Zinc in PDB 5f1c: Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms

The structure of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms, PDB code: 5f1c was solved by G.Kasuya, M.Hattori, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.07 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.458, 139.900, 202.015, 90.00, 90.00, 90.00
R / Rfree (%)	25.5 / 28.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms (pdb code 5f1c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms, PDB code: 5f1c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:52.6 occ:1.00 OD2 A:ASP188 2.2 40.7 1.0 CG A:ASP188 2.3 58.9 1.0 O3G A:ATP409 2.3 33.3 1.0 OD1 A:ASP188 2.5 56.0 1.0 CB A:ASP188 3.1 59.9 1.0 PG A:ATP409 3.5 43.1 1.0 O A:HOH530 3.6 43.1 1.0 O1G A:ATP409 3.7 35.9 1.0 O3B A:ATP409 4.1 33.1 1.0 O1B A:ATP409 4.4 54.2 1.0 NH2 A:ARG313 4.4 39.0 1.0 CA A:ASP188 4.5 54.5 1.0 O2G A:ATP409 4.7 36.4 1.0 NZ A:LYS327 4.8 42.9 1.0 PB A:ATP409 4.8 39.9 1.0 OD2 A:ASP130 4.9 67.8 1.0

Zinc binding site 2 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:38.9 occ:1.00 OE1 A:GLU123 2.4 56.5 1.0 CD A:GLU123 3.4 58.7 1.0 OE2 A:GLU123 3.8 68.9 1.0 CE A:LYS125 4.1 47.6 1.0 NZ A:LYS125 4.5 45.8 1.0 CG A:GLU123 4.6 42.5 1.0

Zinc binding site 3 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:38.5 occ:1.00 OE2 A:GLU141 2.1 42.1 1.0 OE1 A:GLU141 2.2 36.9 1.0 CD A:GLU141 2.4 42.4 1.0 NE2 A:HIS175 2.5 49.8 1.0 CD2 A:HIS175 3.4 49.6 1.0 CE1 A:HIS175 3.4 71.0 1.0 CG A:GLU141 4.0 42.5 1.0 ND1 A:HIS175 4.5 70.1 1.0 CG A:HIS175 4.6 57.4 1.0 CG A:GLN166 4.6 65.2 1.0 CB A:GLN166 4.7 60.3 1.0 CB A:GLU141 4.8 37.9 1.0 C8 A:NAG401 4.8 53.2 1.0 N A:GLU141 4.8 67.0 1.0

Zinc binding site 4 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:70.5 occ:1.00 OE2 A:GLU105 2.5 30.9 1.0 CD A:GLU105 2.5 50.7 1.0 OE2 C:GLU106 2.5 49.3 1.0 OE1 A:GLU105 2.6 58.5 1.0 OE1 C:GLU106 2.7 40.0 1.0 CD C:GLU106 2.9 51.9 1.0 OE1 C:GLN109 3.5 44.6 1.0 CG A:GLU105 3.5 35.3 1.0 O C:HOH514 3.9 53.8 1.0 CG2 C:THR332 4.1 27.6 1.0 OG1 C:THR332 4.2 38.9 1.0 CG C:GLU106 4.4 54.8 1.0 CD C:GLN109 4.5 48.8 1.0 CB A:GLU105 4.6 29.6 1.0 CB C:PHE111 4.7 33.8 1.0 CD C:PRO103 4.7 37.6 1.0 CB C:THR332 4.8 40.0 1.0 N A:SER107 4.9 45.1 1.0 CB A:SER107 4.9 42.1 1.0 CG C:GLN109 4.9 40.4 1.0 CB C:GLU106 5.0 39.8 1.0

Zinc binding site 5 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:66.5 occ:1.00 OE1 B:GLU105 2.4 54.9 1.0 CD B:GLU105 2.4 52.4 1.0 OE2 A:GLU106 2.4 46.1 1.0 OE2 B:GLU105 2.4 32.7 1.0 OE1 A:GLU106 2.6 33.2 1.0 CD A:GLU106 2.8 49.1 1.0 OE1 A:GLN109 3.4 45.1 1.0 CG B:GLU105 3.5 39.5 1.0 CG2 A:THR332 4.0 29.4 1.0 CG A:GLU106 4.3 51.5 1.0 OG1 A:THR332 4.3 39.4 1.0 CD A:GLN109 4.4 44.4 1.0 CB B:SER107 4.5 45.0 1.0 N B:SER107 4.5 44.6 1.0 CB B:GLU105 4.7 31.8 1.0 CA B:SER107 4.8 48.0 1.0 CG A:GLN109 4.8 42.2 1.0 CB A:THR332 4.8 37.9 1.0 CB A:GLU106 4.9 37.1 1.0 CD A:PRO103 5.0 35.1 1.0

