Iron in PDB 5da5: Crystal Structure of Rhodospirillum Rubrum RRU_A0973
Protein crystallography data
The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973, PDB code: 5da5
was solved by
D.He,
S.Vanden Hehier,
A.Georgiev,
K.Altenbach,
E.Tarrant,
C.L.Mackay,
K.J.Waldron,
D.J.Clarke,
J.Marles-Wright,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.63 /
2.06
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.184,
120.533,
140.250,
90.00,
95.36,
90.00
|
R / Rfree (%)
|
17.1 /
20.6
|
Other elements in 5da5:
The structure of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Binding sites:
The binding sites of Iron atom in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
(pdb code 5da5). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 30 binding sites of Iron where determined in the
Crystal Structure of Rhodospirillum Rubrum RRU_A0973, PDB code: 5da5:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 1 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:23.3
occ:1.00
|
OE2
|
J:GLU62
|
2.2
|
32.3
|
1.0
|
OE1
|
A:GLU62
|
2.4
|
21.4
|
1.0
|
OE1
|
A:GLU32
|
2.4
|
20.9
|
1.0
|
OE2
|
A:GLU32
|
2.5
|
24.1
|
1.0
|
O12
|
A:GOA202
|
2.6
|
28.9
|
1.0
|
ND1
|
A:HIS65
|
2.6
|
25.0
|
1.0
|
OE1
|
J:GLU62
|
2.6
|
20.9
|
1.0
|
CD
|
A:GLU32
|
2.8
|
24.7
|
1.0
|
CD
|
J:GLU62
|
2.8
|
31.0
|
1.0
|
CE1
|
A:HIS65
|
3.4
|
23.6
|
1.0
|
HE1
|
A:HIS65
|
3.4
|
28.3
|
1.0
|
HA
|
A:GLU62
|
3.5
|
27.1
|
1.0
|
CD
|
A:GLU62
|
3.5
|
26.3
|
1.0
|
C1
|
A:GOA202
|
3.5
|
26.7
|
1.0
|
FE
|
A:FE204
|
3.5
|
21.6
|
1.0
|
O11
|
A:GOA202
|
3.6
|
38.4
|
1.0
|
HB2
|
A:HIS65
|
3.7
|
23.6
|
1.0
|
CG
|
A:HIS65
|
3.7
|
24.4
|
1.0
|
HE2
|
J:TYR39
|
3.8
|
21.4
|
1.0
|
HB3
|
A:GLU62
|
3.8
|
28.3
|
1.0
|
HB3
|
A:HIS65
|
4.0
|
23.6
|
1.0
|
CB
|
A:HIS65
|
4.0
|
19.6
|
1.0
|
HH
|
J:TYR39
|
4.0
|
32.4
|
1.0
|
OE2
|
A:GLU62
|
4.2
|
29.7
|
1.0
|
HE1
|
J:HIS65
|
4.2
|
31.3
|
1.0
|
O
|
A:HOH301
|
4.2
|
37.1
|
1.0
|
HB3
|
J:ASN58
