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Arsenic in PDB 8d6t: Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)

Protein crystallography data

The structure of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal), PDB code: 8d6t was solved by Z.Chen, S.Zakrzewska, D.L.Minor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.50 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.026, 107.812, 253.579, 90, 90, 90
R / Rfree (%) 20.7 / 23.4

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) (pdb code 8d6t). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal), PDB code: 8d6t:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in 8d6t

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Arsenic binding site 1 out of 6 in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As902

b:154.3
occ:1.00
AS B:CAC902 0.0 154.3 1.0
O1 B:CAC902 1.7 95.0 1.0
O2 B:CAC902 1.7 85.5 1.0
C2 B:CAC902 2.0 128.9 1.0
C1 B:CAC902 2.0 106.2 1.0
NH2 B:ARG150 4.4 62.0 1.0
SG B:CYS122 4.7 62.1 1.0
SG B:CYS129 4.7 59.5 1.0

Arsenic binding site 2 out of 6 in 8d6t

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Arsenic binding site 2 out of 6 in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As903

b:173.1
occ:1.00
AS B:CAC903 0.0 173.1 1.0
O2 B:CAC903 1.7 73.5 1.0
O1 B:CAC903 1.7 81.5 1.0
C2 B:CAC903 2.0 69.5 1.0
C1 B:CAC903 2.0 93.1 1.0
O B:HOH1187 4.3 53.5 1.0
CB B:SER263 4.4 56.5 1.0
O B:HOH1080 4.5 57.7 1.0
CB B:GLU43 4.7 46.3 1.0
OH B:TYR72 4.7 48.3 1.0
OG B:SER263 4.8 61.8 1.0
OE1 B:GLU43 4.9 49.7 1.0
O B:HOH1233 5.0 64.0 1.0

Arsenic binding site 3 out of 6 in 8d6t

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Arsenic binding site 3 out of 6 in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As904

b:177.1
occ:1.00
AS B:CAC904 0.0 177.1 1.0
O2 B:CAC904 1.7 108.5 1.0
O1 B:CAC904 1.7 114.5 1.0
C1 B:CAC904 2.0 115.2 1.0
C2 B:CAC904 2.0 124.1 1.0
O B:HOH1276 4.8 67.0 1.0
O B:HOH1263 4.8 62.0 1.0

Arsenic binding site 4 out of 6 in 8d6t

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Arsenic binding site 4 out of 6 in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As902

b:158.8
occ:1.00
AS A:CAC902 0.0 158.8 1.0
O2 A:CAC902 1.7 129.2 1.0
O1 A:CAC902 1.7 98.8 1.0
C1 A:CAC902 2.0 86.4 1.0
C2 A:CAC902 2.0 89.9 1.0
SG A:CYS122 4.5 52.9 1.0
O A:HOH1256 4.6 58.6 1.0
SG A:CYS129 4.7 44.2 1.0
CB A:CYS122 4.9 48.5 1.0
NH2 A:ARG150 4.9 47.0 1.0

Arsenic binding site 5 out of 6 in 8d6t

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Arsenic binding site 5 out of 6 in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As903

b:162.8
occ:1.00
AS A:CAC903 0.0 162.8 1.0
O1 A:CAC903 1.7 109.8 1.0
O2 A:CAC903 1.7 85.3 1.0
C2 A:CAC903 2.0 94.2 1.0
C1 A:CAC903 2.0 66.2 1.0
CB A:SER263 4.4 51.0 1.0
OG A:SER263 4.6 64.3 1.0
OE1 A:GLU66 4.7 91.5 1.0
CB A:GLU43 4.7 44.0 1.0
OE1 A:GLU43 4.7 46.1 1.0
ND2 A:ASN326 4.8 53.6 1.0
OH A:TYR72 4.9 39.8 1.0

Arsenic binding site 6 out of 6 in 8d6t

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Arsenic binding site 6 out of 6 in the Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Rana Catesbeiana Saxiphilin Mutant - Y558I:Stx (Co-Crystal) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As904

b:186.8
occ:1.00
AS A:CAC904 0.0 186.8 1.0
O2 A:CAC904 1.7 107.7 1.0
O1 A:CAC904 1.7 113.7 1.0
C2 A:CAC904 2.0 110.0 1.0
C1 A:CAC904 2.0 116.9 1.0
O A:LYS279 4.0 64.6 1.0
CA A:SER282 4.5 74.4 1.0
N A:SER282 4.5 67.6 1.0
CB A:SER282 4.6 73.3 1.0
C A:LEU281 4.9 63.9 1.0
C A:LYS279 4.9 61.6 1.0

Reference:

Z.Chen, S.Zakrzewska, H.S.Hajare, A.Alvarez-Buylla, F.Abderemane-Ali, M.Bogan, D.Ramirez, L.A.O'connell, J.Du Bois, D.L.Minor Jr.. Definition of A Saxitoxin (Stx) Binding Code Enables Discovery and Characterization of the Anuran Saxiphilin Family. Proc.Natl.Acad.Sci.Usa V. 119 14119 2022.
ISSN: ESSN 1091-6490
PubMed: 36279441
DOI: 10.1073/PNAS.2210114119
Page generated: Wed Jul 10 13:59:30 2024

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