Iron in PDB 5gn9: Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
Protein crystallography data
The structure of Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B, PDB code: 5gn9
was solved by
E.O.Balogun,
D.K.Inaoka,
T.Shiba,
T.Tsuge,
B.May,
T.Sato,
Y.Kido,
N.Takeshi,
T.Aoki,
T.Honma,
A.Tanaka,
M.Inoue,
S.Matsuoka,
P.A.M.Michels,
Y.Watanabe,
A.L.Moore,
S.Harada,
K.Kita,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.19 /
3.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
150.218,
221.812,
62.611,
90.00,
114.64,
90.00
|
R / Rfree (%)
|
19.2 /
25.2
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
(pdb code 5gn9). 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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B, PDB code: 5gn9:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 1 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:46.0
occ:1.00
|
OE1
|
A:GLU266
|
1.8
|
69.7
|
1.0
|
OAC
|
A:6Y0503
|
2.1
|
38.3
|
1.0
|
OE2
|
A:GLU123
|
2.3
|
55.9
|
1.0
|
OE1
|
A:GLU162
|
2.3
|
48.2
|
1.0
|
OE1
|
A:GLU123
|
2.3
|
47.4
|
1.0
|
OAD
|
A:6Y0503
|
2.4
|
43.9
|
1.0
|
CD
|
A:GLU123
|
2.6
|
50.8
|
1.0
|
CD
|
A:GLU266
|
2.9
|
60.0
|
1.0
|
CAL
|
A:6Y0503
|
3.0
|
47.4
|
1.0
|
CD
|
A:GLU162
|
3.0
|
49.6
|
1.0
|
ND1
|
A:HIS165
|
3.1
|
51.5
|
1.0
|
OE2
|
A:GLU162
|
3.1
|
46.8
|
1.0
|
CAN
|
A:6Y0503
|
3.1
|
50.6
|
1.0
|
FE
|
A:FE502
|
3.3
|
54.5
|
1.0
|
OE2
|
A:GLU266
|
3.6
|
44.4
|
1.0
|
CE1
|
A:HIS165
|
3.7
|
56.0
|
1.0
|
OH
|
A:TYR220
|
3.8
|
47.9
|
1.0
|
CG
|
A:GLU266
|
4.0
|
58.0
|
1.0
|
CB
|
A:ALA126
|
4.0
|
57.3
|
1.0
|
CG
|
A:GLU123
|
4.1
|
48.5
|
1.0
|
CG
|
A:HIS165
|
4.2
|
51.2
|
1.0
|
CAE
|
A:6Y0503
|
4.4
|
55.6
|
1.0
|
CE2
|
A:TYR220
|
4.4
|
52.5
|
1.0
|
CG
|
A:GLU162
|
4.5
|
47.5
|
1.0
|
CAQ
|
A:6Y0503
|
4.5
|
58.4
|
1.0
|
CZ
|
A:TYR220
|
4.6
|
50.9
|
1.0
|
CB
|
A:HIS165
|
4.7
|
52.1
|
1.0
|
OE1
|
A:GLU213
|
4.9
|
43.9
|
1.0
|
CB
|
A:GLU123
|
4.9
|
44.4
|
1.0
|
NE2
|
A:HIS165
|
5.0
|
54.0
|
1.0
|
|
Iron binding site 2 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 2 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe502