|
4.2
|
24.0
|
1.0
|
CA
|
A:GLU62
|
4.3
|
22.6
|
1.0
|
CG
|
A:GLU32
|
4.3
|
21.4
|
1.0
|
CG
|
J:GLU62
|
4.3
|
24.2
|
1.0
|
CB
|
A:GLU62
|
4.3
|
23.6
|
1.0
|
HA
|
A:GLU32
|
4.3
|
25.5
|
1.0
|
CG
|
A:GLU62
|
4.4
|
21.4
|
1.0
|
NE2
|
A:HIS65
|
4.6
|
28.3
|
1.0
|
HG3
|
J:GLU62
|
4.6
|
29.1
|
1.0
|
HG2
|
J:GLU62
|
4.7
|
29.1
|
1.0
|
HG2
|
A:GLU32
|
4.7
|
25.7
|
1.0
|
CE2
|
J:TYR39
|
4.7
|
17.9
|
1.0
|
HG3
|
A:GLU32
|
4.7
|
25.7
|
1.0
|
CD2
|
A:HIS65
|
4.8
|
25.7
|
1.0
|
OH
|
J:TYR39
|
4.8
|
27.0
|
1.0
|
HB1
|
J:ALA35
|
4.9
|
28.5
|
1.0
|
CE1
|
J:HIS65
|
4.9
|
26.1
|
1.0
|
C2
|
A:GOA202
|
4.9
|
35.4
|
1.0
|
HG3
|
A:GLU62
|
4.9
|
25.6
|
1.0
|
HB3
|
A:ALA35
|
5.0
|
25.8
|
1.0
|
HB3
|
A:GLU32
|
5.0
|
23.0
|
1.0
|
|
Iron binding site 2 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 2 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe204
b:21.6
occ:1.00
|
OE1
|
J:GLU62
|
2.2
|
20.9
|
1.0
|
OE2
|
A:GLU62
|
2.3
|
29.7
|
1.0
|
OE2
|
J:GLU32
|
2.4
|
22.6
|
1.0
|
OE1
|
J:GLU32
|
2.4
|
23.5
|
1.0
|
ND1
|
J:HIS65
|
2.5
|
23.7
|
1.0
|
O12
|
A:GOA202
|
2.6
|
28.9
|
1.0
|
OE1
|
A:GLU62
|
2.6
|
21.4
|
1.0
|
CD
|
J:GLU32
|
2.7
|
27.1
|
1.0
|
CD
|
A:GLU62
|
2.8
|
26.3
|
1.0
|
CE1
|
J:HIS65
|
3.3
|
26.1
|
1.0
|
HE1
|
J:HIS65
|
3.3
|
31.3
|
1.0
|
CD
|
J:GLU62
|
3.4
|
31.0
|
1.0
|
HA
|
J:GLU62
|
3.4
|
25.6
|
1.0
|
FE
|
A:FE201
|
3.5
|
23.3
|
1.0
|
O2
|
A:GOA202
|
3.6
|
44.2
|
1.0
|
CG
|
J:HIS65
|
3.6
|
23.4
|
1.0
|
C1
|
A:GOA202
|
3.6
|
26.7
|
1.0
|
HB2
|
J:HIS65
|
3.7
|
25.2
|
1.0
|
HE2
|
A:TYR39
|
3.7
|
27.8
|
1.0
|
HB3
|
J:GLU62
|
3.8
|
26.3
|
1.0
|
HH
|
A:TYR39
|
4.0
|
30.9
|
1.0
|
CB
|
J:HIS65
|
4.0
|
21.0
|
1.0
|
HB3
|
J:HIS65
|
4.0
|
25.2
|
1.0
|
C2
|
A:GOA202
|
4.1
|
35.4
|
1.0
|
OE2
|
J:GLU62
|
4.1
|
32.3
|
1.0
|
CG
|
J:GLU32
|
4.2
|
19.8
|
1.0
|
CA
|
J:GLU62
|
4.3
|
21.4
|
1.0
|
H21
|
A:GOA202
|
4.3
|
42.5
|
1.0
|
HA
|
J:GLU32
|
4.3
|
26.4
|
1.0
|
HB3
|
A:ASN58
|
4.3
|
27.2
|
1.0
|
CB
|
J:GLU62
