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Zinc in PDB 2z3i: Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate

Enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate

All present enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate:
3.5.4.23;

Protein crystallography data

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate, PDB code: 2z3i 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.330, 69.578, 145.990, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22

Other elements in 2z3i:

The structure of Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate also contains other interesting chemical elements:

Arsenic (As) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate (pdb code 2z3i). 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) Mutant E56Q Complexed with Substrate, PDB code: 2z3i:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2z3i

Go back to Zinc Binding Sites List in 2z3i
Zinc binding site 1 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:17.7
occ:1.00
 O A:HOH3138 2.2 40.7 1.0
SG A:CYS91 2.2 27.9 1.0
SG A:CYS54 2.2 17.3 1.0
SG A:CYS88 2.3 12.9 1.0
O A:HOH3063 2.7 17.5 1.0
CB A:CYS54 3.0 13.0 1.0
CB A:CYS88 3.3 12.7 1.0
CB A:CYS91 3.4 15.8 1.0
N A:CYS91 3.6 13.5 1.0
N A:CYS88 3.8 12.4 1.0
CA A:CYS91 3.9 14.6 1.0
CA A:CYS88 4.0 12.1 1.0
O A:HOH3139 4.2 15.5 0.5
C A:CYS88 4.4 11.3 1.0
CA A:CYS54 4.4 12.3 1.0
O A:CYS88 4.5 11.5 1.0
NE A:ARG90 4.5 15.9 0.5
C4 A:BLS2500 4.5 21.1 1.0
NH2 A:ARG90 4.5 15.1 0.5
N3 A:BLS2500 4.6 18.3 1.0
CE2 C:PHE49 4.6 11.0 1.0
CB A:ARG90 4.6 12.6 0.5
C A:ARG90 4.7 12.8 0.5
C A:ARG90 4.7 12.7 0.5
C5 A:BLS2500 4.7 17.9 1.0
CB A:ARG90 4.8 12.4 0.5
OE1 A:GLN56 4.8 18.0 1.0
N A:CYS54 4.8 11.4 1.0
N4 A:BLS2500 4.8 19.9 1.0
C2 A:BLS2500 4.9 17.0 1.0
C6 A:BLS2500 4.9 18.3 1.0
N A:ARG90 5.0 11.0 0.5
N A:ARG90 5.0 11.2 0.5
CA A:ARG90 5.0 12.3 0.5

Zinc binding site 2 out of 4 in 2z3i

Go back to Zinc Binding Sites List in 2z3i
Zinc binding site 2 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:15.6
occ:1.00
 O B:HOH3141 1.6 23.7 1.0
SG B:CYS54 2.3 13.6 1.0
SG B:CYS91 2.3 23.3 1.0
SG B:CYS88 2.3 12.3 1.0
O B:HOH3047 2.5 11.2 1.0
CB B:CYS54 3.0 12.8 1.0
CB B:CYS88 3.3 11.9 1.0
CB B:CYS91 3.5 13.8 1.0
N B:CYS91 3.5 11.9 1.0
CA B:CYS91 3.9 13.2 1.0
N B:CYS88 4.0 11.7 1.0
O C:HOH3150 4.0 13.4 0.5
NH2 B:ARG90 4.1 14.6 0.5
CA B:CYS88 4.1 11.0 1.0
NE B:ARG90 4.3 15.1 0.5
CA B:CYS54 4.4 11.5 1.0
O B:CYS88 4.5 9.5 1.0
C B:CYS88 4.5 10.9 1.0
CB B:ARG90 4.5 12.4 0.5
C B:ARG90 4.5 12.5 0.5
C B:ARG90 4.6 12.0 0.5
C4 B:BLS2501 4.6 18.2 1.0
CE2 D:PHE49 4.6 12.3 1.0
CB B:ARG90 4.6 11.4 0.5
CZ B:ARG90 4.7 15.9 0.5
N B:CYS54 4.7 11.3 1.0
N3 B:BLS2501 4.7 14.2 1.0
C5 B:BLS2501 4.8 16.2 1.0
N B:ARG90 4.8 11.4 0.5
N B:ARG90 4.9 11.0 0.5
CA B:ARG90 4.9 12.4 0.5
CA B:ARG90 4.9 11.4 0.5
OE1 B:GLN56 4.9 16.1 1.0
N4 B:BLS2501 5.0 15.9 1.0

