Zinc in PDB 2z3h: Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Deaminohydroxy Blasticidin S

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

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Deaminohydroxy Blasticidin S, PDB code: 2z3h 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)	50.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.300, 69.275, 146.535, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 18.5

The binding sites of Zinc atom in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Deaminohydroxy Blasticidin S (pdb code 2z3h). 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 Deaminohydroxy Blasticidin S, PDB code: 2z3h:
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) Complexed with Deaminohydroxy 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 Deaminohydroxy Blasticidin S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:7.6 occ:1.00 SG A:CYS91 2.3 8.0 1.0 SG A:CYS88 2.3 6.9 1.0 O1 A:BLO2500 2.3 8.6 1.0 SG A:CYS54 2.4 6.8 1.0 C4 A:BLO2500 2.8 7.4 1.0 CB A:CYS54 3.1 7.1 1.0 O A:HOH2522 3.2 14.1 1.0 CB A:CYS91 3.3 7.1 1.0 CB A:CYS88 3.3 6.8 1.0 C5 A:BLO2500 3.4 8.0 1.0 N3 A:BLO2500 3.4 6.8 1.0 N A:CYS88 3.7 6.5 1.0 N A:CYS91 3.9 7.2 1.0 CA A:CYS88 4.0 6.5 1.0 CA A:CYS91 4.1 6.9 1.0 OE1 A:GLU56 4.4 7.5 1.0 C6 A:BLO2500 4.4 7.8 1.0 C2 A:BLO2500 4.4 7.9 1.0 C A:CYS88 4.5 6.6 1.0 O A:CYS88 4.5 6.4 1.0 CA A:CYS54 4.6 6.7 1.0 CE2 C:PHE49 4.6 7.8 1.0 CD A:GLU56 4.7 7.3 1.0 N1 A:BLO2500 4.8 7.1 1.0 C A:PRO87 4.8 6.9 1.0 NE A:ARG90 4.9 13.0 0.5 OE2 A:GLU56 4.9 8.1 1.0 O A:HOH2665 4.9 5.1 0.5 CB A:ARG90 4.9 8.1 0.5 C A:ARG90 4.9 7.5 0.5 NH2 A:ARG90 5.0 12.5 0.5 C A:ARG90 5.0 6.8 0.5

Zinc binding site 2 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Deaminohydroxy 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 Deaminohydroxy Blasticidin S within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2002 b:7.9 occ:1.00 SG B:CYS91 2.3 8.1 1.0 SG B:CYS88 2.3 7.4 1.0 SG B:CYS54 2.3 7.1 1.0 O1 B:BLO2501 2.3 9.4 1.0 C4 B:BLO2501 2.8 10.1 1.0 CB B:CYS54 3.1 5.9 1.0 O B:HOH2568 3.1 23.9 1.0 CB B:CYS91 3.3 7.2 1.0 CB B:CYS88 3.3 7.7 1.0 C5 B:BLO2501 3.5 7.8 1.0 N3 B:BLO2501 3.5 9.1 1.0 N B:CYS88 3.7 7.5 1.0 N B:CYS91 3.8 7.0 1.0 CA B:CYS88 4.0 7.0 1.0 CA B:CYS91 4.1 7.0 1.0 OE1 B:GLU56 4.4 6.8 1.0 C6 B:BLO2501 4.4 7.9 1.0 C2 B:BLO2501 4.5 8.5 1.0 O B:CYS88 4.5 6.0 1.0 C B:CYS88 4.5 6.9 1.0 CA B:CYS54 4.6 5.5 1.0 CE2 D:PHE49 4.7 8.6 1.0 CD B:GLU56 4.8 8.0 1.0 NE B:ARG90 4.8 9.1 0.5 CB B:ARG90 4.8 7.4 0.5 N1 B:BLO2501 4.8 8.2 1.0 C B:PRO87 4.8 7.9 1.0 C B:ARG90 4.9 7.2 0.5 C B:ARG90 4.9 7.1 0.5 O B:HOH2691 4.9 12.8 0.5 NH2 B:ARG90 4.9 6.8 0.5 OE2 B:GLU56 4.9 8.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Deaminohydroxy Blasticidin S


