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Arsenic in PDB 1wn5: Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid

Enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid

All present enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid:
3.5.4.23;

Protein crystallography data

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid, PDB code: 1wn5 was solved by T.Kumasaka, M.Yamamoto, M.Furuichi, M.Nakasako, M.Kimura, I.Yamaguchi, T.Ueki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.61 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.672, 69.293, 144.714, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22

Other elements in 1wn5:

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid (pdb code 1wn5). 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 Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid, PDB code: 1wn5:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 1wn5

Go back to Arsenic Binding Sites List in 1wn5
Arsenic binding site 1 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid


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 Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2001

b:29.4
occ:0.72
 AS A:CAC2001 0.0 29.4 0.7
O2 A:CAC2001 1.8 19.6 0.7
O1 A:CAC2001 1.8 24.5 0.7
C2 A:CAC2001 2.0 23.9 0.7
C1 A:CAC2001 2.0 26.0 0.7
ZN A:ZN1001 3.4 19.9 1.0
OE1 A:GLU56 3.5 19.2 1.0
OE2 A:GLU56 3.7 17.1 1.0
O A:HOH2043 3.8 17.1 1.0
N A:CYS88 4.0 16.2 1.0
CD A:GLU56 4.1 17.0 1.0
SG A:CYS54 4.1 19.1 1.0
CB A:CYS54 4.2 15.9 1.0
O A:SER86 4.5 17.9 1.0
CB A:CYS88 4.5 13.8 1.0
O A:HOH2023 4.5 19.6 1.0
CA A:PRO87 4.5 16.8 1.0
C A:PRO87 4.7 16.9 1.0
CD1 B:TYR126 4.8 29.5 1.0
CE1 B:TYR126 4.8 30.2 1.0
CA A:CYS88 4.9 16.0 1.0
SG A:CYS91 4.9 19.9 1.0
SG A:CYS88 4.9 17.5 1.0
CB A:ALA76 4.9 13.8 1.0
CG B:TYR126 5.0 29.5 1.0
CG1 A:VAL29 5.0 14.1 1.0
CZ B:TYR126 5.0 30.2 1.0

Arsenic binding site 2 out of 4 in 1wn5

Go back to Arsenic Binding Sites List in 1wn5
Arsenic binding site 2 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid


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 Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As2002

b:31.4
occ:0.71
 AS B:CAC2002 0.0 31.4 0.7
O2 B:CAC2002 1.8 25.1 0.7
O1 B:CAC2002 1.8 20.1 0.7
C2 B:CAC2002 2.0 26.7 0.7
C1 B:CAC2002 2.0 26.4 0.7
ZN B:ZN1002 3.4 21.2 1.0
OE1 B:GLU56 3.6 16.6 1.0
OE2 B:GLU56 3.6 18.9 1.0
O B:HOH2018 3.7 21.3 1.0
CD B:GLU56 4.0 16.8 1.0
N B:CYS88 4.0 15.9 1.0
SG B:CYS54 4.1 18.9 1.0
CB B:CYS54 4.2 15.8 1.0
O B:SER86 4.5 18.0 1.0
CB B:CYS88 4.5 17.6 1.0
CA B:PRO87 4.5 16.6 1.0
O B:HOH2017 4.6 23.3 1.0
C B:PRO87 4.7 16.7 1.0
CD1 A:TYR126 4.8 36.6 1.0
CE1 A:TYR126 4.8 36.2 1.0
CB B:ALA76 4.9 14.6 1.0
SG B:CYS91 4.9 18.8 1.0
CA B:CYS88 4.9 16.8 1.0
SG B:CYS88 4.9 18.1 1.0
CG1 B:VAL29 5.0 15.0 1.0
CG A:TYR126 5.0 37.0 1.0

Arsenic binding site 3 out of 4 in 1wn5

Go back to Arsenic Binding Sites List in 1wn5
Arsenic binding site 3 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid


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 Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As2003

b:30.1
occ:0.58
 AS C:CAC2003 0.0 30.1 0.6
O2 C:CAC2003 1.8 25.9 0.6
O1 C:CAC2003 1.8 19.9 0.6
C2 C:CAC2003 2.0 26.9 0.6
C1 C:CAC2003 2.0 24.9 0.6
ZN C:ZN1003 3.5 24.2 1.0
O C:HOH2016 3.6 19.6 1.0
OE1 C:GLU56 3.6 20.0 1.0
OE2 C:GLU56 3.6 22.8 1.0
N C:CYS88 4.0 21.2 1.0
CD C:GLU56 4.0 20.3 1.0
SG C:CYS54 4.1 19.6 1.0
CB C:CYS54 4.2 16.7 1.0
O C:SER86 4.4 23.1 1.0
CB C:CYS88 4.4 21.3 1.0
CA C:PRO87 4.5 20.5 1.0
O C:HOH2040 4.6 30.2 1.0
C C:PRO87 4.8 21.4 1.0
CA C:CYS88 4.8 20.9 1.0
SG C:CYS88 4.9 22.0 1.0
SG C:CYS91 4.9 22.4 1.0
CB C:ALA76 4.9 18.5 1.0

Arsenic binding site 4 out of 4 in 1wn5

Go back to Arsenic Binding Sites List in 1wn5
Arsenic binding site 4 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid


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 Blasticidin S Deaminase (Bsd) Complexed with Cacodylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As2004

b:32.5
occ:0.58
 AS D:CAC2004 0.0 32.5 0.6
O2 D:CAC2004 1.8 25.7 0.6
O1 D:CAC2004 1.8 22.8 0.6
C2 D:CAC2004 2.0 28.1 0.6
C1 D:CAC2004 2.0 27.1 0.6
ZN D:ZN1004 3.4 25.3 1.0
OE2 D:GLU56 3.6 24.0 1.0
OE1 D:GLU56 3.7 22.1 1.0
O D:HOH2038 3.9 21.8 1.0
SG D:CYS54 4.0 22.3 1.0
N D:CYS88 4.0 22.1 1.0
CD D:GLU56 4.1 21.8 1.0
CB D:CYS54 4.2 18.3 1.0
O D:SER86 4.4 26.8 1.0
O D:HOH2045 4.4 28.5 1.0
CB D:CYS88 4.4 21.2 1.0
CA D:PRO87 4.5 23.5 1.0
C D:PRO87 4.7 24.2 1.0
SG D:CYS88 4.8 21.8 1.0
CA D:CYS88 4.9 21.6 1.0
CD1 C:TYR126 4.9 49.6 1.0
SG D:CYS91 4.9 23.0 1.0
CE1 C:TYR126 4.9 49.7 1.0
CB D:ALA76 5.0 22.1 1.0

Reference:

T.Kumasaka, M.Yamamoto, M.Furuichi, M.Nakasako, A.H.Teh, M.Kimura, I.Yamaguchi, T.Ueki. Crystal Structures of Blasticidin S Deaminase (Bsd): Implications For Dynamic Properties of Catalytic Zinc J.Biol.Chem. V. 282 37103 2007.
ISSN: ISSN 0021-9258
PubMed: 17959604
DOI: 10.1074/JBC.M704476200
Page generated: Wed Jul 10 11:16:10 2024

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