|
4.3
|
21.9
|
1.0
|
H2
|
A:GOA202
|
4.3
|
53.0
|
1.0
|
HE1
|
A:HIS65
|
4.4
|
28.3
|
1.0
|
CG
|
A:GLU62
|
4.4
|
21.4
|
1.0
|
CG
|
J:GLU62
|
4.4
|
24.2
|
1.0
|
NE2
|
J:HIS65
|
4.5
|
24.5
|
1.0
|
HG2
|
J:GLU32
|
4.6
|
23.8
|
1.0
|
CE2
|
A:TYR39
|
4.6
|
23.1
|
1.0
|
HG3
|
J:GLU32
|
4.6
|
23.8
|
1.0
|
HG3
|
A:GLU62
|
4.7
|
25.6
|
1.0
|
O11
|
A:GOA202
|
4.7
|
38.4
|
1.0
|
CD2
|
J:HIS65
|
4.7
|
27.4
|
1.0
|
HG2
|
A:GLU62
|
4.7
|
25.6
|
1.0
|
HB1
|
A:ALA35
|
4.7
|
25.8
|
1.0
|
OH
|
A:TYR39
|
4.8
|
25.7
|
1.0
|
HG3
|
J:GLU62
|
4.9
|
29.1
|
1.0
|
HB3
|
J:GLU32
|
4.9
|
26.3
|
1.0
|
CE1
|
A:HIS65
|
5.0
|
23.6
|
1.0
|
H22
|
A:GOA202
|
5.0
|
42.5
|
1.0
|
|
Iron binding site 3 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 3 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:21.8
occ:1.00
|
OE2
|
C:GLU62
|
2.2
|
31.9
|
1.0
|
OE1
|
B:GLU62
|
2.3
|
21.8
|
1.0
|
OE1
|
B:GLU32
|
2.4
|
24.0
|
1.0
|
OE2
|
B:GLU32
|
2.4
|
22.4
|
1.0
|
O11
|
B:GOA204
|
2.5
|
28.7
|
1.0
|
ND1
|
B:HIS65
|
2.6
|
20.4
|
1.0
|
CD
|
B:GLU32
|
2.7
|
20.8
|
1.0
|
OE1
|
C:GLU62
|
2.7
|
23.4
|
1.0
|
CD
|
C:GLU62
|
2.8
|
26.2
|
1.0
|
C1
|
B:GOA204
|
3.4
|
33.0
|
1.0
|
HA
|
B:GLU62
|
3.4
|
22.8
|
1.0
|
CE1
|
B:HIS65
|
3.4
|
22.9
|
1.0
|
HE1
|
B:HIS65
|
3.4
|
27.5
|
1.0
|
CD
|
B:GLU62
|
3.4
|
24.8
|
1.0
|
O12
|
B:GOA204
|
3.5
|
40.9
|
1.0
|
FE
|
B:FE203
|
3.5
|
20.8
|
1.0
|
HB2
|
B:HIS65
|
3.7
|
21.3
|
1.0
|
CG
|
B:HIS65
|
3.7
|
21.7
|
1.0
|
HE2
|
C:TYR39
|
3.7
|
26.5
|
1.0
|
HB3
|
B:GLU62
|
3.8
|
27.4
|
1.0
|
HH
|
C:TYR39
|
3.9
|
35.2
|
1.0
|
HB3
|
B:HIS65
|
4.1
|
21.3
|
1.0
|
CB
|
B:HIS65
|
4.1
|
17.7
|
1.0
|
OE2
|
B:GLU62
|
4.1
|
35.2
|
1.0
|
CG
|
B:GLU32
|
4.2
|
19.0
|
1.0
|
CA
|
B:GLU62
|
4.3
|
19.0
|
1.0
|
CG
|
C:GLU62
|
4.3
|
20.5
|
1.0
|
HA
|
B:GLU32
|
4.3
|
25.2
|
1.0
|
CB
|
B:GLU62
|
4.3
|
22.8
|
1.0
|
HB3
|
C:ASN58
|
4.3
|
25.6
|
1.0
|
HE1
|
C:HIS65
|
4.4
|
26.4
|
1.0
|
CG
|
B:GLU62
|
4.4
|
22.5
|
1.0
|
HG3
|
C:GLU62
