Zinc in PDB 3bl5: Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
Protein crystallography data
The structure of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis, PDB code: 3bl5
was solved by
N.Cicmil,
R.H.Huang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.95
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
172.057,
75.542,
131.023,
90.00,
94.73,
90.00
|
R / Rfree (%)
|
22.2 /
27.2
|
Other elements in 3bl5:
The structure of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
(pdb code 3bl5). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis, PDB code: 3bl5:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 3bl5
Go back to
Zinc Binding Sites List in 3bl5
Zinc binding site 1 out
of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn300
b:0.7
occ:1.00
|
SG
|
A:CYS198
|
2.3
|
97.9
|
1.0
|
SG
|
A:CYS201
|
2.3
|
88.8
|
1.0
|
SG
|
A:CYS195
|
2.4
|
0.7
|
1.0
|
SG
|
A:CYS186
|
2.4
|
90.9
|
1.0
|
CB
|
A:CYS186
|
3.1
|
90.7
|
1.0
|
N
|
A:CYS195
|
3.3
|
0.6
|
1.0
|
N
|
A:TYR187
|
3.3
|
93.0
|
1.0
|
CA
|
A:CYS186
|
3.4
|
89.4
|
1.0
|
CB
|
A:CYS195
|
3.4
|
0.7
|
1.0
|
OD1
|
A:ASN188
|
3.4
|
99.4
|
1.0
|
CB
|
A:CYS198
|
3.7
|
100.0
|
1.0
|
CB
|
A:CYS201
|
3.8
|
89.5
|
1.0
|
C
|
A:CYS186
|
3.8
|
91.2
|
1.0
|
CA
|
A:CYS195
|
3.8
|
0.7
|
1.0
|
N
|
A:GLY196
|
4.1
|
0.7
|
1.0
|
C
|
A:GLY194
|
4.1
|
0.6
|
1.0
|
CA
|
A:GLY194
|
4.2
|
0.7
|
1.0
|
N
|
A:CYS198
|
4.2
|
0.3
|
1.0
|
CA
|
A:TYR187
|
4.5
|
95.0
|
1.0
|
N
|
A:ASN188
|
4.5
|
96.7
|
1.0
|
CG
|
A:ASN188
|
4.5
|
98.5
|
1.0
|
C
|
A:CYS195
|
4.5
|
0.6
|
1.0
|
CA
|
A:CYS198
|
4.6
|
99.5
|
1.0
|
N
|
A:CYS201
|
4.6
|
90.3
|
1.0
|
N
|
A:CYS186
|
4.7
|
86.8
|
1.0
|
N
|
A:GLU197
|
4.7
|
0.5
|
1.0
|
CA
|
A:CYS201
|
4.7
|
89.8
|
1.0
|
CB
|
A:TYR187
|
4.8
|
95.6
|
1.0
|
C
|
A:TYR187
|
4.8
|
95.9
|
1.0
|
CB
|
A:ASN188
|
5.0
|
97.4
|
1.0
|
|
Zinc binding site 2 out
of 6 in 3bl5
Go back to
Zinc Binding Sites List in 3bl5
Zinc binding site 2 out
of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn300
b:96.0
occ:1.00
|
SG
|
B:CYS186
|
2.2
|
89.5
|
1.0
|
SG
|
B:CYS201
|
2.4
|
93.9
|
1.0
|
SG
|