Zinc binding site 6 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:0.7 occ:1.00 OE1 A:GLU214 2.5 0.8 1.0 ND1 A:HIS219 2.6 0.3 1.0 CE1 A:HIS219 3.4 97.2 1.0 CG A:HIS219 3.5 96.8 1.0 CD A:GLU214 3.6 0.7 1.0 CB A:HIS219 3.8 78.4 1.0 CA A:HIS219 4.1 85.7 1.0 OE2 A:GLU214 4.3 96.1 1.0 NE2 A:HIS219 4.4 0.1 1.0 CD2 A:HIS219 4.5 97.2 1.0 NH1 A:ARG221 4.5 0.7 1.0 CZ A:ARG221 4.6 0.8 1.0 CG A:GLU214 4.6 83.2 1.0 C A:HIS219 4.7 79.1 1.0 NH2 A:ARG221 4.7 99.8 1.0 O A:HIS219 4.9 74.5 1.0

Zinc binding site 7 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:50.5 occ:1.00 OD2 B:ASP188 2.3 40.3 1.0 O1G B:ATP407 2.4 40.9 1.0 CG B:ASP188 2.4 58.6 1.0 OD1 B:ASP188 2.6 50.4 1.0 CB B:ASP188 3.4 65.9 1.0 O3G B:ATP407 3.4 43.9 1.0 PG B:ATP407 3.4 52.5 1.0 O B:HOH548 3.7 43.7 1.0 O1B B:ATP407 3.8 44.1 1.0 NH2 B:ARG313 4.3 48.0 1.0 O3B B:ATP407 4.4 36.0 1.0 PB B:ATP407 4.6 39.2 1.0 O2G B:ATP407 4.6 44.7 1.0 CA B:ASP188 4.7 57.5 1.0 NZ B:LYS327 4.9 49.2 1.0 OD2 B:ASP130 4.9 66.4 1.0

Zinc binding site 8 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:66.5 occ:1.00 OE2 C:GLU105 2.3 27.8 1.0 OE2 B:GLU106 2.4 40.8 1.0 CD C:GLU105 2.4 50.0 1.0 OE1 B:GLU106 2.5 36.8 1.0 OE1 C:GLU105 2.5 59.4 1.0 CD B:GLU106 2.7 47.7 1.0 OE1 B:GLN109 3.6 42.1 1.0 CG C:GLU105 3.6 37.1 1.0 O C:HOH519 3.7 51.4 1.0 CG B:GLU106 4.2 56.3 1.0 O B:HOH521 4.2 34.2 1.0 CG2 B:THR332 4.3 28.7 1.0 OG1 B:THR332 4.5 40.3 1.0 CD B:GLN109 4.5 47.0 1.0 CB C:GLU105 4.6 30.9 1.0 CD B:PRO103 4.6 34.5 1.0 N C:SER107 4.7 40.5 1.0 CB B:GLU106 4.7 34.9 1.0 CB C:SER107 4.8 43.5 1.0 CG B:GLN109 4.9 41.0 1.0 CG B:PRO103 4.9 39.3 1.0 CB B:PHE111 5.0 33.9 1.0

Zinc binding site 9 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:0.8 occ:1.00 OE1 B:GLU214 2.5 98.4 1.0 ND1 B:HIS219 2.7 0.7 1.0 CE1 B:HIS219 3.1 98.7 1.0 CD B:GLU214 3.4 0.1 1.0 OE2 B:GLU214 3.6 99.4 1.0 CG B:HIS219 3.9 93.4 1.0 NE2 B:HIS219 4.3 0.7 1.0 CB B:HIS219 4.6 81.8 1.0 CG B:GLU214 4.7 87.0 1.0 CD2 B:HIS219 4.8 96.4 1.0 CA B:HIS219 4.8 83.5 1.0 NH2 B:ARG221 4.9 93.4 1.0 O B:SER216 5.0 84.8 1.0

Zinc binding site 10 out of 13 in the Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of An Invertebrate P2X Receptor From the Gulf Coast Tick in the Presence of Atp and ZN2+ Ion at 2.9 Angstroms within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:58.4 occ:1.00 OD2 B:ASP24 2.4 40.7 1.0 O B:GLY19 2.4 34.9 1.0 N B:GLY19 2.7 69.7 1.0 CA B:GLY19 2.7 71.9 1.0 C B:GLY19 2.8 46.0 1.0 OD1 B:ASP24 3.1 57.8 1.0 CG B:ASP24 3.1 54.1 1.0 N B:SER20 4.0 53.4 1.0 CB B:ASP24 4.5 53.9 1.0 O B:SER20 5.0 59.3 1.0 CA B:SER20 5.0 45.2 1.0

G.Kasuya, Y.Fujiwara, M.Takemoto, N.Dohmae, Y.Nakada-Nakura, R.Ishitani, M.Hattori, O.Nureki. Structural Insights Into Divalent Cation Modulations of Atp-Gated P2X Receptor Channels Cell Rep V. 14 932 2016.
ISSN: ESSN 2211-1247
PubMed: 26804916
DOI: 10.1016/J.CELREP.2015.12.087