b:54.5
occ:1.00
|
OE2
|
A:GLU162
|
2.0
|
46.8
|
1.0
|
OE2
|
A:GLU213
|
2.3
|
56.9
|
1.0
|
OAC
|
A:6Y0503
|
2.3
|
38.3
|
1.0
|
OE2
|
A:GLU266
|
2.3
|
44.4
|
1.0
|
OE1
|
A:GLU213
|
2.5
|
43.9
|
1.0
|
CD
|
A:GLU213
|
2.7
|
48.9
|
1.0
|
CD
|
A:GLU162
|
2.9
|
49.6
|
1.0
|
OE1
|
A:GLU266
|
3.0
|
69.7
|
1.0
|
CD
|
A:GLU266
|
3.0
|
60.0
|
1.0
|
FE
|
A:FE501
|
3.3
|
46.0
|
1.0
|
CAL
|
A:6Y0503
|
3.4
|
47.4
|
1.0
|
OE1
|
A:GLU162
|
3.5
|
48.2
|
1.0
|
CB
|
A:ALA126
|
3.8
|
57.3
|
1.0
|
CG
|
A:GLU162
|
3.8
|
47.5
|
1.0
|
CAE
|
A:6Y0503
|
3.9
|
55.6
|
1.0
|
ND1
|
A:HIS269
|
4.0
|
54.4
|
1.0
|
CG
|
A:GLU213
|
4.2
|
46.0
|
1.0
|
CG
|
A:GLU266
|
4.5
|
58.0
|
1.0
|
CAN
|
A:6Y0503
|
4.6
|
50.6
|
1.0
|
OE2
|
A:GLU123
|
4.6
|
55.9
|
1.0
|
CA
|
A:ALA126
|
4.7
|
56.5
|
1.0
|
OAD
|
A:6Y0503
|
4.8
|
43.9
|
1.0
|
CE1
|
A:HIS269
|
4.8
|
53.0
|
1.0
|
CB
|
A:ALA216
|
4.8
|
43.8
|
1.0
|
|
Iron binding site 3 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 3 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe501
b:44.6
occ:1.00
|
OE1
|
B:GLU123
|
1.8
|
57.4
|
1.0
|
OE1
|
B:GLU266
|
2.0
|
60.8
|
1.0
|
OAC
|
B:6Y0503
|
2.0
|
46.6
|
1.0
|
OE1
|
B:GLU162
|
2.3
|
47.1
|
1.0
|
CD
|
B:GLU123
|
2.6
|
53.7
|
1.0
|
OE2
|
B:GLU123
|
2.7
|
48.6
|
1.0
|
CD
|
B:GLU266
|
2.8
|
58.2
|
1.0
|
OAD
|
B:6Y0503
|
3.1
|
52.0
|
1.0
|
CD
|
B:GLU162
|
3.1
|
51.3
|
1.0
|
CAL
|
B:6Y0503
|
3.2
|
59.7
|
1.0
|
OE2
|
B:GLU266
|
3.2
|
53.6
|
1.0
|
OE2
|
B:GLU162
|
3.2
|
54.5
|
1.0
|
FE
|
B:FE502
|
3.2
|
48.0
|
1.0
|
ND1
|
B:HIS165
|
3.3
|
39.5
|
1.0
|
CAN
|
B:6Y0503
|
3.6
|
60.6
|
1.0
|
OH
|
B:TYR220
|
4.0
|
57.9
|
1.0
|
CG
|
B:GLU123
|
4.0
|
50.9
|
1.0
|
CG
|
B:GLU266
|
4.0
|
54.4
|
1.0
|
CE1
|
B:HIS165
|
4.0
|
43.9
|
1.0
|
CB
|
B:ALA126
|
4.2
|
49.5
|
1.0
|
CG
|
B:HIS165
|
4.2
|
40.9
|
1.0
|
CAE
|
B:6Y0503
|
4.4
|
70.7
|
1.0
|
CB
|
B:HIS165
|
4.5
|
42.9
|
1.0
|
CG
|
B:GLU162
|
4.6
|
47.0
|
1.0
|
CE2
|
B:TYR220
|
4.6
|
67.9
|
1.0
|
CZ
|
B:TYR220
|
4.7
|
65.6
|
1.0
|
CB
|
B:GLU123
|
4.8
|