|
4.6
|
24.6
|
1.0
|
CE2
|
C:TYR39
|
4.6
|
22.1
|
1.0
|
NE2
|
B:HIS65
|
4.6
|
22.2
|
1.0
|
HG3
|
B:GLU32
|
4.6
|
22.8
|
1.0
|
HG2
|
B:GLU32
|
4.6
|
22.8
|
1.0
|
HG2
|
C:GLU62
|
4.6
|
24.6
|
1.0
|
OH
|
C:TYR39
|
4.7
|
29.4
|
1.0
|
C2
|
B:GOA204
|
4.7
|
37.8
|
1.0
|
HB1
|
C:ALA35
|
4.8
|
25.7
|
1.0
|
CD2
|
B:HIS65
|
4.8
|
18.0
|
1.0
|
HB3
|
B:GLU32
|
4.9
|
21.4
|
1.0
|
O2
|
B:GOA204
|
4.9
|
43.5
|
1.0
|
HG3
|
B:GLU62
|
4.9
|
27.0
|
1.0
|
CE1
|
C:HIS65
|
5.0
|
22.0
|
1.0
|
|
Iron binding site 4 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 4 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe203
b:20.8
occ:1.00
|
OE1
|
C:GLU62
|
2.2
|
23.4
|
1.0
|
OE2
|
B:GLU62
|
2.3
|
35.2
|
1.0
|
OE1
|
C:GLU32
|
2.3
|
23.1
|
1.0
|
OE2
|
C:GLU32
|
2.5
|
21.1
|
1.0
|
ND1
|
C:HIS65
|
2.6
|
16.6
|
1.0
|
O11
|
B:GOA204
|
2.6
|
28.7
|
1.0
|
OE1
|
B:GLU62
|
2.6
|
21.8
|
1.0
|
CD
|
C:GLU32
|
2.7
|
23.8
|
1.0
|
CD
|
B:GLU62
|
2.8
|
24.8
|
1.0
|
O2
|
B:GOA204
|
3.3
|
43.5
|
1.0
|
CD
|
C:GLU62
|
3.3
|
26.2
|
1.0
|
CE1
|
C:HIS65
|
3.4
|
22.0
|
1.0
|
HA
|
C:GLU62
|
3.4
|
23.2
|
1.0
|
HE1
|
C:HIS65
|
3.4
|
26.4
|
1.0
|
FE
|
B:FE201
|
3.5
|
21.8
|
1.0
|
HB2
|
C:HIS65
|
3.7
|
28.3
|
1.0
|
CG
|
C:HIS65
|
3.7
|
18.7
|
1.0
|
HE2
|
B:TYR39
|
3.7
|
26.0
|
1.0
|
C1
|
B:GOA204
|
3.7
|
33.0
|
1.0
|
HB3
|
C:GLU62
|
3.8
|
29.6
|
1.0
|
H2
|
B:GOA204
|
3.9
|
52.2
|
1.0
|
HB3
|
C:HIS65
|
4.0
|
28.3
|
1.0
|
CB
|
C:HIS65
|
4.0
|
23.6
|
1.0
|
HH
|
B:TYR39
|
4.0
|
26.7
|
1.0
|
OE2
|
C:GLU62
|
4.1
|
31.9
|
1.0
|
C2
|
B:GOA204
|
4.1
|
37.8
|
1.0
|
CA
|
C:GLU62
|
4.2
|
19.4
|
1.0
|
CG
|
C:GLU32
|
4.2
|
19.4
|
1.0
|
CB
|
C:GLU62
|
4.3
|
24.7
|
1.0
|
HE1
|
B:HIS65
|
4.3
|
27.5
|
1.0
|
HA
|
C:GLU32
|
4.3
|
21.1
|
1.0
|
CG
|
B:GLU62
|
4.3
|
22.5
|
1.0
|
HB3
|
B:ASN58
|
4.3
|
31.1
|
1.0
|
CG
|
C:GLU62
|
4.4
|
20.5
|
1.0
|
H21
|
B:GOA204
|
4.4
|
45.3
|
1.0
|
CE2
|
B:TYR39
|
4.6
|
21.6
|
1.0
|
NE2
|
C:HIS65
|
4.6
|
20.2
|
1.0
|
HG3
|
