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Zinc in PDB 2z3g: Crystal Structure of Blasticidin S Deaminase (Bsd)

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

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

Protein crystallography data

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd), PDB code: 2z3g 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) 39.80 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.116, 68.762, 146.434, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Blasticidin S Deaminase (Bsd) (pdb code 2z3g). 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), PDB code: 2z3g:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2z3g

Go back to Zinc Binding Sites List in 2z3g
Zinc binding site 1 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:8.5
occ:1.00
O A:HOH2128 2.0 14.1 1.0
SG A:CYS88 2.3 6.8 1.0
SG A:CYS91 2.3 9.6 1.0
SG A:CYS54 2.3 8.7 1.0
CB A:CYS54 3.1 7.9 1.0
O A:HOH2031 3.1 21.6 1.0
CB A:CYS91 3.3 8.0 1.0
CB A:CYS88 3.3 7.1 1.0
O A:HOH2043 3.7 11.8 1.0
N A:CYS88 3.8 6.5 1.0
N A:CYS91 4.0 8.0 1.0
CA A:CYS88 4.1 6.8 1.0
OE1 A:GLU56 4.1 9.3 1.0
CA A:CYS91 4.2 8.1 1.0
O A:CYS88 4.5 6.6 1.0
C A:CYS88 4.5 6.4 1.0
CA A:CYS54 4.5 7.1 1.0
CE2 C:PHE49 4.6 9.1 1.0
CD A:GLU56 4.7 9.4 1.0
OE2 A:GLU56 4.8 9.8 1.0
NE A:ARG90 4.8 13.1 0.5
O A:HOH2035 4.9 8.2 0.5
C A:PRO87 4.9 7.4 1.0
NH2 A:ARG90 4.9 12.0 0.5
CB A:ARG90 5.0 8.1 0.5

Zinc binding site 2 out of 4 in 2z3g

Go back to Zinc Binding Sites List in 2z3g
Zinc binding site 2 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:10.0
occ:1.00
O B:HOH3023 2.1 14.5 1.0
SG B:CYS54 2.3 10.1 1.0
SG B:CYS88 2.3 8.5 1.0
SG B:CYS91 2.3 11.1 1.0
CB B:CYS54 3.1 7.9 1.0
O B:HOH3037 3.1 19.3 1.0
CB B:CYS91 3.3 8.4 1.0
CB B:CYS88 3.3 8.9 1.0
N B:CYS88 3.7 8.1 1.0
N B:CYS91 3.9 7.8 1.0
CA B:CYS88 4.0 8.3 1.0
CA B:CYS91 4.2 8.5 1.0
OE1 B:GLU56 4.4 12.2 1.0
O B:HOH3048 4.4 22.0 1.0
CA B:CYS54 4.6 7.2 1.0
C B:CYS88 4.6 7.3 1.0
O B:CYS88 4.6 8.0 1.0
CE2 D:PHE49 4.6 12.2 1.0
CD B:GLU56 4.8 11.6 1.0
OE2 B:GLU56 4.8 14.2 1.0
O C:HOH2063 4.8 10.4 0.5
C B:PRO87 4.9 8.8 1.0
NH2 B:ARG90 4.9 9.9 0.5
NE B:ARG90 5.0 12.3 0.5
CB B:ARG90 5.0 8.7 0.5
O A:HOH2184 5.0 35.8 1.0

Zinc binding site 3 out of 4 in 2z3g

Go back to Zinc Binding Sites List in 2z3g
Zinc binding site 3 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:11.2
occ:1.00
O C:HOH2023 2.1 17.8 1.0
SG C:CYS88 2.3 8.5 1.0
SG C:CYS91 2.3 12.2 1.0
SG C:CYS54 2.3 10.1 1.0
O C:HOH2049 3.0 18.1 1.0
CB C:CYS54 3.1 8.2 1.0
CB C:CYS91 3.3 9.4 1.0
CB C:CYS88 3.3 9.8 1.0
N C:CYS88 3.7 10.2 1.0
N C:CYS91 3.9 8.6 1.0
CA C:CYS88 4.0 9.4 1.0
CA C:CYS91 4.2 9.1 1.0
OE1 C:GLU56 4.3 12.8 1.0
O C:HOH2184 4.3 27.8 1.0
O C:CYS88 4.5 8.7 1.0
C C:CYS88 4.5 9.0 1.0
CE2 A:PHE49 4.5 11.9 1.0
CA C:CYS54 4.5 7.6 1.0
O C:HOH2189 4.6 39.5 1.0
C C:PRO87 4.8 10.9 1.0
CD C:GLU56 4.8 12.2 1.0
NE C:ARG90 4.9 10.1 0.5
O C:HOH2179 4.9 11.5 0.5
NH2 C:ARG90 4.9 9.3 0.5
CB C:ARG90 5.0 8.8 0.5
O C:HOH2029 5.0 16.6 1.0

Zinc binding site 4 out of 4 in 2z3g

Go back to Zinc Binding Sites List in 2z3g
Zinc binding site 4 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2004

b:10.9
occ:1.00
O D:HOH2075 2.1 19.5 1.0
SG D:CYS88 2.3 9.0 1.0
SG D:CYS91 2.3 11.4 1.0
SG D:CYS54 2.4 9.4 1.0
O D:HOH2047 3.1 20.2 1.0
CB D:CYS54 3.1 8.1 1.0
CB D:CYS91 3.2 8.4 1.0
CB D:CYS88 3.3 9.2 1.0
N D:CYS88 3.7 10.0 1.0
N D:CYS91 3.9 8.2 1.0
CA D:CYS88 4.0 9.2 1.0
CA D:CYS91 4.2 8.4 1.0
O D:HOH2043 4.2 19.9 1.0
O D:HOH2154 4.2 26.3 1.0
C D:CYS88 4.5 8.9 1.0
OE1 D:GLU56 4.5 12.1 1.0
O D:CYS88 4.5 8.6 1.0
CE2 B:PHE49 4.5 11.7 1.0
CA D:CYS54 4.6 7.4 1.0
C D:PRO87 4.8 11.2 1.0
O A:HOH2049 4.9 11.4 0.5
O D:HOH2041 4.9 17.8 1.0
NH2 D:ARG90 4.9 13.1 0.5
NE D:ARG90 5.0 15.6 0.5
CD D:GLU56 5.0 12.9 1.0
CB D:ARG90 5.0 8.6 0.5

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 04:04:14 2020

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