Zinc in PDB 6u9v: Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State (pdb code 6u9v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State, PDB code: 6u9v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6u9v

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Zinc binding site 1 out of 6 in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:82.5
occ:1.00
SG A:CYS499 2.3 63.1 1.0
SG A:CYS506 2.3 66.5 1.0
SG A:CYS479 2.4 70.1 1.0
SG A:CYS572 2.4 64.2 1.0
HB3 A:CYS479 2.9 70.1 1.0
CB A:CYS479 3.0 70.1 1.0
HB2 A:CYS479 3.1 70.1 1.0
HB3 A:CYS499 3.1 63.1 1.0
HB3 A:CYS572 3.1 64.2 1.0
CB A:CYS572 3.2 64.2 1.0
HB2 A:CYS572 3.4 64.2 1.0
CB A:CYS499 3.4 63.1 1.0
H A:CYS499 3.6 63.1 1.0
CB A:CYS506 3.7 66.5 1.0
HB2 A:ASN481 3.8 67.9 1.0
HA A:CYS506 3.8 66.5 1.0
HB2 A:CYS506 3.9 66.5 1.0
H A:ILE507 3.9 61.6 1.0
HB2 A:CYS499 4.0 63.1 1.0
ZN A:ZN703 4.1 89.0 1.0
H A:ASN481 4.2 67.9 1.0
N A:CYS499 4.3 63.1 1.0
CA A:CYS506 4.3 66.5 1.0
HG22 A:ILE507 4.3 61.6 1.0
CA A:CYS499 4.5 63.1 1.0
SG A:CYS498 4.5 61.9 1.0
HB3 A:CYS506 4.5 66.5 1.0
CA A:CYS479 4.5 70.1 1.0
H A:CYS572 4.5 64.2 1.0
HD22 A:ASN481 4.6 67.9 1.0
H A:CYS479 4.6 70.1 1.0
SG A:CYS482 4.6 69.8 1.0
N A:ILE507 4.6 61.6 1.0
H A:THR508 4.7 63.5 1.0
CA A:CYS572 4.7 64.2 1.0
CB A:ASN481 4.7 67.9 1.0
H A:GLY480 4.8 72.0 1.0
H A:CYS482 4.8 69.8 1.0
HB2 A:PRO570 4.8 58.8 1.0
N A:ASN481 4.9 67.9 1.0
C A:CYS506 5.0 66.5 1.0

Zinc binding site 2 out of 6 in 6u9v

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Zinc binding site 2 out of 6 in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:89.0
occ:1.00
HB2 A:CYS477 1.5 69.6 1.0
CB A:CYS477 2.1 69.6 1.0
SG A:CYS482 2.3 69.8 1.0
SG A:CYS477 2.3 69.6 1.0
SG A:CYS479 2.3 70.1 1.0
SG A:CYS498 2.4 61.9 1.0
HB3 A:CYS477 2.7 69.6 1.0
H A:CYS479 2.8 70.1 1.0
HB2 A:CYS482 3.0 69.8 1.0
CB A:CYS482 3.3 69.8 1.0
CA A:CYS477 3.3 69.6 1.0
H A:GLN478 3.5 68.5 1.0
N A:CYS479 3.5 70.1 1.0
HA A:CYS477 3.5 69.6 1.0
CB A:CYS479 3.6 70.1 1.0
H A:CYS482 3.7 69.8 1.0
CB A:CYS498 3.7 61.9 1.0
HB2 A:CYS498 3.7 61.9 1.0
N A:GLN478 3.7 68.5 1.0
HA A:CYS498 3.7 61.9 1.0
C A:CYS477 3.8 69.6 1.0
HB3 A:CYS479 3.9 70.1 1.0
CA A:CYS479 3.9 70.1 1.0
H A:CYS499 3.9 63.1 1.0
HB3 A:CYS482 4.0 69.8 1.0
ZN A:ZN702 4.1 82.5 1.0
C A:CYS479 4.1 70.1 1.0
O A:CYS479 4.2 70.1 1.0
N A:CYS482 4.2 69.8 1.0
CA A:CYS498 4.3 61.9 1.0
CA A:CYS482 4.3 69.8 1.0
HB2 A:CYS479 4.4 70.1 1.0
HB3 A:CYS498 4.5 61.9 1.0
C A:GLN478 4.5 68.5 1.0
HZ3 A:TRP476 4.5 67.7 1.0
HB3 A:CYS572 4.5 64.2 1.0
N A:CYS477 4.6 69.6 1.0
HA A:CYS482 4.6 69.8 1.0
O A:CYS477 4.6 69.6 1.0
H A:CYS477 4.7 69.6 1.0
N A:CYS499 4.7 63.1 1.0
CA A:GLN478 4.7 68.5 1.0
N A:GLY480 4.8 72.0 1.0
SG A:CYS572 4.8 64.2 1.0
H A:ASN481 4.8 67.9 1.0
HA A:CYS479 4.9 70.1 1.0
SG A:CYS499 4.9 63.1 1.0

