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Zinc 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:

Arsenic (As) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 1wn5

Go back to Zinc Binding Sites List in 1wn5
Zinc 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 Zinc with other atoms in the Zn 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:Zn1001

b:19.9
occ:1.00
O2 A:CAC2001 2.0 19.6 0.7
SG A:CYS91 2.3 19.9 1.0
SG A:CYS54 2.3 19.1 1.0
SG A:CYS88 2.3 17.5 1.0
CB A:CYS54 3.0 15.9 1.0
CB A:CYS91 3.3 17.8 1.0
CB A:CYS88 3.3 13.8 1.0
AS A:CAC2001 3.4 29.4 0.7
O A:HOH2059 3.5 31.6 1.0
N A:CYS88 3.7 16.2 1.0
N A:CYS91 4.0 15.4 1.0
CA A:CYS88 4.0 16.0 1.0
C2 A:CAC2001 4.2 23.9 0.7
CA A:CYS91 4.2 16.5 1.0
O1 A:CAC2001 4.2 24.5 0.7
OE1 A:GLU56 4.3 19.2 1.0
O A:CYS88 4.5 16.1 1.0
C A:CYS88 4.5 16.1 1.0
CA A:CYS54 4.5 14.1 1.0
CE2 C:PHE49 4.6 17.9 1.0
CD A:GLU56 4.7 17.0 1.0
C A:PRO87 4.8 16.9 1.0
OE2 A:GLU56 4.9 17.1 1.0
O A:HOH2009 4.9 27.3 1.0

Zinc binding site 2 out of 4 in 1wn5

Go back to Zinc Binding Sites List in 1wn5
Zinc 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 Zinc with other atoms in the Zn 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:Zn1002

b:21.2
occ:1.00
O1 B:CAC2002 2.1 20.1 0.7
SG B:CYS88 2.3 18.1 1.0
SG B:CYS91 2.3 18.8 1.0
SG B:CYS54 2.4 18.9 1.0
CB B:CYS54 3.1 15.8 1.0
CB B:CYS88 3.3 17.6 1.0
CB B:CYS91 3.3 17.1 1.0
AS B:CAC2002 3.4 31.4 0.7
O B:HOH2057 3.4 32.5 1.0
N B:CYS88 3.7 15.9 1.0
C1 B:CAC2002 3.9 26.4 0.7
N B:CYS91 3.9 14.2 1.0
CA B:CYS88 4.0 16.8 1.0
CA B:CYS91 4.2 14.0 1.0
O2 B:CAC2002 4.2 25.1 0.7
OE1 B:GLU56 4.4 16.6 1.0
C B:CYS88 4.5 15.1 1.0
O B:CYS88 4.5 15.1 1.0
CA B:CYS54 4.6 15.0 1.0
CE2 D:PHE49 4.6 22.7 1.0
OE2 B:GLU56 4.7 18.9 1.0
CD B:GLU56 4.7 16.8 1.0
C B:PRO87 4.8 16.7 1.0
O B:HOH2031 4.8 34.0 1.0

Zinc binding site 3 out of 4 in 1wn5

Go back to Zinc Binding Sites List in 1wn5
Zinc 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 Zinc with other atoms in the Zn 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:Zn1003

b:24.2
occ:1.00
O1 C:CAC2003 2.1 19.9 0.6
SG C:CYS88 2.2 22.0 1.0
SG C:CYS91 2.3 22.4 1.0
SG C:CYS54 2.4 19.6 1.0
CB C:CYS54 3.1 16.7 1.0
CB C:CYS88 3.2 21.3 1.0
CB C:CYS91 3.3 20.4 1.0
AS C:CAC2003 3.5 30.1 0.6
O C:HOH2093 3.5 31.5 1.0
N C:CYS88 3.7 21.2 1.0
C1 C:CAC2003 3.8 24.9 0.6
N C:CYS91 3.9 17.6 1.0
CA C:CYS88 3.9 20.9 1.0
CA C:CYS91 4.2 17.8 1.0
O2 C:CAC2003 4.3 25.9 0.6
O C:CYS88 4.4 18.5 1.0
C C:CYS88 4.4 20.2 1.0
OE1 C:GLU56 4.4 20.0 1.0
CA C:CYS54 4.5 15.4 1.0
CE2 A:PHE49 4.6 21.4 1.0
OE2 C:GLU56 4.7 22.8 1.0
CD C:GLU56 4.7 20.3 1.0
C C:PRO87 4.8 21.4 1.0
O C:HOH2055 4.8 29.6 1.0

Zinc binding site 4 out of 4 in 1wn5

Go back to Zinc Binding Sites List in 1wn5
Zinc 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 Zinc with other atoms in the Zn 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:Zn1004

b:25.3
occ:1.00
O1 D:CAC2004 2.1 22.8 0.6
SG D:CYS88 2.3 21.8 1.0
SG D:CYS91 2.3 23.0 1.0
SG D:CYS54 2.3 22.3 1.0
CB D:CYS54 3.1 18.3 1.0
CB D:CYS91 3.2 20.9 1.0
CB D:CYS88 3.3 21.2 1.0
AS D:CAC2004 3.4 32.5 0.6
O D:HOH2046 3.5 28.4 1.0
N D:CYS88 3.7 22.1 1.0
C1 D:CAC2004 3.8 27.1 0.6
N D:CYS91 3.9 18.4 1.0
CA D:CYS88 4.0 21.6 1.0
O2 D:CAC2004 4.1 25.7 0.6
CA D:CYS91 4.2 20.6 1.0
OE1 D:GLU56 4.4 22.1 1.0
C D:CYS88 4.5 21.0 1.0
O D:CYS88 4.5 20.7 1.0
CA D:CYS54 4.5 17.6 1.0
OE2 D:GLU56 4.6 24.0 1.0
CE2 B:PHE49 4.6 22.4 1.0
CD D:GLU56 4.7 21.8 1.0
C D:PRO87 4.8 24.2 1.0
O D:HOH2042 4.9 30.4 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 Dec 16 03:10:15 2020

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