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:
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: Thu Oct 24 10:37:31 2024
|