B:CYS198
|
2.4
|
0.3
|
1.0
|
SG
|
B:CYS195
|
2.4
|
0.7
|
1.0
|
CB
|
B:CYS186
|
3.0
|
93.5
|
1.0
|
N
|
B:CYS195
|
3.2
|
0.1
|
1.0
|
CA
|
B:CYS186
|
3.3
|
93.1
|
1.0
|
CB
|
B:CYS195
|
3.3
|
0.2
|
1.0
|
N
|
B:TYR187
|
3.3
|
95.4
|
1.0
|
OD1
|
B:ASN188
|
3.4
|
0.7
|
1.0
|
CB
|
B:CYS198
|
3.8
|
0.3
|
1.0
|
CB
|
B:CYS201
|
3.8
|
93.7
|
1.0
|
C
|
B:CYS186
|
3.8
|
94.4
|
1.0
|
CA
|
B:CYS195
|
3.8
|
0.2
|
1.0
|
C
|
B:GLY194
|
4.0
|
0.5
|
1.0
|
N
|
B:GLY196
|
4.1
|
0.5
|
1.0
|
CA
|
B:GLY194
|
4.1
|
0.5
|
1.0
|
N
|
B:CYS198
|
4.3
|
0.6
|
1.0
|
N
|
B:ASN188
|
4.4
|
98.1
|
1.0
|
CG
|
B:ASN188
|
4.5
|
99.9
|
1.0
|
CA
|
B:TYR187
|
4.5
|
96.9
|
1.0
|
C
|
B:CYS195
|
4.5
|
0.5
|
1.0
|
N
|
B:CYS201
|
4.6
|
94.7
|
1.0
|
N
|
B:CYS186
|
4.6
|
91.3
|
1.0
|
CA
|
B:CYS198
|
4.6
|
0.2
|
1.0
|
N
|
B:GLU197
|
4.7
|
0.7
|
1.0
|
CA
|
B:CYS201
|
4.8
|
93.8
|
1.0
|
CB
|
B:TYR187
|
4.8
|
96.9
|
1.0
|
C
|
B:TYR187
|
4.8
|
97.5
|
1.0
|
CB
|
B:ASN188
|
4.9
|
99.5
|
1.0
|
O
|
B:CYS186
|
5.0
|
94.4
|
1.0
|
|
Zinc binding site 3 out
of 6 in 3bl5
Go back to
Zinc Binding Sites List in 3bl5
Zinc binding site 3 out
of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn300
b:63.0
occ:1.00
|
SG
|
C:CYS195
|
2.1
|
66.1
|
1.0
|
SG
|
C:CYS201
|
2.3
|
64.4
|
1.0
|
SG
|
C:CYS198
|
2.3
|
58.1
|
1.0
|
SG
|
C:CYS186
|
2.3
|
61.9
|
1.0
|
CB
|
C:CYS201
|
3.0
|
68.6
|
1.0
|
CB
|
C:CYS186
|
3.2
|
62.1
|
1.0
|
CB
|
C:CYS195
|
3.2
|
66.2
|
1.0
|
N
|
C:CYS195
|
3.4
|
65.2
|
1.0
|
CB
|
C:CYS198
|
3.5
|
62.3
|
1.0
|
CA
|
C:CYS186
|
3.6
|
63.0
|
1.0
|
N
|
C:GLY196
|
3.6
|
66.9
|
1.0
|
CA
|
C:CYS195
|
3.6
|
66.5
|
1.0
|
N
|
C:CYS198
|
3.9
|
64.8
|
1.0
|
C
|
C:CYS195
|
4.0
|
66.8
|
1.0
|
N
|
C:TYR187
|
4.1
|
65.3
|
1.0
|
CA
|
C:CYS201
|
4.2
|
68.9
|
1.0
|
CA
|
C:CYS198
|
4.2
|
62.9
|
1.0
|
ND2
|
C:ASN188
|
4.2
|
69.6
|
1.0
|
N
|
C:CYS201
|
4.3
|
69.5
|
1.0
|
C
|
C:CYS186
|
4.3
|
63.3
|
1.0
|
N
|
C:GLU197
|
4.4
|
66.6
|
1.0
|
C
|
C:GLY194
|
4.4
|
65.6
|
1.0
|
O
|
C:CYS198
|
4.4
|
62.3
|
1.0
|
CA
|
C:GLY196
|
4.6
|
66.5
|
1.0
|
C
|
C:CYS198
|
4.7
|
63.1
|
1.0
|
N
|
C:CYS186
|
4.8
|
63.3
|
1.0
|
CA
|
C:GLY194
|
4.8
|
