Iron in PDB 3d19: Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Protein crystallography data
The structure of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19
was solved by
J.B.Bonanno,
Y.Patskovsky,
J.Freeman,
K.T.Bain,
S.Chang,
S.Ozyurt,
D.Smith,
S.Wasserman,
J.M.Sauder,
S.K.Burley,
S.C.Almo,
New York Sgx Researchcenter For Structural Genomics (Nysgxrc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.825,
136.378,
87.060,
90.00,
102.84,
90.00
|
R / Rfree (%)
|
20.6 /
26.8
|
Other elements in 3d19:
The structure of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
(pdb code 3d19). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 3d19
Go back to
Iron Binding Sites List in 3d19
Iron binding site 1 out
of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:41.7
occ:1.00
|
OE2
|
A:GLU259
|
2.1
|
38.5
|
1.0
|
OE1
|
A:GLU128
|
2.1
|
47.1
|
1.0
|
NE2
|
A:HIS37
|
2.3
|
39.0
|
1.0
|
NE2
|
A:HIS255
|
2.3
|
35.2
|
1.0
|
O
|
A:HOH327
|
2.4
|
42.1
|
1.0
|
CD
|
A:GLU128
|
3.0
|
45.8
|
1.0
|
MG
|
A:MG301
|
3.0
|
31.0
|
1.0
|
CD
|
A:GLU259
|
3.1
|
37.5
|
1.0
|
CE1
|
A:HIS37
|
3.2
|
40.8
|
1.0
|
CD2
|
A:HIS255
|
3.2
|
37.4
|
1.0
|
OE2
|
A:GLU128
|
3.2
|
49.5
|
1.0
|
CD2
|
A:HIS37
|
3.3
|
37.4
|
1.0
|
CE1
|
A:HIS255
|
3.3
|
41.1
|
1.0
|
OE1
|
A:GLU259
|
3.5
|
40.0
|
1.0
|
CG2
|
A:ILE33
|
3.6
|
27.8
|
1.0
|
ND1
|
A:HIS37
|
4.3
|
40.4
|
1.0
|
CG
|
A:HIS255
|
4.4
|
35.6
|
1.0
|
CG
|
A:HIS37
|
4.4
|
37.6
|
1.0
|
CG
|
A:GLU128
|
4.4
|
38.5
|
1.0
|
CG
|
A:GLU259
|
4.4
|
36.1
|
1.0
|
ND1
|
A:HIS255
|
4.4
|
37.7
|
1.0
|
CD1
|
A:ILE33
|
4.6
|
26.1
|
1.0
|
NE2
|
A:HIS124
|
4.7
|
27.7
|
1.0
|
CD2
|
A:HIS124
|
4.9
|
28.7
|
1.0
|
CB
|
A:ILE33
|
4.9
|
31.1
|
1.0
|
CB
|
A:GLU128
|
4.9
|
36.8
|
1.0
|
NE2
|
A:HIS165
|
4.9
|
37.2
|
1.0
|
|
Iron binding site 2 out
of 6 in 3d19
Go back to
Iron Binding Sites List in 3d19
Iron binding site 2 out
of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe302
b:42.1
occ:1.00
|
OE2
|
B:GLU259
|
2.1
|
31.6
|
1.0
|
OE1
|
B:GLU128
|
2.1
|
36.0
|
1.0
|
NE2
|
B:HIS37
|
2.2
|
30.4
|
1.0
|
NE2
|
B:HIS255
|
2.3
|
38.8
|
1.0
|
O
|
B:HOH341
|
2.6
|
43.8
|
1.0
|
MG
|
B:MG301
|
3.0
|
37.2
|
1.0
|
CD
|
B:GLU128
|
3.0
|
34.1
|
1.0
|
CD
|
B:GLU259
|
3.0
|
30.4
|
1.0
|
CE1
|
B:HIS37
|
3.1
|
33.1
|
1.0
|
OE2
|
B:GLU128
|
3.2
|
35.6
|
1.0
|
CE1
|
B:HIS255
|
3.2
|
37.0
|
1.0
|
OE1
|
B:GLU259
|
3.3
|
26.8
|
1.0
|
CD2
|
B:HIS37
|
3.3
|
33.4
|
1.0
|
CD2
|
B:HIS255
|
3.3
|
38.6
|
1.0
|
CG2
|
B:ILE33
|
3.4
|
32.7
|
1.0
|
ND1
|
B:HIS37
|
4.3
|
32.6
|
1.0
|
ND1
|
B:HIS255
|
4.4
|
38.2
|
1.0
|
CG
|
B:GLU259