Zinc binding site 3 out of 4 in 2z3i

Go back to Zinc Binding Sites List in 2z3i
Zinc binding site 3 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:20.2
occ:1.00
 O C:HOH3149 2.0 43.6 1.0
SG C:CYS54 2.2 15.6 1.0
SG C:CYS91 2.3 27.1 1.0
SG C:CYS88 2.3 15.1 1.0
O C:HOH3063 2.6 22.6 1.0
CB C:CYS54 3.0 12.6 1.0
CB C:CYS91 3.3 17.5 1.0
CB C:CYS88 3.3 15.2 1.0
N C:CYS91 3.6 15.7 1.0
N C:CYS88 3.9 16.3 1.0
CA C:CYS91 3.9 16.6 1.0
CA C:CYS88 4.1 15.3 1.0
NE C:ARG90 4.3 16.8 0.5
O C:HOH3151 4.4 19.3 0.5
CA C:CYS54 4.4 11.6 1.0
NH2 C:ARG90 4.4 13.6 0.5
O C:CYS88 4.5 14.3 1.0
C C:CYS88 4.5 15.6 1.0
CB C:ARG90 4.6 14.7 0.5
C4 C:BLS2502 4.6 24.1 1.0
N3 C:BLS2502 4.6 24.4 1.0
CE2 A:PHE49 4.6 15.2 1.0
C C:ARG90 4.7 15.1 0.5
C C:ARG90 4.7 14.9 0.5
N C:CYS54 4.8 11.2 1.0
OE1 C:GLN56 4.8 16.4 1.0
C5 C:BLS2502 4.8 22.1 1.0
CB C:ARG90 4.8 14.5 0.5
CZ C:ARG90 4.9 15.2 0.5
N4 C:BLS2502 4.9 22.4 1.0
C2 C:BLS2502 4.9 21.4 1.0
N C:ARG90 5.0 13.9 0.5
N C:ARG90 5.0 13.8 0.5
CA C:ARG90 5.0 15.0 0.5

Zinc binding site 4 out of 4 in 2z3i

Go back to Zinc Binding Sites List in 2z3i
Zinc binding site 4 out of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd) Mutant E56Q Complexed with Substrate


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) Mutant E56Q Complexed with Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2004

b:21.4
occ:1.00
 O D:HOH3139 1.9 34.5 1.0
SG D:CYS54 2.2 18.3 1.0
SG D:CYS91 2.3 29.2 1.0
SG D:CYS88 2.3 17.0 1.0
O D:HOH3049 2.5 21.3 1.0
CB D:CYS54 3.0 15.7 1.0
CB D:CYS91 3.3 18.2 1.0
CB D:CYS88 3.4 18.6 1.0
N D:CYS91 3.6 14.9 1.0
CA D:CYS91 3.9 17.2 1.0
N D:CYS88 4.0 19.1 1.0
O A:HOH3140 4.2 16.4 0.5
CA D:CYS88 4.2 17.7 1.0
CA D:CYS54 4.4 15.1 1.0
NE D:ARG90 4.4 17.5 0.5
NH2 D:ARG90 4.5 19.1 0.5
CE2 B:PHE49 4.6 16.8 1.0
C D:CYS88 4.6 16.7 1.0
CB D:ARG90 4.6 14.2 0.5
O D:CYS88 4.6 16.6 1.0
C4 D:BLS2503 4.6 25.5 1.0
N3 D:BLS2503 4.6 24.0 1.0
C D:ARG90 4.7 14.8 0.5
N D:CYS54 4.7 14.0 1.0
C D:ARG90 4.7 14.5 0.5
CB D:ARG90 4.8 13.8 0.5
OE1 D:GLN56 4.8 22.2 1.0
C5 D:BLS2503 4.9 26.4 1.0
C2 D:BLS2503 4.9 25.0 1.0
N4 D:BLS2503 5.0 23.8 1.0
CZ D:ARG90 5.0 18.5 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 04:04:16 2020

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