Zinc binding site 3 out of 6 in 6u9v

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Zinc binding site 3 out of 6 in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:78.9
occ:1.00
SG B:CYS499 2.3 62.4 1.0
SG B:CYS506 2.3 64.9 1.0
SG B:CYS572 2.3 62.9 1.0
SG B:CYS479 2.4 69.4 1.0
HB3 B:CYS479 2.8 69.4 1.0
CB B:CYS479 2.9 69.4 1.0
HB2 B:CYS479 3.0 69.4 1.0
HB3 B:CYS572 3.2 62.9 1.0
HB3 B:CYS499 3.2 62.4 1.0
CB B:CYS572 3.3 62.9 1.0
CB B:CYS499 3.4 62.4 1.0
HB2 B:CYS572 3.5 62.9 1.0
H B:CYS499 3.6 62.4 1.0
CB B:CYS506 3.8 64.9 1.0
HA B:CYS506 3.8 64.9 1.0
HB2 B:ASN481 3.9 66.5 1.0
HB2 B:CYS506 3.9 64.9 1.0
H B:ILE507 3.9 60.5 1.0
HB2 B:CYS499 4.1 62.4 1.0
ZN B:ZN703 4.2 89.7 1.0
H B:ASN481 4.2 66.5 1.0
HG22 B:ILE507 4.2 60.5 1.0
N B:CYS499 4.3 62.4 1.0
CA B:CYS506 4.3 64.9 1.0
CA B:CYS479 4.4 69.4 1.0
H B:CYS572 4.5 62.9 1.0
HB3 B:CYS506 4.5 64.9 1.0
CA B:CYS499 4.5 62.4 1.0
H B:CYS479 4.5 69.4 1.0
SG B:CYS498 4.6 62.5 1.0
N B:ILE507 4.6 60.5 1.0
HD22 B:ASN481 4.6 66.5 1.0
H B:THR508 4.7 62.5 1.0
HB2 B:PRO570 4.7 57.9 1.0
CA B:CYS572 4.7 62.9 1.0
H B:GLY480 4.7 70.4 1.0
CB B:ASN481 4.8 66.5 1.0
H B:CYS482 4.8 69.1 1.0
SG B:CYS482 4.8 69.1 1.0
N B:ASN481 4.9 66.5 1.0
HA B:CYS479 5.0 69.4 1.0
N B:CYS479 5.0 69.4 1.0
C B:CYS506 5.0 64.9 1.0

