Zinc in PDB 2z3g: Crystal Structure of Blasticidin S Deaminase (Bsd)
Enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd)
All present enzymatic activity of Crystal Structure of Blasticidin S Deaminase (Bsd):
3.5.4.23;
Protein crystallography data
The structure of Crystal Structure of Blasticidin S Deaminase (Bsd), PDB code: 2z3g
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)
|
39.80 /
1.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.116,
68.762,
146.434,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.4 /
19.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Blasticidin S Deaminase (Bsd)
(pdb code 2z3g). 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), PDB code: 2z3g:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2z3g
Go back to
Zinc Binding Sites List in 2z3g
Zinc binding site 1 out
of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)
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) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2001
b:8.5
occ:1.00
|
O
|
A:HOH2128
|
2.0
|
14.1
|
1.0
|
SG
|
A:CYS88
|
2.3
|
6.8
|
1.0
|
SG
|
A:CYS91
|
2.3
|
9.6
|
1.0
|
SG
|
A:CYS54
|
2.3
|
8.7
|
1.0
|
CB
|
A:CYS54
|
3.1
|
7.9
|
1.0
|
O
|
A:HOH2031
|
3.1
|
21.6
|
1.0
|
CB
|
A:CYS91
|
3.3
|
8.0
|
1.0
|
CB
|
A:CYS88
|
3.3
|
7.1
|
1.0
|
O
|
A:HOH2043
|
3.7
|
11.8
|
1.0
|
N
|
A:CYS88
|
3.8
|
6.5
|
1.0
|
N
|
A:CYS91
|
4.0
|
8.0
|
1.0
|
CA
|
A:CYS88
|
4.1
|
6.8
|
1.0
|
OE1
|
A:GLU56
|
4.1
|
9.3
|
1.0
|
CA
|
A:CYS91
|
4.2
|
8.1
|
1.0
|
O
|
A:CYS88
|
4.5
|
6.6
|
1.0
|
C
|
A:CYS88
|
4.5
|
6.4
|
1.0
|
CA
|
A:CYS54
|
4.5
|
7.1
|
1.0
|
CE2
|
C:PHE49
|
4.6
|
9.1
|
1.0
|
CD
|
A:GLU56
|
4.7
|
9.4
|
1.0
|
OE2
|
A:GLU56
|
4.8
|
9.8
|
1.0
|
NE
|
A:ARG90
|
4.8
|
13.1
|
0.5
|
O
|
A:HOH2035
|
4.9
|
8.2
|
0.5
|
C
|
A:PRO87
|
4.9
|
7.4
|
1.0
|
NH2
|
A:ARG90
|
4.9
|
12.0
|
0.5
|
CB
|
A:ARG90
|
5.0
|
8.1
|
0.5
|
|
Zinc binding site 2 out
of 4 in 2z3g
Go back to
Zinc Binding Sites List in 2z3g
Zinc binding site 2 out
of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)
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) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2002
b:10.0
occ:1.00
|
O
|
B:HOH3023
|
2.1
|
14.5
|
1.0
|
SG
|
B:CYS54
|
2.3
|
10.1
|
1.0
|
SG
|
B:CYS88
|
2.3
|
8.5
|
1.0
|
SG
|
B:CYS91
|
2.3
|
11.1
|
1.0
|
CB
|
B:CYS54
|
3.1
|
7.9
|
1.0
|
O
|
B:HOH3037
|
3.1
|
19.3
|
1.0
|
CB
|
B:CYS91
|
3.3
|
8.4
|
1.0
|
CB
|
B:CYS88
|
3.3
|
8.9
|
1.0
|
N
|
B:CYS88
|
3.7
|
8.1
|
1.0
|
N
|
B:CYS91
|
3.9
|
7.8
|
1.0
|
CA
|
B:CYS88
|
4.0
|
8.3
|
1.0
|
CA
|
B:CYS91
|
4.2
|
8.5
|
1.0
|
OE1
|
B:GLU56
|
4.4
|
12.2
|
1.0
|
O
|
B:HOH3048
|
4.4
|
22.0
|
1.0
|
CA
|
B:CYS54
|
4.6
|
7.2
|
1.0
|
C
|
B:CYS88
|
4.6
|
7.3
|
1.0
|
O
|
B:CYS88
|
4.6
|
8.0
|
1.0
|
CE2
|
D:PHE49
