Iron in PDB 3q1g: Crystal Structure of Boxb Crystallized with Peg
Enzymatic activity of Crystal Structure of Boxb Crystallized with Peg
All present enzymatic activity of Crystal Structure of Boxb Crystallized with Peg:
1.14.12.21;
Protein crystallography data
The structure of Crystal Structure of Boxb Crystallized with Peg, PDB code: 3q1g
was solved by
T.Weinert,
L.Rather,
G.Fuchs,
U.Ermler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.70 /
2.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
209.660,
76.770,
147.830,
90.00,
109.43,
90.00
|
R / Rfree (%)
|
20.6 /
23.5
|
Other elements in 3q1g:
The structure of Crystal Structure of Boxb Crystallized with Peg also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Boxb Crystallized with Peg
(pdb code 3q1g). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Crystal Structure of Boxb Crystallized with Peg, PDB code: 3q1g:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 1 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
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 Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1001
b:38.0
occ:1.00
|
OE1
|
A:GLU150
|
2.0
|
44.7
|
1.0
|
O
|
A:OH1003
|
2.0
|
41.5
|
1.0
|
OE1
|
A:GLU120
|
2.2
|
46.3
|
1.0
|
ND1
|
A:HIS153
|
2.4
|
44.4
|
1.0
|
O
|
A:HOH562
|
2.8
|
44.8
|
1.0
|
CD
|
A:GLU120
|
3.0
|
39.8
|
1.0
|
CD
|
A:GLU150
|
3.0
|
40.5
|
1.0
|
OE2
|
A:GLU120
|
3.1
|
40.8
|
1.0
|
CE1
|
A:HIS153
|
3.2
|
43.6
|
1.0
|
OE2
|
A:GLU150
|
3.4
|
46.8
|
1.0
|
FE
|
A:FE1002
|
3.5
|
39.3
|
1.0
|
CG
|
A:HIS153
|
3.5
|
39.1
|
1.0
|
OE2
|
A:GLU240
|
3.5
|
54.0
|
1.0
|
CB
|
A:HIS153
|
4.0
|
36.3
|
1.0
|
OE1
|
A:GLU240
|
4.1
|
51.1
|
1.0
|
CD
|
A:GLU240
|
4.2
|
48.5
|
1.0
|
NE2
|
A:HIS153
|
4.4
|
42.0
|
1.0
|
CG
|
A:GLU150
|
4.4
|
37.5
|
1.0
|
CG
|
A:GLU120
|
4.4
|
38.8
|
1.0
|
CD2
|
A:HIS153
|
4.6
|
39.6
|
1.0
|
CE1
|
A:HIS243
|
4.6
|
41.8
|
1.0
|
CA
|
A:GLU150
|
4.7
|
36.2
|
1.0
|
ND1
|
A:HIS243
|
4.7
|
43.6
|
1.0
|
CB
|
A:GLU150
|
4.7
|
35.5
|
1.0
|
CB
|
A:GLU120
|
4.9
|
36.8
|
1.0
|
CE
|
A:MET236
|
4.9
|
35.6
|
1.0
|
|
Iron binding site 2 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 2 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