66.8
|
1.0
|
N
|
C:ASN188
|
4.8
|
67.5
|
1.0
|
C
|
C:GLU197
|
4.9
|
66.3
|
1.0
|
C
|
C:GLY196
|
4.9
|
66.6
|
1.0
|
|
Zinc binding site 4 out
of 6 in 3bl5
Go back to
Zinc Binding Sites List in 3bl5
Zinc binding site 4 out
of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
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 Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn300
b:75.2
occ:1.00
|
SG
|
D:CYS195
|
2.1
|
72.5
|
1.0
|
SG
|
D:CYS186
|
2.2
|
73.4
|
1.0
|
SG
|
D:CYS198
|
2.3
|
68.1
|
1.0
|
SG
|
D:CYS201
|
2.3
|
73.1
|
1.0
|
CB
|
D:CYS201
|
3.0
|
71.4
|
1.0
|
CB
|
D:CYS186
|
3.2
|
69.2
|
1.0
|
CB
|
D:CYS195
|
3.2
|
69.9
|
1.0
|
CB
|
D:CYS198
|
3.4
|
69.1
|
1.0
|
N
|
D:CYS195
|
3.5
|
68.5
|
1.0
|
N
|
D:GLY196
|
3.6
|
71.6
|
1.0
|
CA
|
D:CYS186
|
3.6
|
67.7
|
1.0
|
CA
|
D:CYS195
|
3.7
|
69.3
|
1.0
|
N
|
D:CYS198
|
3.8
|
72.3
|
1.0
|
C
|
D:CYS195
|
4.0
|
70.8
|
1.0
|
N
|
D:TYR187
|
4.1
|
68.5
|
1.0
|
CA
|
D:CYS201
|
4.1
|
71.4
|
1.0
|
CA
|
D:CYS198
|
4.1
|
70.5
|
1.0
|
ND2
|
D:ASN188
|
4.2
|
68.3
|
1.0
|
N
|
D:CYS201
|
4.2
|
70.0
|
1.0
|
N
|
D:GLU197
|
4.3
|
71.7
|
1.0
|
C
|
D:CYS186
|
4.3
|
67.6
|
1.0
|
O
|
D:CYS198
|
4.4
|
69.4
|
1.0
|
C
|
D:GLY194
|
4.4
|
69.5
|
1.0
|
CA
|
D:GLY196
|
4.6
|
71.0
|
1.0
|
C
|
D:CYS198
|
4.6
|
69.2
|
1.0
|
C
|
D:GLU197
|
4.8
|
74.0
|
1.0
|
N
|
D:CYS186
|
4.8
|
68.4
|
1.0
|
C
|
D:GLY196
|
4.8
|
71.1
|
1.0
|
CA
|
D:GLY194
|
4.9
|
70.5
|
1.0
|
N
|
D:ASN188
|
4.9
|
70.5
|
1.0
|
|
Zinc binding site 5 out
of 6 in 3bl5
Go back to
Zinc Binding Sites List in 3bl5
Zinc binding site 5 out
of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn300
b:0.7
occ:1.00
|
SG
|
E:CYS195
|
2.2
|
0.7
|
1.0
|
SG
|
E:CYS201
|
2.3
|
97.5
|
1.0
|
SG
|
E:CYS198
|
2.3
|
0.7
|
1.0
|
SG
|
E:CYS186
|
2.6
|
94.1
|
1.0
|
CB
|
E:CYS186
|
2.9
|
93.1
|
1.0
|
N
|
E:CYS195
|
3.1
|
0.6
|
1.0
|
CA
|
E:CYS186
|
3.4
|
92.6
|
1.0
|
CB
|
E:CYS201
|
3.4
|
97.2
|
1.0
|
CB
|
E:CYS195
|
3.5
|
0.7
|
1.0
|
CB
|
E:CYS198
|
3.6
|
0.7
|
1.0
|
N
|
E:GLY196
|
3.6
|
0.7
|
1.0
|
CA
|
E:CYS195
|
3.7
|
0.4
|
1.0
|
ND2
|
E:ASN188
|
3.8
|
0.1
|
1.0
|
N
|
E:CYS198
|
