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Arsenic in PDB 2z3j: Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant

Enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant

All present enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant:
3.5.4.23;

Protein crystallography data

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant, PDB code: 2z3j was solved by A.H.Teh, 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) 43.81 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.802, 69.952, 145.844, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 21.4

Other elements in 2z3j:

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant (pdb code 2z3j). 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) R90K Mutant, PDB code: 2z3j:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 2z3j

Go back to Arsenic Binding Sites List in 2z3j
Arsenic binding site 1 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant


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) R90K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2501

b:13.4
occ:1.00
AS A:CAC2501 0.0 13.4 1.0
O2 A:CAC2501 1.7 12.1 1.0
O1 A:CAC2501 1.7 11.7 1.0
C1 A:CAC2501 1.9 11.1 1.0
C2 A:CAC2501 2.0 12.9 1.0
ZN A:ZN2001 3.3 12.1 1.0
OE1 A:GLU56 3.6 10.5 1.0
OE2 A:GLU56 3.7 11.7 1.0
O A:HOH3003 3.9 11.7 1.0
N A:CYS88 4.0 10.4 1.0
SG A:CYS54 4.0 12.6 1.0
CD A:GLU56 4.1 12.0 1.0
CB A:CYS54 4.3 10.1 1.0
CB A:CYS88 4.4 9.4 1.0
O A:SER86 4.4 11.1 1.0
CA A:PRO87 4.5 11.0 1.0
CE1 B:TYR126 4.6 15.8 1.0
CD1 B:TYR126 4.7 15.6 1.0
C A:PRO87 4.7 10.6 1.0
O A:HOH3058 4.7 16.5 1.0
SG A:CYS91 4.8 12.9 1.0
CB A:ALA76 4.8 11.2 1.0
SG A:CYS88 4.8 10.4 1.0
CZ B:TYR126 4.9 15.7 1.0
CA A:CYS88 4.9 10.2 1.0
CG1 A:VAL29 4.9 11.8 1.0

Arsenic binding site 2 out of 4 in 2z3j

Go back to Arsenic Binding Sites List in 2z3j
Arsenic binding site 2 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant


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) R90K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As2502

b:16.9
occ:1.00
AS B:CAC2502 0.0 16.9 1.0
O1 B:CAC2502 1.7 13.9 1.0
O2 B:CAC2502 1.7 13.9 1.0
C1 B:CAC2502 2.0 15.0 1.0
C2 B:CAC2502 2.0 15.7 1.0
ZN B:ZN2002 3.3 13.6 1.0
OE1 B:GLU56 3.5 11.5 1.0
OE2 B:GLU56 3.6 11.2 1.0
O B:HOH2505 3.9 14.8 1.0
N B:CYS88 4.0 11.4 1.0
CD B:GLU56 4.0 9.8 1.0
SG B:CYS54 4.0 13.4 1.0
CB B:CYS54 4.3 10.6 1.0
CA B:PRO87 4.4 11.8 1.0
CB B:CYS88 4.5 11.0 1.0
O B:SER86 4.5 12.6 1.0
O B:HOH2561 4.6 15.4 1.0
CD1 A:TYR126 4.7 23.6 1.0
C B:PRO87 4.7 10.9 1.0
CE1 A:TYR126 4.7 23.9 1.0
SG B:CYS88 4.8 12.6 1.0
CB B:ALA76 4.8 10.2 1.0
SG B:CYS91 4.8 13.7 1.0
CA B:CYS88 4.9 11.0 1.0
CG A:TYR126 5.0 25.5 1.0
CZ A:TYR126 5.0 25.0 1.0
CG1 B:VAL29 5.0 11.3 1.0

Arsenic binding site 3 out of 4 in 2z3j

Go back to Arsenic Binding Sites List in 2z3j
Arsenic binding site 3 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant


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) R90K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As2503

b:17.1
occ:1.00
AS C:CAC2503 0.0 17.1 1.0
O1 C:CAC2503 1.7 15.3 1.0
O2 C:CAC2503 1.7 16.1 1.0
C2 C:CAC2503 2.0 16.6 1.0
C1 C:CAC2503 2.0 14.4 1.0
ZN C:ZN2003 3.3 14.8 1.0
OE1 C:GLU56 3.6 10.9 1.0
OE2 C:GLU56 3.7 12.4 1.0
O C:HOH2525 3.8 10.8 1.0
N C:CYS88 4.0 14.2 1.0
SG C:CYS54 4.0 14.6 1.0
CD C:GLU56 4.0 11.8 1.0
CB C:CYS54 4.2 8.8 1.0
CB C:CYS88 4.4 13.1 1.0
O C:SER86 4.4 16.7 1.0
CA C:PRO87 4.5 15.4 1.0
O C:HOH2561 4.7 17.3 1.0
CD1 D:TYR126 4.7 23.8 1.0
CE1 D:TYR126 4.7 22.6 1.0
C C:PRO87 4.7 14.8 1.0
SG C:CYS91 4.8 13.0 1.0
CB C:ALA76 4.8 12.1 1.0
CA C:CYS88 4.8 13.5 1.0
SG C:CYS88 4.9 13.8 1.0
CZ D:TYR126 5.0 24.1 1.0
CG D:TYR126 5.0 24.7 1.0

Arsenic binding site 4 out of 4 in 2z3j

Go back to Arsenic Binding Sites List in 2z3j
Arsenic binding site 4 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) R90K Mutant


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) R90K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As2504

b:19.0
occ:1.00
AS D:CAC2504 0.0 19.0 1.0
O2 D:CAC2504 1.7 16.0 1.0
O1 D:CAC2504 1.7 16.4 1.0
C2 D:CAC2504 2.0 17.0 1.0
C1 D:CAC2504 2.0 14.3 1.0
ZN D:ZN2004 3.3 15.9 1.0
OE1 D:GLU56 3.6 12.3 1.0
OE2 D:GLU56 3.6 14.5 1.0
O D:HOH2513 3.9 13.7 1.0
N D:CYS88 4.0 14.0 1.0
CD D:GLU56 4.0 13.5 1.0
SG D:CYS54 4.0 16.0 1.0
CB D:CYS54 4.3 10.5 1.0
CA D:PRO87 4.4 15.0 1.0
O D:SER86 4.4 15.3 1.0
CB D:CYS88 4.6 12.7 1.0
CE1 C:TYR126 4.6 25.9 1.0
CD1 C:TYR126 4.6 25.1 1.0
O D:HOH2553 4.6 17.2 1.0
C D:PRO87 4.7 14.5 1.0
SG D:CYS88 4.8 14.2 1.0
SG D:CYS91 4.8 15.0 1.0
CB D:ALA76 4.9 15.2 1.0
CA D:CYS88 4.9 12.9 1.0
CZ C:TYR126 4.9 26.2 1.0
CG C:TYR126 5.0 27.1 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: Tue Oct 27 16:49:49 2020

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