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 Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe1002
b:39.3
occ:1.00
|
OE1
|
A:GLU240
|
1.9
|
51.1
|
1.0
|
OD2
|
A:ASP211
|
1.9
|
48.2
|
1.0
|
OE2
|
A:GLU150
|
2.0
|
46.8
|
1.0
|
O
|
A:OH1003
|
2.0
|
41.5
|
1.0
|
ND1
|
A:HIS243
|
2.2
|
43.6
|
1.0
|
O
|
A:HOH562
|
2.5
|
44.8
|
1.0
|
CD
|
A:GLU240
|
2.9
|
48.5
|
1.0
|
CD
|
A:GLU150
|
3.0
|
40.5
|
1.0
|
CG
|
A:ASP211
|
3.0
|
42.4
|
1.0
|
CE1
|
A:HIS243
|
3.0
|
41.8
|
1.0
|
OE2
|
A:GLU240
|
3.3
|
54.0
|
1.0
|
CG
|
A:HIS243
|
3.3
|
40.6
|
1.0
|
OE1
|
A:GLU150
|
3.4
|
44.7
|
1.0
|
FE
|
A:FE1001
|
3.5
|
38.0
|
1.0
|
CB
|
A:HIS243
|
3.7
|
39.4
|
1.0
|
CB
|
A:ASP211
|
3.7
|
39.2
|
1.0
|
OD1
|
A:ASP211
|
3.9
|
44.1
|
1.0
|
O
|
A:HOH547
|
4.1
|
47.3
|
1.0
|
NE2
|
A:HIS243
|
4.2
|
42.9
|
1.0
|
CG
|
A:GLU150
|
4.2
|
37.5
|
1.0
|
CG
|
A:GLU240
|
4.3
|
44.7
|
1.0
|
CD2
|
A:HIS243
|
4.4
|
42.0
|
1.0
|
CA
|
A:ASP211
|
4.5
|
37.9
|
1.0
|
CE1
|
A:HIS153
|
4.9
|
43.6
|
1.0
|
CA
|
A:GLU240
|
4.9
|
42.0
|
1.0
|
ND1
|
A:HIS153
|
5.0
|
44.4
|
1.0
|
|
Iron binding site 3 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 3 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
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 Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1001
b:37.6
occ:1.00
|
OE1
|
B:GLU150
|
1.9
|
44.1
|
1.0
|
O
|
B:OH1003
|
2.1
|
34.6
|
1.0
|
OE1
|
B:GLU120
|
2.2
|
46.9
|
1.0
|
ND1
|
B:HIS153
|
2.4
|
45.1
|
1.0
|
O
|
B:HOH578
|
2.6
|
38.1
|
1.0
|
CD
|
B:GLU150
|
3.0
|
39.9
|
1.0
|
CD
|
B:GLU120
|
3.0
|
40.2
|
1.0
|
CE1
|
B:HIS153
|
3.2
|
44.9
|
1.0
|
OE2
|
B:GLU120
|
3.2
|
41.7
|
1.0
|
FE
|
B:FE1002
|
3.4
|
34.7
|
1.0
|
OE2
|
B:GLU150
|
3.4
|
47.3
|
1.0
|
CG
|
B:HIS153
|
3.5
|
39.7
|
1.0
|
OE2
|
B:GLU240
|
3.7
|
55.9
|
1.0
|
OE1
|
B:GLU240
|
3.8
|
51.8
|
1.0
|
CB
|
B:HIS153
|
4.0
|
36.6
|
1.0
|
CD
|
B:GLU240
|
4.2
|
49.9
|
1.0
|
NE2
|
B:HIS153
|
4.4
|
43.0
|
1.0
|
CG
|
B:GLU150
|
4.4
|
36.9
|
1.0
|
CG
|
B:GLU120
|
4.5
|
38.9
|
1.0
|
CD2
|
B:HIS153
|
4.6
|
40.0
|
1.0
|
CE1
|
B:HIS243
|
4.6
|
42.0
|
1.0
|
CA
|
B:GLU150
|
4.7
|
35.0
|
1.0
|
ND1
|