|
4.6
|
12.2
|
1.0
|
CD
|
B:GLU56
|
4.8
|
11.6
|
1.0
|
OE2
|
B:GLU56
|
4.8
|
14.2
|
1.0
|
O
|
C:HOH2063
|
4.8
|
10.4
|
0.5
|
C
|
B:PRO87
|
4.9
|
8.8
|
1.0
|
NH2
|
B:ARG90
|
4.9
|
9.9
|
0.5
|
NE
|
B:ARG90
|
5.0
|
12.3
|
0.5
|
CB
|
B:ARG90
|
5.0
|
8.7
|
0.5
|
O
|
A:HOH2184
|
5.0
|
35.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2z3g
Go back to
Zinc Binding Sites List in 2z3g
Zinc binding site 3 out
of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)
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) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn2003
b:11.2
occ:1.00
|
O
|
C:HOH2023
|
2.1
|
17.8
|
1.0
|
SG
|
C:CYS88
|
2.3
|
8.5
|
1.0
|
SG
|
C:CYS91
|
2.3
|
12.2
|
1.0
|
SG
|
C:CYS54
|
2.3
|
10.1
|
1.0
|
O
|
C:HOH2049
|
3.0
|
18.1
|
1.0
|
CB
|
C:CYS54
|
3.1
|
8.2
|
1.0
|
CB
|
C:CYS91
|
3.3
|
9.4
|
1.0
|
CB
|
C:CYS88
|
3.3
|
9.8
|
1.0
|
N
|
C:CYS88
|
3.7
|
10.2
|
1.0
|
N
|
C:CYS91
|
3.9
|
8.6
|
1.0
|
CA
|
C:CYS88
|
4.0
|
9.4
|
1.0
|
CA
|
C:CYS91
|
4.2
|
9.1
|
1.0
|
OE1
|
C:GLU56
|
4.3
|
12.8
|
1.0
|
O
|
C:HOH2184
|
4.3
|
27.8
|
1.0
|
O
|
C:CYS88
|
4.5
|
8.7
|
1.0
|
C
|
C:CYS88
|
4.5
|
9.0
|
1.0
|
CE2
|
A:PHE49
|
4.5
|
11.9
|
1.0
|
CA
|
C:CYS54
|
4.5
|
7.6
|
1.0
|
O
|
C:HOH2189
|
4.6
|
39.5
|
1.0
|
C
|
C:PRO87
|
4.8
|
10.9
|
1.0
|
CD
|
C:GLU56
|
4.8
|
12.2
|
1.0
|
NE
|
C:ARG90
|
4.9
|
10.1
|
0.5
|
O
|
C:HOH2179
|
4.9
|
11.5
|
0.5
|
NH2
|
C:ARG90
|
4.9
|
9.3
|
0.5
|
CB
|
C:ARG90
|
5.0
|
8.8
|
0.5
|
O
|
C:HOH2029
|
5.0
|
16.6
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2z3g
Go back to
Zinc Binding Sites List in 2z3g
Zinc binding site 4 out
of 4 in the Crystal Structure of Blasticidin S Deaminase (Bsd)
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) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn2004
b:10.9
occ:1.00
|
O
|
D:HOH2075
|
2.1
|
19.5
|
1.0
|
SG
|
D:CYS88
|
2.3
|
9.0
|
1.0
|
SG
|
D:CYS91
|
2.3
|
11.4
|
1.0
|
SG
|
D:CYS54
|
2.4
|
9.4
|
1.0
|
O
|
D:HOH2047
|
3.1
|
20.2
|
1.0
|
CB
|
D:CYS54
|
3.1
|
8.1
|
1.0
|
CB
|
D:CYS91
|
3.2
|
8.4
|
1.0
|
CB
|
D:CYS88
|
3.3
|
9.2
|
1.0
|
N
|
D:CYS88
|
3.7
|
10.0
|
1.0
|
N
|
D:CYS91
|
3.9
|
8.2
|
1.0
|
CA
|
D:CYS88
|
4.0
|
9.2
|
1.0
|
CA
|
D:CYS91
|
4.2
|
8.4
|
1.0
|
O
|
D:HOH2043
|
4.2
|
19.9
|
1.0
|
O
|
D:HOH2154
|
4.2
|
26.3
|
1.0
|
C
|
D:CYS88
|
4.5
|
8.9
|
1.0
|
OE1
|
D:GLU56
|
4.5
|
12.1
|
1.0
|
O
|
D:CYS88
|
4.5
|
8.6
|
1.0
|
CE2
|
B:PHE49
|
4.5
|
11.7
|
1.0
|
CA
|
D:CYS54
|
4.6
|
7.4
|
1.0
|
C
|
D:PRO87
|
4.8
|
11.2
|
1.0
|
O
|
A:HOH2049
|
4.9
|
11.4
|
0.5
|
O
|
D:HOH2041
|
4.9
|
17.8
|
1.0
|
NH2
|
D:ARG90
|
4.9
|
13.1
|
0.5
|
NE
|
D:ARG90
|
5.0
|
15.6
|
0.5
|
CD
|
D:GLU56
|
5.0
|
12.9
|
1.0
|
CB
|
D:ARG90
|
5.0
|
8.6
|
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 10:36:46 2024
|