C:GLU32
|
4.6
|
23.3
|
1.0
|
HG2
|
C:GLU32
|
4.7
|
23.3
|
1.0
|
HG3
|
B:GLU62
|
4.7
|
27.0
|
1.0
|
HG2
|
B:GLU62
|
4.7
|
27.0
|
1.0
|
CD2
|
C:HIS65
|
4.7
|
22.2
|
1.0
|
O12
|
B:GOA204
|
4.8
|
40.9
|
1.0
|
HB1
|
B:ALA35
|
4.8
|
21.9
|
1.0
|
OH
|
B:TYR39
|
4.8
|
22.3
|
1.0
|
HG3
|
C:GLU62
|
4.8
|
24.6
|
1.0
|
HB3
|
C:GLU32
|
4.9
|
23.7
|
1.0
|
H22
|
B:GOA204
|
4.9
|
45.3
|
1.0
|
CE1
|
B:HIS65
|
4.9
|
22.9
|
1.0
|
CB
|
C:GLU32
|
5.0
|
19.7
|
1.0
|
HB3
|
C:ALA35
|
5.0
|
25.7
|
1.0
|
|
Iron binding site 5 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 5 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:20.0
occ:1.00
|
OE1
|
D:GLU62
|
2.3
|
17.6
|
1.0
|
OE1
|
D:GLU32
|
2.3
|
23.4
|
1.0
|
OE2
|
E:GLU62
|
2.3
|
32.2
|
1.0
|
OE2
|
D:GLU32
|
2.4
|
21.1
|
1.0
|
ND1
|
D:HIS65
|
2.5
|
23.4
|
1.0
|
O11
|
D:GOA202
|
2.7
|
30.9
|
1.0
|
CD
|
D:GLU32
|
2.7
|
19.9
|
1.0
|
OE1
|
E:GLU62
|
2.8
|
22.3
|
1.0
|
CD
|
E:GLU62
|
2.9
|
28.9
|
1.0
|
O2
|
D:GOA202
|
3.2
|
41.7
|
1.0
|
CE1
|
D:HIS65
|
3.3
|
26.3
|
1.0
|
HE1
|
D:HIS65
|
3.4
|
31.5
|
1.0
|
CD
|
D:GLU62
|
3.4
|
21.8
|
1.0
|
HA
|
D:GLU62
|
3.4
|
26.2
|
1.0
|
FE
|
D:FE205
|
3.5
|
20.6
|
1.0
|
C1
|
D:GOA202
|
3.6
|
30.6
|
1.0
|
CG
|
D:HIS65
|
3.6
|
21.6
|
1.0
|
HB2
|
D:HIS65
|
3.7
|
24.0
|
1.0
|
HE2
|
E:TYR39
|
3.7
|
23.8
|
1.0
|
H2
|
D:GOA202
|
3.8
|
50.0
|
1.0
|
C2
|
D:GOA202
|
3.8
|
34.6
|
1.0
|
HB3
|
D:GLU62
|
3.9
|
24.7
|
1.0
|
HB3
|
D:HIS65
|
4.0
|
24.0
|
1.0
|
CB
|
D:HIS65
|
4.0
|
20.0
|
1.0
|
HH
|
E:TYR39
|
4.0
|
26.9
|
1.0
|
H21
|
D:GOA202
|
4.0
|
41.5
|
1.0
|
OE2
|
D:GLU62
|
4.1
|
32.5
|
1.0
|
CG
|
D:GLU32
|
4.2
|
21.8
|
1.0
|
CA
|
D:GLU62
|
4.3
|
21.9
|
1.0
|
CB
|
D:GLU62
|
4.3
|
20.6
|
1.0
|
CG
|
E:GLU62
|
4.4
|
20.4
|
1.0
|
CG
|
D:GLU62
|
4.4
|
21.9
|
1.0
|
HE1
|
E:HIS65
|
4.4
|
30.1
|
1.0
|
HA
|
D:GLU32
|
4.4
|
19.6
|
1.0
|
HB3
|
E:ASN58
|
4.4
|
30.0
|
1.0
|
NE2
|
D:HIS65
|
4.5
|
26.6
|
1.0
|
HG3
|
D:GLU32
|
4.6
|
26.1
|
1.0
|
CE2
|
