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Zinc 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:

Arsenic (As) 4 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 2z3j

Go back to Zinc Binding Sites List in 2z3j
Zinc 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 Zinc with other atoms in the Zn 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:Zn2001

b:12.1
occ:1.00
O1 A:CAC2501 2.0 11.7 1.0
SG A:CYS91 2.3 12.9 1.0
SG A:CYS88 2.3 10.4 1.0
SG A:CYS54 2.4 12.6 1.0
CB A:CYS54 3.1 10.1 1.0
CB A:CYS88 3.3 9.4 1.0
AS A:CAC2501 3.3 13.4 1.0
CB A:CYS91 3.3 11.3 1.0
N A:CYS88 3.7 10.4 1.0
O2 A:CAC2501 3.8 12.1 1.0
O A:HOH3014 3.9 18.4 1.0
N A:CYS91 4.0 10.4 1.0
C1 A:CAC2501 4.0 11.1 1.0
CA A:CYS88 4.0 10.2 1.0
CA A:CYS91 4.2 10.7 1.0
OE1 A:GLU56 4.4 10.5 1.0
CE2 C:PHE49 4.5 13.7 1.0
O A:CYS88 4.5 9.5 1.0
C A:CYS88 4.5 9.6 1.0
CA A:CYS54 4.6 9.2 1.0
CD A:GLU56 4.7 12.0 1.0
OE2 A:GLU56 4.8 11.7 1.0
C A:PRO87 4.8 10.6 1.0
C2 A:CAC2501 5.0 12.9 1.0

Zinc binding site 2 out of 4 in 2z3j

Go back to Zinc Binding Sites List in 2z3j
Zinc 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 Zinc with other atoms in the Zn 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:Zn2002

b:13.6
occ:1.00
O1 B:CAC2502 2.0 13.9 1.0
SG B:CYS88 2.3 12.6 1.0
SG B:CYS91 2.3 13.7 1.0
SG B:CYS54 2.4 13.4 1.0
CB B:CYS54 3.1 10.6 1.0
CB B:CYS91 3.2 10.7 1.0
CB B:CYS88 3.3 11.0 1.0
AS B:CAC2502 3.3 16.9 1.0
N B:CYS88 3.7 11.4 1.0
O2 B:CAC2502 3.9 13.9 1.0
O B:HOH2522 3.9 16.1 1.0
N B:CYS91 3.9 8.5 1.0
CA B:CYS88 4.0 11.0 1.0
C1 B:CAC2502 4.1 15.0 1.0
CA B:CYS91 4.2 10.1 1.0
OE1 B:GLU56 4.3 11.5 1.0
O B:CYS88 4.5 10.2 1.0
C B:CYS88 4.5 11.0 1.0
CA B:CYS54 4.6 10.1 1.0
CE2 D:PHE49 4.6 16.3 1.0
CD B:GLU56 4.7 9.8 1.0
OE2 B:GLU56 4.8 11.2 1.0
C B:PRO87 4.8 10.9 1.0
C2 B:CAC2502 5.0 15.7 1.0

Zinc binding site 3 out of 4 in 2z3j

Go back to Zinc Binding Sites List in 2z3j
Zinc 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 Zinc with other atoms in the Zn 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:Zn2003

b:14.8
occ:1.00
O1 C:CAC2503 1.9 15.3 1.0
SG C:CYS91 2.3 13.0 1.0
SG C:CYS88 2.4 13.8 1.0
SG C:CYS54 2.4 14.6 1.0
CB C:CYS54 3.1 8.8 1.0
CB C:CYS91 3.2 11.3 1.0
CB C:CYS88 3.3 13.1 1.0
AS C:CAC2503 3.3 17.1 1.0
N C:CYS88 3.7 14.2 1.0
O2 C:CAC2503 3.9 16.1 1.0
N C:CYS91 3.9 11.3 1.0
O C:HOH2527 4.0 17.6 1.0
CA C:CYS88 4.0 13.5 1.0
C1 C:CAC2503 4.1 14.4 1.0
CA C:CYS91 4.2 11.1 1.0
OE1 C:GLU56 4.4 10.9 1.0
O C:CYS88 4.5 13.0 1.0
C C:CYS88 4.5 13.8 1.0
CA C:CYS54 4.5 8.7 1.0
CE2 A:PHE49 4.6 14.7 1.0
CD C:GLU56 4.8 11.8 1.0
C C:PRO87 4.8 14.8 1.0
OE2 C:GLU56 4.8 12.4 1.0
C2 C:CAC2503 4.9 16.6 1.0

Zinc binding site 4 out of 4 in 2z3j

Go back to Zinc Binding Sites List in 2z3j
Zinc 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 Zinc with other atoms in the Zn 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:Zn2004

b:15.9
occ:1.00
O1 D:CAC2504 2.1 16.4 1.0
SG D:CYS88 2.3 14.2 1.0
SG D:CYS91 2.3 15.0 1.0
SG D:CYS54 2.4 16.0 1.0
CB D:CYS54 3.1 10.5 1.0
CB D:CYS91 3.2 12.0 1.0
AS D:CAC2504 3.3 19.0 1.0
CB D:CYS88 3.4 12.7 1.0
N D:CYS88 3.7 14.0 1.0
O2 D:CAC2504 3.8 16.0 1.0
O D:HOH2524 3.9 17.9 1.0
N D:CYS91 3.9 11.7 1.0
CA D:CYS88 4.0 12.9 1.0
C1 D:CAC2504 4.1 14.3 1.0
CA D:CYS91 4.2 12.2 1.0
OE1 D:GLU56 4.3 12.3 1.0
O D:CYS88 4.5 12.6 1.0
C D:CYS88 4.5 12.7 1.0
CE2 B:PHE49 4.5 17.0 1.0
CA D:CYS54 4.6 11.1 1.0
CD D:GLU56 4.7 13.5 1.0
OE2 D:GLU56 4.7 14.5 1.0
C D:PRO87 4.8 14.5 1.0
C2 D:CAC2504 5.0 17.0 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 04:04:17 2020

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