Zinc in PDB 2z3j: 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;

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

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

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 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 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 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 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

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