48.9
|
1.0
|
CA
|
B:GLU123
|
5.0
|
50.8
|
1.0
|
|
Iron binding site 4 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 4 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe502
b:48.0
occ:1.00
|
OE2
|
B:GLU266
|
2.2
|
53.6
|
1.0
|
OE1
|
B:GLU213
|
2.3
|
34.1
|
1.0
|
OE2
|
B:GLU162
|
2.5
|
54.5
|
1.0
|
OAC
|
B:6Y0503
|
2.6
|
46.6
|
1.0
|
OE2
|
B:GLU213
|
2.6
|
37.7
|
1.0
|
CD
|
B:GLU213
|
2.8
|
38.6
|
1.0
|
CD
|
B:GLU162
|
3.1
|
51.3
|
1.0
|
CD
|
B:GLU266
|
3.2
|
58.2
|
1.0
|
FE
|
B:FE501
|
3.2
|
44.6
|
1.0
|
CAL
|
B:6Y0503
|
3.4
|
59.7
|
1.0
|
OE1
|
B:GLU266
|
3.5
|
60.8
|
1.0
|
OE1
|
B:GLU162
|
3.5
|
47.1
|
1.0
|
CAE
|
B:6Y0503
|
3.6
|
70.7
|
1.0
|
CB
|
B:ALA126
|
3.8
|
49.5
|
1.0
|
CG
|
B:GLU162
|
4.1
|
47.0
|
1.0
|
CG
|
B:GLU213
|
4.2
|
41.0
|
1.0
|
CG
|
B:GLU266
|
4.5
|
54.4
|
1.0
|
ND1
|
B:HIS269
|
4.5
|
48.9
|
1.0
|
CAN
|
B:6Y0503
|
4.7
|
60.6
|
1.0
|
CB
|
B:ALA216
|
4.8
|
52.0
|
1.0
|
CB
|
B:GLU266
|
4.9
|
54.1
|
1.0
|
CA
|
B:ALA126
|
4.9
|
48.9
|
1.0
|
OE2
|
B:GLU123
|
5.0
|
48.6
|
1.0
|
OE1
|
B:GLU123
|
5.0
|
57.4
|
1.0
|
CAF
|
B:6Y0503
|
5.0
|
73.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 5 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:61.5
occ:1.00
|
OE1
|
C:GLU266
|
1.9
|
46.5
|
1.0
|
OAC
|
C:6Y0503
|
2.0
|
65.9
|
1.0
|
OE2
|
C:GLU123
|
2.2
|
59.1
|
1.0
|
OE1
|
C:GLU123
|
2.6
|
55.8
|
1.0
|
CD
|
C:GLU266
|
2.7
|
52.4
|
1.0
|
OAD
|
C:6Y0503
|
2.7
|
85.7
|
1.0
|
CD
|
C:GLU123
|
2.8
|
61.5
|
1.0
|
FE
|
C:FE502
|
3.0
|
56.0
|
1.0
|
OE2
|
C:GLU266
|
3.0
|
48.8
|
1.0
|
CAL
|
C:6Y0503
|
3.1
|
85.0
|
1.0
|
CAN
|
C:6Y0503
|
3.3
|
88.7
|
1.0
|
OE1
|
C:GLU162
|
3.3
|
71.2
|
1.0
|
OE2
|
C:GLU162
|
3.6
|
56.6
|
1.0
|
CD
|
C:GLU162
|
3.6
|
64.1
|
1.0
|
ND1
|
C:HIS165
|
3.8
|
52.0
|
1.0
|
CG
|
C:GLU266
|
4.0
|
53.4
|
1.0
|
CB
|
C:ALA126
|
4.1
|
74.0
|
1.0
|
CG
|
C:GLU123
|
4.3
|
67.0
|
1.0
|
CE1
|
C:HIS165
|
4.3
|
54.8
|
1.0
|
CAE
|
C:6Y0503
|
4.4
|
94.7
|
1.0
|
OH
|
C:TYR220
|
4.5
|
83.8
|
1.0
|
CG
|
C:GLU162
|
4.6
|
63.0
|
1.0
|
CE2
|
C:TYR220
|
4.7
|
82.7
|
1.0
|
CB
|