B:HIS243
|
4.7
|
44.0
|
1.0
|
CB
|
B:GLU150
|
4.8
|
34.4
|
1.0
|
CE
|
B:MET236
|
4.8
|
37.4
|
1.0
|
CB
|
B:GLU120
|
4.9
|
36.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 4 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
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 Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe1002
b:34.7
occ:1.00
|
OE1
|
B:GLU240
|
1.9
|
51.8
|
1.0
|
OD2
|
B:ASP211
|
2.0
|
47.5
|
1.0
|
OE2
|
B:GLU150
|
2.0
|
47.3
|
1.0
|
O
|
B:OH1003
|
2.0
|
34.6
|
1.0
|
ND1
|
B:HIS243
|
2.2
|
44.0
|
1.0
|
CD
|
B:GLU240
|
2.8
|
49.9
|
1.0
|
O
|
B:HOH578
|
2.9
|
38.1
|
1.0
|
CD
|
B:GLU150
|
3.0
|
39.9
|
1.0
|
CG
|
B:ASP211
|
3.0
|
43.1
|
1.0
|
CE1
|
B:HIS243
|
3.1
|
42.0
|
1.0
|
OE2
|
B:GLU240
|
3.1
|
55.9
|
1.0
|
OE1
|
B:GLU150
|
3.3
|
44.1
|
1.0
|
CG
|
B:HIS243
|
3.4
|
40.9
|
1.0
|
FE
|
B:FE1001
|
3.4
|
37.6
|
1.0
|
CB
|
B:ASP211
|
3.7
|
39.8
|
1.0
|
CB
|
B:HIS243
|
3.8
|
39.8
|
1.0
|
OD1
|
B:ASP211
|
4.0
|
45.4
|
1.0
|
O
|
B:HOH499
|
4.0
|
43.4
|
1.0
|
CG
|
B:GLU240
|
4.2
|
45.9
|
1.0
|
NE2
|
B:HIS243
|
4.3
|
43.4
|
1.0
|
CG
|
B:GLU150
|
4.3
|
36.9
|
1.0
|
CD2
|
B:HIS243
|
4.4
|
42.8
|
1.0
|
CA
|
B:ASP211
|
4.4
|
39.0
|
1.0
|
CE1
|
B:HIS153
|
4.8
|
44.9
|
1.0
|
CA
|
B:GLU240
|
4.9
|
43.6
|
1.0
|
ND1
|
B:HIS153
|
4.9
|
45.1
|
1.0
|
CB
|
B:GLU240
|
5.0
|
43.9
|
1.0
|
|
Iron binding site 5 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 5 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
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 Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1001
b:37.1
occ:1.00
|
OE1
|
C:GLU150
|
2.0
|
45.4
|
1.0
|
O
|
C:OH1003
|
2.0
|
36.4
|
1.0
|
OE1
|
C:GLU120
|
2.1
|
48.1
|
1.0
|
O
|
C:HOH544
|
2.4
|
38.7
|
1.0
|
ND1
|
C:HIS153
|
2.4
|
44.5
|
1.0
|
CD
|
C:GLU120
|
2.9
|
41.8
|
1.0
|
CD
|
C:GLU150
|
3.0
|
41.4
|
1.0
|
OE2
|
C:GLU120
|
3.1
|
42.6
|
1.0
|
CE1
|
C:HIS153
|
3.2
|
43.4
|
1.0
|
FE
|
C:FE1002
|
3.4
|
38.9
|
1.0
|
OE2
|
C:GLU150
|
3.4
|
48.5
|
1.0
|
CG
|
C:HIS153
|
3.5
|
39.0
|
1.0
|
OE2
|
C:GLU240
|
3.7
|
56.2
|
1.0
|
CB
|
C:HIS153
|
4.0
|
36.3
|
1.0
|
OE1
|
C:GLU240
|
4.0
|
51.7
|
1.0
|
O
|
C:HOH516
|
4.2
|
47.5
|