4.0
|
0.7
|
1.0
|
N
|
E:TYR187
|
4.1
|
96.5
|
1.0
|
C
|
E:GLY194
|
4.1
|
0.7
|
1.0
|
C
|
E:CYS195
|
4.1
|
0.0
|
1.0
|
C
|
E:CYS186
|
4.2
|
94.5
|
1.0
|
CA
|
E:GLY194
|
4.2
|
0.7
|
1.0
|
CA
|
E:CYS198
|
4.3
|
0.6
|
1.0
|
N
|
E:GLU197
|
4.4
|
0.7
|
1.0
|
O
|
E:CYS198
|
4.5
|
0.9
|
1.0
|
N
|
E:CYS186
|
4.5
|
90.3
|
1.0
|
CA
|
E:CYS201
|
4.6
|
98.1
|
1.0
|
CA
|
E:GLY196
|
4.7
|
0.3
|
1.0
|
N
|
E:CYS201
|
4.7
|
98.4
|
1.0
|
C
|
E:CYS198
|
4.8
|
0.5
|
1.0
|
C
|
E:GLU197
|
4.9
|
0.7
|
1.0
|
O
|
E:ASP193
|
5.0
|
0.7
|
1.0
|
CG
|
E:ASN188
|
5.0
|
0.5
|
1.0
|
|
Zinc binding site 6 out
of 6 in 3bl5
Go back to
Zinc Binding Sites List in 3bl5
Zinc binding site 6 out
of 6 in the Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in PREQ1 Biosynthesis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn300
b:0.7
occ:1.00
|
SG
|
F:CYS198
|
2.7
|
0.7
|
1.0
|
SG
|
F:CYS201
|
2.9
|
0.7
|
1.0
|
N
|
F:CYS195
|
2.9
|
0.7
|
1.0
|
SG
|
F:CYS195
|
3.0
|
0.5
|
1.0
|
SG
|
F:CYS186
|
3.0
|
0.7
|
1.0
|
N
|
F:GLY196
|
3.1
|
0.7
|
1.0
|
CB
|
F:CYS201
|
3.1
|
0.7
|
1.0
|
CB
|
F:CYS186
|
3.4
|
0.7
|
1.0
|
CA
|
F:CYS186
|
3.6
|
0.7
|
1.0
|
CA
|
F:CYS195
|
3.6
|
0.7
|
1.0
|
CB
|
F:CYS195
|
3.7
|
0.4
|
1.0
|
C
|
F:CYS195
|
3.7
|
0.7
|
1.0
|
C
|
F:GLY194
|
3.9
|
0.7
|
1.0
|
CB
|
F:CYS198
|
4.0
|
0.7
|
1.0
|
CA
|
F:GLY194
|
4.0
|
0.7
|
1.0
|
N
|
F:CYS201
|
4.0
|
0.7
|
1.0
|
CA
|
F:GLY196
|
4.1
|
0.7
|
1.0
|
ND2
|
F:ASN188
|
4.1
|
0.7
|
1.0
|
N
|
F:CYS198
|
4.2
|
0.7
|
1.0
|
CA
|
F:CYS201
|
4.2
|
0.7
|
1.0
|
N
|
F:TYR187
|
4.3
|
0.3
|
1.0
|
N
|
F:GLU197
|
4.3
|
0.7
|
1.0
|
C
|
F:CYS186
|
4.4
|
0.6
|
1.0
|
CA
|
F:CYS198
|
4.6
|
0.7
|
1.0
|
C
|
F:GLY196
|
4.6
|
0.7
|
1.0
|
N
|
F:CYS186
|
4.7
|
0.7
|
1.0
|
O
|
F:CYS198
|
4.7
|
0.7
|
1.0
|
O
|
F:CYS195
|
4.9
|
0.7
|
1.0
|
O
|
F:ASP193
|
4.9
|
0.7
|
1.0
|
O
|
F:GLY194
|
5.0
|
0.5
|
1.0
|
|
Reference:
N.Cicmil,
R.H.Huang.
Crystal Structure of Quec From Bacillus Subtilis: An Enzyme Involved in Preq(1) Biosynthesis. Proteins V. 72 1084 2008.
ISSN: ISSN 0887-3585
PubMed: 18491386
DOI: 10.1002/PROT.22098
Page generated: Thu Oct 24 11:32:30 2024
|