C:GLU162
|
4.7
|
60.1
|
1.0
|
CAQ
|
C:6Y0503
|
4.7
|
97.5
|
1.0
|
OE1
|
C:GLU213
|
4.8
|
45.7
|
1.0
|
CG
|
C:HIS165
|
4.9
|
52.2
|
1.0
|
CA
|
C:GLU123
|
5.0
|
80.8
|
1.0
|
|
Iron binding site 6 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 6 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe502
b:56.0
occ:1.00
|
OE2
|
C:GLU266
|
2.0
|
48.8
|
1.0
|
OE2
|
C:GLU162
|
2.0
|
56.6
|
1.0
|
OAC
|
C:6Y0503
|
2.4
|
65.9
|
1.0
|
OE1
|
C:GLU213
|
2.5
|
45.7
|
1.0
|
OE2
|
C:GLU213
|
2.6
|
52.1
|
1.0
|
CD
|
C:GLU213
|
2.9
|
50.1
|
1.0
|
FE
|
C:FE501
|
3.0
|
61.5
|
1.0
|
CD
|
C:GLU266
|
3.0
|
52.4
|
1.0
|
CD
|
C:GLU162
|
3.1
|
64.1
|
1.0
|
OE1
|
C:GLU266
|
3.4
|
46.5
|
1.0
|
CAL
|
C:6Y0503
|
3.6
|
85.0
|
1.0
|
OE1
|
C:GLU162
|
3.6
|
71.2
|
1.0
|
CB
|
C:ALA126
|
3.7
|
74.0
|
1.0
|
CAE
|
C:6Y0503
|
4.1
|
94.7
|
1.0
|
CG
|
C:GLU162
|
4.3
|
63.0
|
1.0
|
CG
|
C:GLU266
|
4.3
|
53.4
|
1.0
|
CG
|
C:GLU213
|
4.4
|
55.2
|
1.0
|
ND1
|
C:HIS269
|
4.4
|
48.2
|
1.0
|
OE2
|
C:GLU123
|
4.6
|
59.1
|
1.0
|
CAN
|
C:6Y0503
|
4.7
|
88.7
|
1.0
|
CB
|
C:GLU266
|
4.7
|
47.3
|
1.0
|
CA
|
C:GLU266
|
4.9
|
46.2
|
1.0
|
OAD
|
C:6Y0503
|
4.9
|
85.7
|
1.0
|
CB
|
C:ALA216
|
4.9
|
62.1
|
1.0
|
|
Iron binding site 7 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 7 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe501
b:66.5
occ:1.00
|
OE1
|
D:GLU266
|
1.9
|
60.0
|
1.0
|
OAC
|
D:6Y0503
|
2.0
|
62.7
|
1.0
|
OE1
|
D:GLU162
|
2.1
|
70.4
|
1.0
|
OAD
|
D:6Y0503
|
2.2
|
95.2
|
1.0
|
OE2
|
D:GLU123
|
2.3
|
55.6
|
1.0
|
OE1
|
D:GLU123
|
2.5
|
43.4
|
1.0
|
CD
|
D:GLU123
|
2.7
|
54.3
|
1.0
|
CAL
|
D:6Y0503
|
2.8
|
84.3
|
1.0
|
CAN
|
D:6Y0503
|
2.9
|
92.5
|
1.0
|
CD
|
D:GLU266
|
2.9
|
57.6
|
1.0
|
FE
|
D:FE502
|
3.1
|
56.1
|
1.0
|
CD
|
D:GLU162
|
3.2
|
65.6
|
1.0
|
OE2
|
D:GLU266
|
3.3
|
52.1
|
1.0
|
ND1
|
D:HIS165
|
3.4
|
49.6
|
1.0
|
OE2
|
D:GLU162
|
3.8
|
54.6
|
1.0
|
CB
|
D:ALA126
|
3.9
|
73.5
|
1.0
|
CE1
|
D:HIS165
|
3.9
|
51.1
|
1.0
|
OH
|
D:TYR220
|
4.1
|
82.3
|
1.0
|
CAE
|
D:6Y0503
|
4.2
|
98.8
|
1.0
|
CG
|
D:GLU123
|
4.2
|
61.9