1.0
|
CD
|
C:GLU240
|
4.2
|
49.7
|
1.0
|
NE2
|
C:HIS153
|
4.4
|
41.3
|
1.0
|
CG
|
C:GLU120
|
4.4
|
40.7
|
1.0
|
CG
|
C:GLU150
|
4.4
|
38.2
|
1.0
|
CD2
|
C:HIS153
|
4.6
|
39.2
|
1.0
|
CE1
|
C:HIS243
|
4.7
|
41.8
|
1.0
|
CA
|
C:GLU150
|
4.7
|
36.2
|
1.0
|
CB
|
C:GLU150
|
4.8
|
36.3
|
1.0
|
CE
|
C:MET236
|
4.8
|
36.4
|
1.0
|
ND1
|
C:HIS243
|
4.8
|
44.2
|
1.0
|
CB
|
C:GLU120
|
4.9
|
38.6
|
1.0
|
|
Iron binding site 6 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 6 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
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 Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe1002
b:38.9
occ:1.00
|
OE1
|
C:GLU240
|
1.9
|
51.7
|
1.0
|
OE2
|
C:GLU150
|
1.9
|
48.5
|
1.0
|
OD2
|
C:ASP211
|
2.0
|
49.4
|
1.0
|
O
|
C:OH1003
|
2.0
|
36.4
|
1.0
|
ND1
|
C:HIS243
|
2.3
|
44.2
|
1.0
|
O
|
C:HOH544
|
2.8
|
38.7
|
1.0
|
CD
|
C:GLU240
|
2.8
|
49.7
|
1.0
|
CD
|
C:GLU150
|
2.9
|
41.4
|
1.0
|
CG
|
C:ASP211
|
3.0
|
44.9
|
1.0
|
OE2
|
C:GLU240
|
3.1
|
56.2
|
1.0
|
CE1
|
C:HIS243
|
3.1
|
41.8
|
1.0
|
OE1
|
C:GLU150
|
3.3
|
45.4
|
1.0
|
FE
|
C:FE1001
|
3.4
|
37.1
|
1.0
|
CG
|
C:HIS243
|
3.4
|
40.8
|
1.0
|
CB
|
C:ASP211
|
3.7
|
41.9
|
1.0
|
O
|
C:HOH511
|
3.8
|
39.5
|
1.0
|
CB
|
C:HIS243
|
3.9
|
39.8
|
1.0
|
OD1
|
C:ASP211
|
4.0
|
47.4
|
1.0
|
CG
|
C:GLU240
|
4.2
|
45.4
|
1.0
|
CG
|
C:GLU150
|
4.2
|
38.2
|
1.0
|
NE2
|
C:HIS243
|
4.3
|
42.8
|
1.0
|
CA
|
C:ASP211
|
4.4
|
41.0
|
1.0
|
CD2
|
C:HIS243
|
4.5
|
41.8
|
1.0
|
CE1
|
C:HIS153
|
4.8
|
43.4
|
1.0
|
ND1
|
C:HIS153
|
4.9
|
44.5
|
1.0
|
CA
|
C:GLU240
|
4.9
|
41.6
|
1.0
|
O
|
C:ASP211
|
5.0
|
41.2
|
1.0
|
|
Iron binding site 7 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 7 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1001
b:44.1
occ:1.00
|
O
|
D:OH1003
|
1.9
|
43.3
|
1.0
|
OE1
|
D:GLU150
|
2.0
|
63.0
|
1.0
|
OE1
|
D:GLU120
|
2.0
|
65.0
|
1.0
|
ND1
|
D:HIS153
|
2.4
|
63.5
|
1.0
|
CD
|
D:GLU120
|
2.8
|
58.1
|
1.0
|
OE2
|
D:GLU120
|
3.0
|
59.2
|
1.0
|
CD
|
D:GLU150
|
3.0
|
58.3
|
1.0
|
O
|
D:HOH514
|
3.2
|
53.3
|
1.0
|
CE1
|
D:HIS153
|
3.2
|
62.5
|
1.0
|
FE
|
D:FE1002
|
3.4
|
44.5
|
1.0
|
OE2
|
D:GLU150
|
3.4
|
