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Arsenic in PDB 2z3i: Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate

Enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate

All present enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate:
3.5.4.23;

Protein crystallography data

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate, PDB code: 2z3i 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) 50.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.330, 69.578, 145.990, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22

Other elements in 2z3i:

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate 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) Mutant E56Q Complexed with Substrate (pdb code 2z3i). 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) Mutant E56Q Complexed with Substrate, PDB code: 2z3i:
Jump to Arsenic binding site number: 1; 2; 3; 4;

Arsenic binding site 1 out of 4 in 2z3i

Go back to Arsenic Binding Sites List in 2z3i
Arsenic binding site 1 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As3001

b:0.7
occ:1.00
AS A:CAC3001 0.0 0.7 1.0
O2 A:CAC3001 1.7 0.5 1.0
O1 A:CAC3001 1.7 0.7 1.0
C2 A:CAC3001 2.0 0.7 1.0
C1 A:CAC3001 2.0 0.6 1.0
SG A:CYS73 3.7 20.4 1.0
CB A:CYS73 3.7 18.7 1.0
CG A:GLU7 3.8 41.0 1.0
O A:HOH3076 4.1 53.4 1.0
CB A:ALA115 4.6 20.4 1.0
OE1 A:GLU7 4.7 43.0 1.0
N A:GLU7 4.7 40.2 1.0
CG A:GLU6 4.7 45.6 1.0
CD A:GLU7 4.8 40.8 1.0
CA A:GLU7 4.8 39.3 1.0
OG A:SER4 4.8 49.1 1.0
CB A:GLU7 4.9 39.5 1.0

Arsenic binding site 2 out of 4 in 2z3i

Go back to Arsenic Binding Sites List in 2z3i
Arsenic binding site 2 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:As3002

b:0.2
occ:1.00
AS B:CAC3002 0.0 0.2 1.0
O1 B:CAC3002 1.7 0.1 1.0
O2 B:CAC3002 1.7 0.3 1.0
C1 B:CAC3002 2.0 0.2 1.0
C2 B:CAC3002 2.0 0.2 1.0
OE2 B:GLU7 3.4 45.0 1.0
O B:HOH3021 3.5 35.9 1.0
CD B:GLU7 3.8 41.7 1.0
SG B:CYS73 4.0 17.8 1.0
CB B:GLU7 4.1 38.9 1.0
CB B:ALA115 4.1 18.9 1.0
CB B:CYS73 4.2 14.2 1.0
O B:HOH3051 4.2 48.7 1.0
CD B:LYS103 4.3 24.3 1.0
CG B:GLU7 4.3 41.3 1.0
OE1 B:GLU7 4.4 46.4 1.0
OG B:SER4 4.7 51.5 1.0
NZ B:LYS103 4.9 34.4 1.0

Arsenic binding site 3 out of 4 in 2z3i

Go back to Arsenic Binding Sites List in 2z3i
Arsenic binding site 3 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As3003

b:29.2
occ:1.00
AS C:CAC3003 0.0 29.2 1.0
O1 C:CAC3003 1.7 38.5 1.0
O2 C:CAC3003 1.7 35.0 1.0
C2 C:CAC3003 2.0 34.5 1.0
C1 C:CAC3003 2.0 31.2 1.0
SG C:CYS73 2.4 17.2 1.0
CB C:CYS73 3.3 15.6 1.0
CG C:GLU7 3.8 24.3 1.0
CB C:ALA115 3.8 25.7 1.0
CG1 C:ILE105 4.1 19.0 1.0
CD1 C:ILE105 4.1 19.6 1.0
O C:HOH3120 4.4 33.4 1.0
OE1 C:GLU7 4.6 26.0 1.0
CA C:CYS73 4.7 14.9 1.0
CA C:GLU7 4.7 23.5 1.0
CD C:GLU7 4.8 25.5 1.0
O C:HOH3119 4.8 46.1 1.0
CB C:GLU7 4.8 23.7 1.0
N C:GLU7 4.9 23.6 1.0
O C:HOH3086 4.9 53.8 1.0
CD1 C:LEU10 4.9 21.8 1.0

Arsenic binding site 4 out of 4 in 2z3i

Go back to Arsenic Binding Sites List in 2z3i
Arsenic binding site 4 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As3004

b:0.7
occ:1.00
AS D:CAC3004 0.0 0.7 1.0
O1 D:CAC3004 1.7 0.5 1.0
O2 D:CAC3004 1.7 0.6 1.0
C1 D:CAC3004 2.0 0.7 1.0
C2 D:CAC3004 2.0 0.7 1.0
SG D:CYS73 3.4 25.1 1.0
OE1 D:GLU7 3.8 60.6 1.0
CB D:CYS73 3.8 21.1 1.0
O D:HOH3116 3.9 38.7 1.0
CB D:GLU7 3.9 53.5 1.0
CB D:ALA115 4.0 33.0 1.0
CD D:GLU7 4.1 59.8 1.0
O D:HOH3082 4.4 59.3 1.0
OE2 D:GLU7 4.6 61.2 1.0
CG D:GLU7 4.6 56.0 1.0
CA D:GLU7 4.7 52.9 1.0
CE D:LYS103 4.7 36.5 1.0
N D:GLU7 4.8 54.5 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 16:49:50 2020

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