|
1.0
|
CAQ
|
D:6Y0503
|
4.2
|
0.0
|
1.0
|
CG
|
D:GLU266
|
4.3
|
56.6
|
1.0
|
CG
|
D:GLU162
|
4.4
|
64.5
|
1.0
|
CE2
|
D:TYR220
|
4.5
|
81.2
|
1.0
|
CG
|
D:HIS165
|
4.6
|
52.3
|
1.0
|
CB
|
D:GLU162
|
4.6
|
61.6
|
1.0
|
CZ
|
D:TYR220
|
4.8
|
84.2
|
1.0
|
OAK
|
D:6Y0503
|
4.8
|
99.2
|
1.0
|
CA
|
D:GLU123
|
4.8
|
70.8
|
1.0
|
CB
|
D:GLU123
|
4.9
|
67.2
|
1.0
|
CA
|
D:GLU162
|
4.9
|
62.6
|
1.0
|
|
Iron binding site 8 out
of 8 in 5gn9
Go back to
Iron Binding Sites List in 5gn9
Iron binding site 8 out
of 8 in the Crystal Structure of Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B
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 Alternative Oxidase From Trypanosoma Brucei Brucei Complexed with Cumarin Derivative-17B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe502
b:56.1
occ:1.00
|
OAC
|
D:6Y0503
|
2.0
|
62.7
|
1.0
|
OE2
|
D:GLU266
|
2.0
|
52.1
|
1.0
|
OE2
|
D:GLU162
|
2.3
|
54.6
|
1.0
|
OE1
|
D:GLU213
|
2.3
|
41.9
|
1.0
|
OE2
|
D:GLU213
|
2.4
|
55.4
|
1.0
|
CD
|
D:GLU213
|
2.7
|
50.0
|
1.0
|
CD
|
D:GLU266
|
2.9
|
57.6
|
1.0
|
CD
|
D:GLU162
|
2.9
|
65.6
|
1.0
|
CAL
|
D:6Y0503
|
3.0
|
84.3
|
1.0
|
OE1
|
D:GLU162
|
3.1
|
70.4
|
1.0
|
FE
|
D:FE501
|
3.1
|
66.5
|
1.0
|
OE1
|
D:GLU266
|
3.1
|
60.0
|
1.0
|
CAE
|
D:6Y0503
|
3.5
|
98.8
|
1.0
|
CB
|
D:ALA126
|
4.0
|
73.5
|
1.0
|
CAN
|
D:6Y0503
|
4.1
|
92.5
|
1.0
|
CG
|
D:GLU213
|
4.2
|
56.0
|
1.0
|
CG
|
D:GLU162
|
4.2
|
64.5
|
1.0
|
CG
|
D:GLU266
|
4.3
|
56.6
|
1.0
|
ND1
|
D:HIS269
|
4.4
|
55.1
|
1.0
|
OAD
|
D:6Y0503
|
4.4
|
95.2
|
1.0
|
CB
|
D:ALA216
|
4.5
|
73.6
|
1.0
|
CB
|
D:GLU266
|
4.7
|
52.5
|
1.0
|
CAF
|
D:6Y0503
|
4.9
|
0.1
|
1.0
|
OE2
|
D:GLU123
|
5.0
|
55.6
|
1.0
|
|
Reference:
E.O.Balogun,
D.K.Inaoka,
T.Shiba,
T.Tsuge,
B.May,
T.Sato,
Y.Kido,
N.Takeshi,
T.Aoki,
T.Honma,
A.Tanaka,
M.Inoue,
S.Matsuoka,
P.A.M.Michels,
Y.Watanabe,
A.L.Moore,
S.Harada,
K.Kita.
Discovery of Trypanocidal Coumarins with Dual-Inhibition For African Trypanosomes Glycerol Kinase and Alternative Oxidase To Be Published.
Page generated: Tue Aug 6 01:33:56 2024
|