65.1
|
1.0
|
CG
|
D:HIS153
|
3.5
|
58.5
|
1.0
|
OE1
|
D:GLU240
|
3.7
|
69.2
|
1.0
|
CB
|
D:HIS153
|
3.9
|
55.1
|
1.0
|
OE2
|
D:GLU240
|
4.1
|
72.0
|
1.0
|
CG
|
D:GLU120
|
4.3
|
56.3
|
1.0
|
CD
|
D:GLU240
|
4.3
|
66.3
|
1.0
|
NE2
|
D:HIS153
|
4.4
|
61.2
|
1.0
|
CG
|
D:GLU150
|
4.4
|
55.5
|
1.0
|
CD2
|
D:HIS153
|
4.6
|
58.9
|
1.0
|
CE
|
D:MET236
|
4.7
|
54.8
|
1.0
|
CA
|
D:GLU150
|
4.7
|
54.4
|
1.0
|
CE1
|
D:HIS243
|
4.7
|
60.4
|
1.0
|
CB
|
D:GLU150
|
4.8
|
53.5
|
1.0
|
CB
|
D:GLU120
|
4.8
|
54.4
|
1.0
|
ND1
|
D:HIS243
|
4.9
|
62.0
|
1.0
|
CA
|
D:GLU120
|
5.0
|
53.5
|
1.0
|
|
Iron binding site 8 out
of 8 in 3q1g
Go back to
Iron Binding Sites List in 3q1g
Iron binding site 8 out
of 8 in the Crystal Structure of Boxb Crystallized with Peg
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Boxb Crystallized with Peg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe1002
b:44.5
occ:1.00
|
O
|
D:OH1003
|
1.9
|
43.3
|
1.0
|
OE2
|
D:GLU150
|
2.0
|
65.1
|
1.0
|
OD2
|
D:ASP211
|
2.1
|
65.4
|
1.0
|
OE1
|
D:GLU240
|
2.3
|
69.2
|
1.0
|
O
|
D:HOH514
|
2.4
|
53.3
|
1.0
|
ND1
|
D:HIS243
|
2.4
|
62.0
|
1.0
|
OE2
|
D:GLU240
|
2.6
|
72.0
|
1.0
|
CD
|
D:GLU240
|
2.8
|
66.3
|
1.0
|
CD
|
D:GLU150
|
3.0
|
58.3
|
1.0
|
CG
|
D:ASP211
|
3.0
|
59.3
|
1.0
|
CE1
|
D:HIS243
|
3.2
|
60.4
|
1.0
|
OE1
|
D:GLU150
|
3.3
|
63.0
|
1.0
|
FE
|
D:FE1001
|
3.4
|
44.1
|
1.0
|
CG
|
D:HIS243
|
3.5
|
58.9
|
1.0
|
CB
|
D:ASP211
|
3.7
|
56.2
|
1.0
|
OD1
|
D:ASP211
|
3.9
|
61.2
|
1.0
|
CB
|
D:HIS243
|
3.9
|
57.3
|
1.0
|
O
|
D:HOH505
|
4.1
|
64.2
|
1.0
|
CG
|
D:GLU240
|
4.2
|
62.4
|
1.0
|
CG
|
D:GLU150
|
4.3
|
55.5
|
1.0
|
CA
|
D:ASP211
|
4.4
|
54.7
|
1.0
|
NE2
|
D:HIS243
|
4.4
|
61.7
|
1.0
|
CD2
|
D:HIS243
|
4.6
|
60.8
|
1.0
|
CE1
|
D:HIS153
|
4.9
|
62.5
|
1.0
|
ND1
|
D:HIS153
|
4.9
|
63.5
|
1.0
|
CA
|
D:GLU240
|
5.0
|
60.6
|
1.0
|
O
|
D:ASP211
|
5.0
|
55.1
|
1.0
|
|
Reference:
L.J.Rather,
T.Weinert,
U.Demmer,
E.Bill,
W.Ismail,
G.Fuchs,
U.Ermler.
Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase Boxb. J.Biol.Chem. V. 286 29241 2011.
ISSN: ISSN 0021-9258
PubMed: 21632537
DOI: 10.1074/JBC.M111.236893
Page generated: Sun Aug 4 18:30:56 2024
|