Zinc binding site 4 out of 6 in 6u9v

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Zinc binding site 4 out of 6 in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:89.7
occ:1.00
HB2 B:CYS477 1.5 69.9 1.0
CB B:CYS477 2.1 69.9 1.0
SG B:CYS482 2.3 69.1 1.0
SG B:CYS477 2.3 69.9 1.0
SG B:CYS479 2.3 69.4 1.0
SG B:CYS498 2.3 62.5 1.0
H B:CYS479 2.6 69.4 1.0
HB3 B:CYS477 2.7 69.9 1.0
HB2 B:CYS482 2.9 69.1 1.0
H B:GLN478 3.0 68.2 1.0
CB B:CYS482 3.2 69.1 1.0
N B:CYS479 3.3 69.4 1.0
CA B:CYS477 3.4 69.9 1.0
HA B:CYS477 3.5 69.9 1.0
N B:GLN478 3.5 68.2 1.0
CB B:CYS479 3.6 69.4 1.0
CB B:CYS498 3.7 62.5 1.0
HB2 B:CYS498 3.8 62.5 1.0
H B:CYS482 3.8 69.1 1.0
HA B:CYS498 3.8 62.5 1.0
C B:CYS477 3.8 69.9 1.0
HB3 B:CYS479 3.9 69.4 1.0
HB3 B:CYS482 3.9 69.1 1.0
CA B:CYS479 3.9 69.4 1.0
H B:CYS499 4.0 62.4 1.0
C B:CYS479 4.1 69.4 1.0
ZN B:ZN702 4.2 78.9 1.0
O B:CYS479 4.2 69.4 1.0
CA B:CYS482 4.3 69.1 1.0
N B:CYS482 4.3 69.1 1.0
CA B:CYS498 4.3 62.5 1.0
C B:GLN478 4.4 68.2 1.0
HZ3 B:TRP476 4.4 67.7 1.0
HB2 B:CYS479 4.4 69.4 1.0
HA B:CYS482 4.5 69.1 1.0
HB3 B:CYS498 4.5 62.5 1.0
CA B:GLN478 4.5 68.2 1.0
N B:CYS477 4.6 69.9 1.0
H B:CYS477 4.6 69.9 1.0
N B:CYS499 4.8 62.4 1.0
HA B:CYS479 4.8 69.4 1.0
HB3 B:CYS572 4.9 62.9 1.0
CZ3 B:TRP476 4.9 67.7 1.0
N B:GLY480 4.9 70.4 1.0
O B:CYS477 4.9 69.9 1.0
SG B:CYS499 4.9 62.4 1.0
SG B:CYS572 5.0 62.9 1.0

Zinc binding site 5 out of 6 in 6u9v

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Zinc binding site 5 out of 6 in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:81.9
occ:1.00
SG C:CYS499 2.3 62.5 1.0
SG C:CYS506 2.3 65.8 1.0
SG C:CYS572 2.3 63.5 1.0
SG C:CYS479 2.4 69.4 1.0
HB3 C:CYS479 2.9 69.4 1.0
CB C:CYS479 3.1 69.4 1.0
HB2 C:CYS479 3.1 69.4 1.0
HB3 C:CYS499 3.2 62.5 1.0
HB3 C:CYS572 3.2 63.5 1.0
CB C:CYS572 3.3 63.5 1.0
CB C:CYS499 3.4 62.5 1.0
HB2 C:CYS572 3.4 63.5 1.0
H C:CYS499 3.6 62.5 1.0
CB C:CYS506 3.7 65.8 1.0
HB2 C:CYS506 3.8 65.8 1.0
HA C:CYS506 3.8 65.8 1.0
HB2 C:ASN481 3.8 66.7 1.0
H C:ILE507 3.9 61.1 1.0
HB2 C:CYS499 4.0 62.5 1.0
ZN C:ZN703 4.1 90.2 1.0
H C:ASN481 4.2 66.7 1.0
HG22 C:ILE507 4.2 61.1 1.0
CA C:CYS506 4.3 65.8 1.0
N C:CYS499 4.3 62.5 1.0
HB3 C:CYS506 4.5 65.8 1.0
CA C:CYS499 4.5 62.5 1.0
H C:CYS572 4.5 63.5 1.0
CA C:CYS479 4.5 69.4 1.0
N C:ILE507 4.6 61.1 1.0
SG C:CYS498 4.6 61.6 1.0
H C:CYS479 4.6 69.4 1.0
HD22 C:ASN481 4.6 66.7 1.0
H C:THR508 4.6 62.9 1.0
HB2 C:PRO570 4.7 58.1 1.0
SG C:CYS482 4.7 68.8 1.0
CA C:CYS572 4.7 63.5 1.0
CB C:ASN481 4.8 66.7 1.0
H C:GLY480 4.8 71.1 1.0
H C:CYS482 4.8 68.8 1.0
N C:ASN481 5.0 66.7 1.0
C C:CYS506 5.0 65.8 1.0

