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Zinc in PDB 1wn6: Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S

Enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S

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

Protein crystallography data

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S, PDB code: 1wn6 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) 19.64 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 54.690, 54.690, 197.632, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.3

Other elements in 1wn6:

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

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S (pdb code 1wn6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S, PDB code: 1wn6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1wn6

Go back to Zinc Binding Sites List in 1wn6
Zinc binding site 1 out of 2 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S


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 Tetrahedral Intermediate of Blasticidin S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:25.8
occ:1.00
 SG A:CYS91 2.1 28.8 1.0
SG A:CYS54 2.2 21.1 1.0
SG A:CYS88 2.3 20.9 1.0
O A:HOH1021 2.6 24.9 1.0
O6 A:BST1003 2.7 32.9 1.0
CB A:CYS54 3.0 20.6 1.0
CB A:CYS91 3.3 24.8 1.0
CB A:CYS88 3.3 20.7 1.0
N A:CYS91 3.7 21.1 1.0
C4 A:BST1003 3.9 28.3 1.0
CA A:CYS91 4.0 22.7 1.0
N A:CYS88 4.0 20.3 1.0
CA A:CYS88 4.1 20.3 1.0
N3 A:BST1003 4.2 25.0 1.0
C5 A:BST1003 4.3 27.9 1.0
CA A:CYS54 4.4 18.4 1.0
C A:CYS88 4.5 19.5 1.0
O A:CYS88 4.6 19.8 1.0
C A:ARG90 4.8 21.1 1.0
CB A:ARG90 4.8 21.0 1.0
C2 A:BST1003 4.8 21.8 1.0
N A:CYS54 4.8 18.5 1.0
OE1 A:GLU56 4.9 22.8 1.0
C6 A:BST1003 4.9 25.5 1.0
N A:ARG90 5.0 18.4 1.0

Zinc binding site 2 out of 2 in 1wn6

Go back to Zinc Binding Sites List in 1wn6
Zinc binding site 2 out of 2 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Tetrahedral Intermediate of Blasticidin S


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 Tetrahedral Intermediate of Blasticidin S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:25.9
occ:1.00
 SG B:CYS91 2.2 30.9 1.0
SG B:CYS54 2.2 21.1 1.0
SG B:CYS88 2.4 21.3 1.0
O B:HOH1011 2.5 27.9 1.0
O6 B:BST1004 2.9 31.5 1.0
CB B:CYS54 3.0 20.2 1.0
CB B:CYS91 3.3 22.6 1.0
CB B:CYS88 3.4 20.0 1.0
N B:CYS91 3.7 21.1 1.0
N B:CYS88 4.0 22.9 1.0
C4 B:BST1004 4.0 29.0 1.0
CA B:CYS91 4.0 20.8 1.0
CA B:CYS88 4.2 21.0 1.0
N3 B:BST1004 4.2 27.6 1.0
CA B:CYS54 4.4 18.2 1.0
C5 B:BST1004 4.4 28.5 1.0
C B:CYS88 4.6 21.1 1.0
O B:CYS88 4.6 21.2 1.0
C B:ARG90 4.8 20.3 1.0
N B:CYS54 4.8 16.6 1.0
CB B:ARG90 4.8 21.6 1.0
C2 B:BST1004 4.8 23.9 1.0
OE1 B:GLU56 4.9 23.3 1.0
C6 B:BST1004 4.9 27.0 1.0
N B:ARG90 5.0 19.1 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 Oct 16 20:07:11 2024

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