E:TYR39
|
4.6
|
19.8
|
1.0
|
HG2
|
D:GLU32
|
4.7
|
26.1
|
1.0
|
HG3
|
E:GLU62
|
4.7
|
24.5
|
1.0
|
HG2
|
E:GLU62
|
4.7
|
24.5
|
1.0
|
CD2
|
D:HIS65
|
4.7
|
22.1
|
1.0
|
H22
|
D:GOA202
|
4.7
|
41.5
|
1.0
|
O12
|
D:GOA202
|
4.8
|
32.1
|
1.0
|
HB1
|
E:ALA35
|
4.8
|
25.7
|
1.0
|
OH
|
E:TYR39
|
4.8
|
22.4
|
1.0
|
HG3
|
D:GLU62
|
4.9
|
26.2
|
1.0
|
HB3
|
D:GLU32
|
4.9
|
23.9
|
1.0
|
CE1
|
E:HIS65
|
5.0
|
25.1
|
1.0
|
ND1
|
E:HIS65
|
5.0
|
18.9
|
1.0
|
|
Iron binding site 6 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 6 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe205
b:20.6
occ:1.00
|
OE2
|
D:GLU62
|
2.2
|
32.5
|
1.0
|
OE1
|
E:GLU62
|
2.3
|
22.3
|
1.0
|
OE2
|
E:GLU32
|
2.4
|
20.6
|
1.0
|
OE1
|
E:GLU32
|
2.4
|
22.7
|
1.0
|
O11
|
D:GOA202
|
2.5
|
30.9
|
1.0
|
ND1
|
E:HIS65
|
2.6
|
18.9
|
1.0
|
OE1
|
D:GLU62
|
2.6
|
17.6
|
1.0
|
CD
|
E:GLU32
|
2.7
|
25.9
|
1.0
|
CD
|
D:GLU62
|
2.8
|
21.8
|
1.0
|
CD
|
E:GLU62
|
3.4
|
28.9
|
1.0
|
CE1
|
E:HIS65
|
3.5
|
25.1
|
1.0
|
HA
|
E:GLU62
|
3.5
|
24.2
|
1.0
|
HE1
|
E:HIS65
|
3.5
|
30.1
|
1.0
|
FE
|
D:FE201
|
3.5
|
20.0
|
1.0
|
HB2
|
E:HIS65
|
3.6
|
25.1
|
1.0
|
C1
|
D:GOA202
|
3.6
|
30.6
|
1.0
|
CG
|
E:HIS65
|
3.6
|
25.3
|
1.0
|
HE2
|
D:TYR39
|
3.7
|
27.8
|
1.0
|
HB3
|
E:GLU62
|
3.8
|
24.6
|
1.0
|
HB3
|
E:HIS65
|
3.8
|
25.1
|
1.0
|
CB
|
E:HIS65
|
3.9
|
20.9
|
1.0
|
O12
|
D:GOA202
|
3.9
|
32.1
|
1.0
|
HH
|
D:TYR39
|
4.0
|
25.9
|
1.0
|
OE2
|
E:GLU62
|
4.1
|
32.2
|
1.0
|
CG
|
E:GLU32
|
4.2
|
20.1
|
1.0
|
CG
|
D:GLU62
|
4.3
|
21.9
|
1.0
|
CA
|
E:GLU62
|
4.3
|
20.2
|
1.0
|
HE1
|
D:HIS65
|
4.3
|
31.5
|
1.0
|
HA
|
E:GLU32
|
4.3
|
23.6
|
1.0
|
CB
|
E:GLU62
|
4.3
|
20.5
|
1.0
|
HB3
|
D:ASN58
|
4.3
|
24.2
|
1.0
|
CG
|
E:GLU62
|
4.4
|
20.4
|
1.0
|
HG3
|
D:GLU62
|
4.6
|
26.2
|
1.0
|
HG3
|
E:GLU32
|
4.6
|
24.1
|
1.0
|
CE2
|
D:TYR39
|
4.6
|
23.2
|
1.0
|
HG2
|
E:GLU32
|
4.6
|
24.1
|
1.0
|
NE2
|
E:HIS65
|
4.6
|
20.2
|
1.0
|
HG2
|
D:GLU62
|
4.6
|
26.2
|
1.0
|
CD2