Zinc binding site 6 out of 6 in 6u9v

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Zinc binding site 6 out of 6 in the Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo Electron Microscopy Structure of the Atp-Gated Rat P2X7 Ion Channel in the Apo, Closed State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn703

b:90.2
occ:1.00
HB2 C:CYS477 1.8 68.8 1.0
SG C:CYS482 2.3 68.8 1.0
SG C:CYS477 2.3 68.8 1.0
SG C:CYS498 2.3 61.6 1.0
SG C:CYS479 2.3 69.4 1.0
CB C:CYS477 2.4 68.8 1.0
H C:CYS479 2.6 69.4 1.0
HB2 C:CYS482 2.9 68.8 1.0
HB3 C:CYS477 3.0 68.8 1.0
H C:GLN478 3.1 68.0 1.0
CB C:CYS482 3.2 68.8 1.0
N C:CYS479 3.4 69.4 1.0
CB C:CYS479 3.6 69.4 1.0
CA C:CYS477 3.6 68.8 1.0
N C:GLN478 3.6 68.0 1.0
CB C:CYS498 3.7 61.6 1.0
H C:CYS482 3.7 68.8 1.0
HA C:CYS498 3.8 61.6 1.0
HB2 C:CYS498 3.8 61.6 1.0
HA C:CYS477 3.8 68.8 1.0
HB3 C:CYS479 3.8 69.4 1.0
CA C:CYS479 3.8 69.4 1.0
HB3 C:CYS482 3.9 68.8 1.0
H C:CYS499 3.9 62.5 1.0
C C:CYS477 4.0 68.8 1.0
ZN C:ZN702 4.1 81.9 1.0
C C:CYS479 4.1 69.4 1.0
O C:CYS479 4.1 69.4 1.0
N C:CYS482 4.2 68.8 1.0
CA C:CYS482 4.3 68.8 1.0
CA C:CYS498 4.3 61.6 1.0
HB2 C:CYS479 4.4 69.4 1.0
C C:GLN478 4.4 68.0 1.0
HB3 C:CYS498 4.5 61.6 1.0
HA C:CYS482 4.5 68.8 1.0
HZ3 C:TRP476 4.6 67.0 1.0
CA C:GLN478 4.6 68.0 1.0
HB3 C:CYS572 4.6 63.5 1.0
N C:CYS499 4.7 62.5 1.0
HA C:CYS479 4.8 69.4 1.0
N C:GLY480 4.8 71.1 1.0
SG C:CYS572 4.8 63.5 1.0
SG C:CYS499 4.8 62.5 1.0
N C:CYS477 4.8 68.8 1.0
H C:CYS477 4.9 68.8 1.0
H C:ASN481 4.9 66.7 1.0

Reference:

A.E.Mccarthy, C.Yoshioka, S.E.Mansoor. Full-Length P2X7STRUCTURES Reveal How Palmitoylation Prevents Channel Desensitization. Cell V. 179 659 2019.
ISSN: ISSN 1097-4172
PubMed: 31587896
DOI: 10.1016/J.CELL.2019.09.017
Page generated: Wed Dec 16 12:58:14 2020

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