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Arsenic in PDB 1p13: Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk)

Enzymatic activity of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk)

All present enzymatic activity of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk):
2.7.1.112;

Protein crystallography data

The structure of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk), PDB code: 1p13 was solved by E.D.Sonnenburg, A.Bilwes, T.Hunter, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.88 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.384, 58.793, 62.662, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.2

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk) (pdb code 1p13). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 4 binding sites of Arsenic where determined in the Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk), PDB code: 1p13:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 1p13

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Arsenic binding site 1 out of 4 in the Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As398

b:32.5
occ:1.00
AS A:CAC398 0.0 32.5 1.0
O1 A:CAC398 1.8 53.0 1.0
C2 A:CAC398 1.9 43.7 1.0
C1 A:CAC398 1.9 38.5 1.0
SG A:CYS198 2.4 22.2 1.0
CB A:CYS198 3.2 14.7 1.0
N A:CYS198 3.5 15.4 1.0
C A:TYR197 3.6 14.1 1.0
O A:ALA196 3.8 21.0 1.0
N A:SER190 3.8 22.8 1.0
CA A:CYS198 3.9 12.1 1.0
O A:TYR197 3.9 16.2 1.0
CA A:TYR197 4.1 16.0 1.0
C A:GLU189 4.2 22.3 1.0
CA A:SER190 4.2 25.4 1.0
O A:ARG188 4.2 15.0 1.0
C A:ALA196 4.4 20.7 1.0
N A:TYR197 4.5 17.5 1.0
NH1 A:ARG188 4.5 14.6 1.0
CB A:SER190 4.6 27.3 1.0
CA A:GLU189 4.6 16.6 1.0
O A:GLU189 4.7 21.8 1.0
C A:ARG188 4.7 16.6 1.0
O A:HOH411 4.8 17.2 1.0
CG A:ARG188 4.8 14.1 1.0
O2P D:PTR3 4.8 25.7 1.0
O A:HOH476 4.9 41.2 1.0
N A:GLU189 4.9 17.9 1.0
O A:HOH448 5.0 33.6 1.0

Arsenic binding site 2 out of 4 in 1p13

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Arsenic binding site 2 out of 4 in the Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As351

b:76.5
occ:1.00
AS A:CAC351 0.0 76.5 1.0
O1 A:CAC351 1.8 80.8 1.0
C2 A:CAC351 1.9 78.7 1.0
C1 A:CAC351 1.9 80.1 1.0
SG A:CYS251 2.5 26.6 1.0
CB A:CYS251 3.2 22.0 1.0
O A:HOH438 3.9 31.9 1.0
CA A:CYS251 3.9 15.3 1.0
O A:HOH429 4.4 23.3 1.0
N A:CYS251 4.7 15.8 1.0
O A:HOH459 5.0 29.2 1.0

Arsenic binding site 3 out of 4 in 1p13

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Arsenic binding site 3 out of 4 in the Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As399

b:30.0
occ:1.00
AS B:CAC399 0.0 30.0 1.0
O1 B:CAC399 1.8 44.3 1.0
C1 B:CAC399 1.9 42.1 1.0
C2 B:CAC399 1.9 33.3 1.0
SG B:CYS198 2.4 18.4 1.0
CB B:CYS198 3.2 14.2 1.0
N B:CYS198 3.5 12.7 1.0
C B:TYR197 3.7 11.8 1.0
CA B:CYS198 3.9 10.9 1.0
N B:SER190 4.0 14.3 1.0
O B:TYR197 4.0 13.0 1.0
CA B:SER190 4.1 21.9 1.0
CA B:TYR197 4.2 14.0 1.0
O B:ALA196 4.2 17.2 1.0
NH1 B:ARG188 4.3 14.4 1.0
O B:ARG188 4.3 9.5 1.0
C B:GLU189 4.3 14.6 1.0
CB B:SER190 4.4 18.5 1.0
O2P C:PTR3 4.4 45.7 1.0
O B:HOH400 4.6 16.6 1.0
N B:TYR197 4.6 13.4 1.0
C B:ALA196 4.6 15.1 1.0
O B:GLU189 4.7 14.7 1.0
CG B:ARG188 4.7 8.4 1.0
CZ B:ARG188 4.8 17.4 1.0
C B:ARG188 4.9 9.0 1.0
CA B:GLU189 4.9 17.0 1.0
OH C:PTR3 5.0 41.1 1.0

Arsenic binding site 4 out of 4 in 1p13

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Arsenic binding site 4 out of 4 in the Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Crystal Structure of the Src SH2 Domain Complexed with Peptide (Sdpyanfk) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As352

b:92.1
occ:1.00
AS B:CAC352 0.0 92.1 1.0
O1 B:CAC352 1.8 88.7 1.0
C2 B:CAC352 1.9 87.7 1.0
C1 B:CAC352 1.9 87.2 1.0
SG B:CYS251 2.8 24.1 1.0
O B:HOH508 3.0 45.5 1.0
CB B:CYS251 3.8 19.1 1.0
CA B:CYS251 4.3 13.6 1.0
O B:HOH421 4.5 22.1 1.0

Reference:

E.D.Sonnenburg, A.Bilwes, T.Hunter, J.P.Noel. The Structure of the Membrane Distal Phosphatase Domain of Rptpalpha Reveals Interdomain Flexibility and An SH2 Domain Interaction Region. Biochemistry V. 42 7904 2003.
ISSN: ISSN 0006-2960
PubMed: 12834342
DOI: 10.1021/BI0340503
Page generated: Tue Oct 27 16:47:00 2020

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