.9 0.0 1.0
CZ3 I:TRP123 5.0 0.0 1.0

Zinc binding site 7 out of 17 in 6o9l

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Zinc binding site 7 out of 17 in the Human Holo-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 Holo-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:CYS10 2.6 0.0 1.0
SG J:CYS44 2.8 0.0 1.0
O J:CYS44 2.9 0.0 1.0
C J:CYS44 2.9 0.0 1.0
SG J:CYS7 3.0 0.0 1.0
CB J:CYS7 3.1 0.0 1.0
CB J:CYS44 3.1 0.0 1.0
N J:CYS45 3.1 0.0 1.0
SG J:CYS45 3.3 0.0 1.0
CA J:CYS45 3.4 0.0 1.0
CA J:CYS44 3.6 0.0 1.0
CB J:CYS10 3.7 0.0 1.0
N J:CYS10 3.9 0.0 1.0
CB J:CYS45 4.0 0.0 1.0
CA J:CYS10 4.4 0.0 1.0
CA J:CYS7 4.6 0.0 1.0
CB J:THR9 4.6 0.0 1.0
N J:CYS44 4.7 0.0 1.0
N J:GLY11 4.7 0.0 1.0
C J:CYS45 4.8 0.0 1.0

Zinc binding site 8 out of 17 in 6o9l

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Zinc binding site 8 out of 17 in the Human Holo-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 Holo-Pic in the Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 SG L:CYS36 2.6 0.0 1.0
SG L:CYS19 2.6 0.0 1.0
CB L:CYS39 2.9 0.0 1.0
O L:ARG37 3.1 0.0 1.0
SG L:CYS22 3.2 0.0 1.0
CB L:CYS36 3.3 0.0 1.0
CB L:CYS19 3.3 0.0 1.0
O L:CYS39 3.6 0.0 1.0
CA L:CYS39 3.8 0.0 1.0
N L:CYS39 3.8 0.0 1.0
SG L:CYS39 3.9 0.0 1.0
C L:CYS39 4.0 0.0 1.0
C L:ARG37 4.3 0.0 1.0
N L:ARG37 4.4 0.0 1.0
OG1 L:THR24 4.4 0.0 1.0
C L:CYS36 4.5 0.0 1.0
CA L:CYS36 4.5 0.0 1.0
CB L:CYS22 4.6 0.0 1.0
CA L:CYS19 4.7 0.0 1.0
CG L:GLU38 4.9 0.0 1.0
CA L:ARG37 5.0 0.0 1.0

Zinc binding site 9 out of 17 in 6o9l

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Zinc binding site 9 out of 17 in the Human Holo-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 Holo-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 2.4 0.0 1.0
NE2 M:HIS18 2.4 0.0 1.0
SG M:CYS15 2.5 0.0 1.0
SG M:CYS37 2.6 0.0 1.0
SG M:CYS34 3.1 0.0 1.0
CB M:CYS15 3.5 0.0 1.0
ND1 M:HIS18 3.5 0.0 1.0
CD2 M:HIS18 3.6 0.0 1.0
OE2 M:GLU36 3.7 0.0 1.0
CB M:CYS37 3.9 0.0 1.0
CB M:CYS34 4.1 0.0 1.0
CG M:ASP20 4.1 0.0 1.0
CG M:HIS18 4.2 0.0 1.0
CD M:GLU36 4.3 0.0 1.0
CG M:GLU36 4.3 0.0 1.0
OD1 M:ASP20 4.3 0.0 1.0
OD2 M:ASP20 4.4 0.0 1.0
CB M:ASP20 4.4 0.0 1.0
OD1 M:ASN17 4.4 0.0 1.0
CA M:ASP20 4.8 0.0 1.0
O M:HIS18 4.8 0.0 1.0
N M:CYS37 4.9 0.0 1.0
CA M:CYS15 5.0 0.0 1.0

Zinc binding site 10 out of 17 in 6o9l

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Zinc binding site 10 out of 17 in the Human Holo-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 Holo-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 2.6 0.0 1.0
SG Q:CYS129 2.6 0.0 1.0
SG Q:CYS132 2.6 0.0 1.0
OG1 Q:THR159 2.9 0.0 1.0
CB Q:CYS154 2.9 0.0 1.0
SG Q:CYS157 3.2 0.0 1.0
CB Q:CYS129 3.2 0.0 1.0
CB Q:CYS132 3.8 0.0 1.0
CB Q:THR159 4.3 0.0 1.0
CA Q:CYS154 4.3 0.0 1.0
N Q:CYS132 4.3 0.0 1.0
CA Q:CYS132 4.7 0.0 1.0
CA Q:CYS129 4.7 0.0 1.0
CG2 Q:THR159 4.8 0.0 1.0
CE2 Q:PHE136 4.8 0.0 1.0
CB Q:CYS157 5.0 0.0 1.0

Reference:

C.Yan, T.Dodd, Y.He, J.A.Tainer, S.E.Tsutakawa, I.Ivanov. Transcription Preinitiation Complex Structure and Dynamics Provide Insight Into Genetic Diseases. Nat.Struct.Mol.Biol. V. 26 397 2019.
ISSN: ESSN 1545-9985
PubMed: 31110295
DOI: 10.1038/S41594-019-0220-3
Page generated: Tue Oct 29 04:09:49 2024

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