|
4.4
|
32.0
|
1.0
|
CG
|
B:HIS37
|
4.4
|
34.5
|
1.0
|
CG
|
B:HIS255
|
4.4
|
39.1
|
1.0
|
CG
|
B:GLU128
|
4.4
|
32.9
|
1.0
|
NE2
|
B:HIS124
|
4.5
|
33.6
|
1.0
|
CD2
|
B:HIS124
|
4.6
|
32.2
|
1.0
|
CB
|
B:ILE33
|
4.8
|
30.5
|
1.0
|
NE2
|
B:HIS165
|
4.9
|
28.5
|
1.0
|
CB
|
B:GLU128
|
4.9
|
34.4
|
1.0
|
CD1
|
B:ILE33
|
4.9
|
25.1
|
1.0
|
|
Iron binding site 3 out
of 6 in 3d19
Go back to
Iron Binding Sites List in 3d19
Iron binding site 3 out
of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe302
b:38.7
occ:1.00
|
OE1
|
C:GLU128
|
2.1
|
33.2
|
1.0
|
NE2
|
C:HIS37
|
2.1
|
37.2
|
1.0
|
OE2
|
C:GLU259
|
2.2
|
33.4
|
1.0
|
O
|
C:HOH312
|
2.3
|
40.5
|
1.0
|
NE2
|
C:HIS255
|
2.3
|
28.5
|
1.0
|
CD
|
C:GLU128
|
3.0
|
32.6
|
1.0
|
MG
|
C:MG301
|
3.0
|
35.3
|
1.0
|
CE1
|
C:HIS37
|
3.1
|
34.8
|
1.0
|
CE1
|
C:HIS255
|
3.2
|
30.1
|
1.0
|
OE2
|
C:GLU128
|
3.2
|
33.5
|
1.0
|
CD2
|
C:HIS37
|
3.2
|
34.6
|
1.0
|
CD
|
C:GLU259
|
3.2
|
30.4
|
1.0
|
CD2
|
C:HIS255
|
3.4
|
30.8
|
1.0
|
CG2
|
C:ILE33
|
3.5
|
30.4
|
1.0
|
OE1
|
C:GLU259
|
3.6
|
30.6
|
1.0
|
ND1
|
C:HIS37
|
4.2
|
33.0
|
1.0
|
CG
|
C:HIS37
|
4.3
|
33.7
|
1.0
|
ND1
|
C:HIS255
|
4.3
|
27.4
|
1.0
|
CG
|
C:GLU128
|
4.4
|
31.2
|
1.0
|
NE2
|
C:HIS124
|
4.4
|
37.0
|
1.0
|
CG
|
C:HIS255
|
4.5
|
30.9
|
1.0
|
CD1
|
C:ILE33
|
4.5
|
28.7
|
1.0
|
CG
|
C:GLU259
|
4.6
|
33.7
|
1.0
|
CD2
|
C:HIS124
|
4.6
|
35.4
|
1.0
|
CB
|
C:GLU128
|
4.8
|
33.5
|
1.0
|
CB
|
C:ILE33
|
4.8
|
33.0
|
1.0
|
|
Iron binding site 4 out
of 6 in 3d19
Go back to
Iron Binding Sites List in 3d19
Iron binding site 4 out
of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe302
b:47.0
occ:1.00
|
OE1
|
D:GLU128
|
2.1
|
53.3
|
1.0
|
O
|
D:HOH310
|
2.2
|
39.7
|
1.0
|
OE2
|
D:GLU259
|
2.2
|
38.3
|
1.0
|
NE2
|
D:HIS255
|
2.2
|
41.7
|
1.0
|
NE2
|
D:HIS37
|
2.3
|
42.0
|
1.0
|
CD
|
D:GLU259
|
3.0
|
39.5
|
1.0
|
MG
|
D:MG301
|
3.0
|
35.9
|
1.0
|
CE1
|
D:HIS37
|
3.1
|
43.6
|
1.0
|
CD
|
D:GLU128
|
3.1
|
48.7
|
1.0
|
OE1
|
D:GLU259
|
3.1
|
38.7
|
1.0
|
CD2
|
D:HIS255
|
3.1
|
43.1
|
1.0
|
OE2
|
D:GLU128
|
3.3
|
49.5
|
1.0
|
CE1
|
D:HIS255
|
3.3
|
39.8
|
1.0
|
CD2
|
D:HIS37
|
3.4
|
42.5
|
1.0
|
CG2
|
D:ILE33
|
3.6
|
38.8
|
1.0
|
ND1
|
D:HIS37
|
4.3
|
43.6
|
1.0
|
CG
|
D:HIS255
|
4.3
|
39.5
|
1.0
|
ND1
|
D:HIS255
|
4.4
|
40.6
|
1.0
|
CG
|
D:GLU128
|
4.5
|
45.5
|
1.0
|
CG
|
D:HIS37
|
4.5
|
44.4
|
1.0
|
CG
|
D:GLU259
|
4.5
|
37.9
|
1.0
|
NE2
|
D:HIS124
|
4.5
|
45.3
|
1.0
|
CD2
|
D:HIS124
|
4.7
|
45.3
|
1.0
|
CD1
|
D:ILE33
|
4.8
|
39.0
|
1.0
|
CB
|
D:GLU128
|
4.8
|
43.5
|
1.0
|
CB
|
D:ILE33
|
4.8
|
40.9
|
1.0
|
CG2
|
D:THR125
|