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 Deaminohydroxy Blasticidin S within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2003 b:8.8 occ:1.00 SG C:CYS88 2.3 7.9 1.0 SG C:CYS91 2.3 8.8 1.0 O1 C:BLO2502 2.3 9.8 1.0 SG C:CYS54 2.3 7.5 1.0 C4 C:BLO2502 2.8 8.2 1.0 CB C:CYS54 3.1 6.3 1.0 O C:HOH2519 3.1 13.7 1.0 CB C:CYS91 3.3 8.0 1.0 CB C:CYS88 3.3 8.6 1.0 C5 C:BLO2502 3.5 9.7 1.0 N3 C:BLO2502 3.5 8.2 1.0 N C:CYS88 3.7 9.1 1.0 N C:CYS91 3.8 7.9 1.0 CA C:CYS88 4.0 8.5 1.0 CA C:CYS91 4.1 8.4 1.0 OE1 C:GLU56 4.4 8.3 1.0 C6 C:BLO2502 4.5 8.2 1.0 O C:CYS88 4.5 7.5 1.0 C2 C:BLO2502 4.5 8.6 1.0 C C:CYS88 4.5 8.0 1.0 CA C:CYS54 4.6 6.0 1.0 CE2 A:PHE49 4.6 11.1 1.0 CD C:GLU56 4.8 7.9 1.0 C C:PRO87 4.8 9.7 1.0 NE C:ARG90 4.8 11.0 0.5 CB C:ARG90 4.8 8.1 0.5 N1 C:BLO2502 4.9 8.2 1.0 C C:ARG90 4.9 8.2 0.5 NH2 C:ARG90 4.9 10.1 0.5 C C:ARG90 5.0 7.7 0.5 OE2 C:GLU56 5.0 9.0 1.0 O C:HOH2657 5.0 5.5 0.5

Zinc binding site 4 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Complexed with Deaminohydroxy Blasticidin S


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 Deaminohydroxy Blasticidin S within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2004 b:9.7 occ:1.00 SG D:CYS91 2.3 9.7 1.0 O1 D:BLO2503 2.3 9.2 1.0 SG D:CYS88 2.3 8.8 1.0 SG D:CYS54 2.4 8.5 1.0 C4 D:BLO2503 2.8 8.9 1.0 O D:HOH2617 3.0 29.1 1.0 CB D:CYS54 3.1 7.4 1.0 CB D:CYS91 3.2 8.6 1.0 CB D:CYS88 3.4 8.7 1.0 C5 D:BLO2503 3.4 9.8 1.0 N3 D:BLO2503 3.5 9.6 1.0 N D:CYS88 3.7 9.2 1.0 N D:CYS91 3.8 8.5 1.0 CA D:CYS88 4.0 8.8 1.0 CA D:CYS91 4.1 8.1 1.0 OE1 D:GLU56 4.3 8.6 1.0 C6 D:BLO2503 4.4 9.3 1.0 C2 D:BLO2503 4.4 9.4 1.0 O D:CYS88 4.5 8.6 1.0 C D:CYS88 4.5 8.5 1.0 CA D:CYS54 4.6 7.5 1.0 CE2 B:PHE49 4.7 9.7 1.0 NE D:ARG90 4.7 11.9 0.5 CD D:GLU56 4.8 9.6 1.0 NH2 D:ARG90 4.8 7.8 0.5 C D:PRO87 4.8 10.5 1.0 CB D:ARG90 4.8 9.2 0.5 N1 D:BLO2503 4.8 9.1 1.0 C D:ARG90 4.9 8.6 0.5 C D:ARG90 4.9 8.6 0.5 OE2 D:GLU56 4.9 10.3 1.0 O A:HOH2666 5.0 9.6 0.5

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