5.0
|
40.2
|
1.0
|
|
Iron binding site 5 out
of 6 in 3d19
Go back to
Iron Binding Sites List in 3d19
Iron binding site 5 out
of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe302
b:53.8
occ:1.00
|
OE1
|
E:GLU128
|
2.0
|
45.0
|
1.0
|
OE2
|
E:GLU259
|
2.1
|
55.5
|
1.0
|
NE2
|
E:HIS255
|
2.2
|
50.1
|
1.0
|
NE2
|
E:HIS37
|
2.3
|
43.9
|
1.0
|
O
|
E:HOH308
|
2.6
|
43.6
|
1.0
|
CD
|
E:GLU128
|
2.8
|
44.5
|
1.0
|
MG
|
E:MG301
|
2.9
|
40.2
|
1.0
|
OE2
|
E:GLU128
|
3.0
|
44.6
|
1.0
|
CD
|
E:GLU259
|
3.1
|
55.1
|
1.0
|
CE1
|
E:HIS37
|
3.1
|
42.4
|
1.0
|
CE1
|
E:HIS255
|
3.1
|
50.9
|
1.0
|
CD2
|
E:HIS255
|
3.2
|
51.4
|
1.0
|
OE1
|
E:GLU259
|
3.3
|
58.0
|
1.0
|
CD2
|
E:HIS37
|
3.4
|
44.4
|
1.0
|
CG2
|
E:ILE33
|
3.5
|
46.9
|
1.0
|
CG
|
E:GLU128
|
4.3
|
45.3
|
1.0
|
ND1
|
E:HIS255
|
4.3
|
51.4
|
1.0
|
ND1
|
E:HIS37
|
4.3
|
43.6
|
1.0
|
CG
|
E:HIS255
|
4.4
|
50.9
|
1.0
|
CG
|
E:GLU259
|
4.5
|
52.5
|
1.0
|
CG
|
E:HIS37
|
4.5
|
45.3
|
1.0
|
NE2
|
E:HIS124
|
4.6
|
39.8
|
1.0
|
CD2
|
E:HIS124
|
4.7
|
41.0
|
1.0
|
CB
|
E:GLU128
|
4.7
|
45.5
|
1.0
|
CB
|
E:ILE33
|
4.9
|
47.9
|
1.0
|
CD1
|
E:ILE33
|
5.0
|
42.5
|
1.0
|
NE2
|
E:HIS165
|
5.0
|
42.6
|
1.0
|
|
Iron binding site 6 out
of 6 in 3d19
Go back to
Iron Binding Sites List in 3d19
Iron binding site 6 out
of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe302
b:45.1
occ:1.00
|
NE2
|
F:HIS37
|
2.1
|
38.7
|
1.0
|
OE2
|
F:GLU259
|
2.2
|
36.8
|
1.0
|
OE1
|
F:GLU128
|
2.2
|
44.3
|
1.0
|
O
|
F:HOH316
|
2.3
|
52.0
|
1.0
|
NE2
|
F:HIS255
|
2.4
|
43.1
|
1.0
|
CE1
|
F:HIS37
|
2.8
|
38.8
|
1.0
|
CD
|
F:GLU128
|
3.0
|
42.8
|
1.0
|
MG
|
F:MG301
|
3.1
|
36.4
|
1.0
|
CD
|
F:GLU259
|
3.2
|
39.0
|
1.0
|
OE2
|
F:GLU128
|
3.2
|
43.2
|
1.0
|
CD2
|
F:HIS37
|
3.2
|
37.4
|
1.0
|
CD2
|
F:HIS255
|
3.4
|
42.6
|
1.0
|
OE1
|
F:GLU259
|
3.4
|
43.7
|
1.0
|
CE1
|
F:HIS255
|
3.4
|
43.3
|
1.0
|
CG2
|
F:ILE33
|
3.6
|
41.9
|
1.0
|
ND1
|
F:HIS37
|
4.0
|
40.0
|
1.0
|
CG
|
F:HIS37
|
4.3
|
39.8
|
1.0
|
CG
|
F:GLU128
|
4.5
|
42.0
|
1.0
|
NE2
|
F:HIS124
|
4.5
|
38.1
|
1.0
|
ND1
|
F:HIS255
|
4.5
|
39.3
|
1.0
|
CG
|
F:HIS255
|
4.5
|
40.4
|
1.0
|
CG
|
F:GLU259
|
4.6
|
41.3
|
1.0
|
CD2
|
F:HIS124
|
4.6
|
38.1
|
1.0
|
CD1
|
F:ILE33
|
4.7
|
42.6
|
1.0
|
CB
|
F:ILE33
|
4.8
|
43.3
|
1.0
|
CB
|
F:GLU128
|
4.9
|
42.5
|
1.0
|
CG2
|
F:THR125
|
5.0
|
38.9
|
1.0
|
|
Reference:
J.B.Bonanno,
Y.Patskovsky,
J.Freeman,
K.T.Bain,
S.Chang,
S.Ozyurt,
D.Smith,
S.Wasserman,
J.M.Sauder,
S.K.Burley,
S.C.Almo.
Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus. To Be Published.
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