|
E:HIS65
|
4.7
|
18.4
|
1.0
|
HB1
|
D:ALA35
|
4.8
|
24.4
|
1.0
|
OH
|
D:TYR39
|
4.8
|
21.6
|
1.0
|
HB3
|
E:GLU32
|
4.9
|
25.4
|
1.0
|
C2
|
D:GOA202
|
4.9
|
34.6
|
1.0
|
HG3
|
E:GLU62
|
4.9
|
24.5
|
1.0
|
CE1
|
D:HIS65
|
4.9
|
26.3
|
1.0
|
|
Iron binding site 7 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 7 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:21.2
occ:1.00
|
OE2
|
H:GLU62
|
2.3
|
29.7
|
1.0
|
OE1
|
F:GLU32
|
2.3
|
23.1
|
1.0
|
OE1
|
F:GLU62
|
2.4
|
19.1
|
1.0
|
OE2
|
F:GLU32
|
2.4
|
20.1
|
1.0
|
O11
|
F:GOA202
|
2.4
|
30.4
|
1.0
|
ND1
|
F:HIS65
|
2.6
|
21.2
|
1.0
|
CD
|
F:GLU32
|
2.7
|
19.6
|
1.0
|
OE1
|
H:GLU62
|
2.8
|
21.4
|
1.0
|
CD
|
H:GLU62
|
2.9
|
27.6
|
1.0
|
O2
|
F:GOA202
|
3.3
|
43.2
|
1.0
|
CE1
|
F:HIS65
|
3.4
|
25.2
|
1.0
|
HE1
|
F:HIS65
|
3.4
|
30.3
|
1.0
|
HA
|
F:GLU62
|
3.4
|
22.3
|
1.0
|
CD
|
F:GLU62
|
3.5
|
24.5
|
1.0
|
C1
|
F:GOA202
|
3.5
|
30.9
|
1.0
|
FE
|
F:FE204
|
3.6
|
21.8
|
1.0
|
HE2
|
H:TYR39
|
3.6
|
24.2
|
1.0
|
HB2
|
F:HIS65
|
3.7
|
24.3
|
1.0
|
CG
|
F:HIS65
|
3.7
|
19.3
|
1.0
|
HB3
|
F:GLU62
|
3.8
|
25.1
|
1.0
|
HH
|
H:TYR39
|
3.8
|
28.6
|
1.0
|
HB3
|
F:HIS65
|
4.0
|
24.3
|
1.0
|
C2
|
F:GOA202
|
4.0
|
36.0
|
1.0
|
CB
|
F:HIS65
|
4.0
|
20.3
|
1.0
|
H2
|
F:GOA202
|
4.1
|
51.8
|
1.0
|
OE2
|
F:GLU62
|
4.2
|
30.9
|
1.0
|
CG
|
F:GLU32
|
4.2
|
17.7
|
1.0
|
HB3
|
H:ASN58
|
4.3
|
32.2
|
1.0
|
CA
|
F:GLU62
|
4.3
|
18.6
|
1.0
|
HE1
|
H:HIS65
|
4.3
|
27.0
|
1.0
|
CB
|
F:GLU62
|
4.3
|
20.9
|
1.0
|
HA
|
F:GLU32
|
4.3
|
24.4
|
1.0
|
CG
|
H:GLU62
|
4.3
|
23.6
|
1.0
|
H22
|
F:GOA202
|
4.4
|
43.1
|
1.0
|
CG
|
F:GLU62
|
4.4
|
23.7
|
1.0
|
CE2
|
H:TYR39
|
4.5
|
20.2
|
1.0
|
HG3
|
F:GLU32
|
4.6
|
21.3
|
1.0
|
O12
|
F:GOA202
|
4.6
|
48.2
|
1.0
|
NE2
|
F:HIS65
|
4.6
|
24.7
|
1.0
|
OH
|
H:TYR39
|
4.6
|
23.9
|
1.0
|
HG2
|
F:GLU32
|
4.6
|
21.3
|
1.0
|
HG3
|
H:GLU62
|
4.6
|
28.3
|
1.0
|
HG2
|
H:GLU62
|
4.7
|
28.3
|
1.0
|
HB1
|
H:ALA35
|
4.7
|
27.6
|
1.0
|
CD2
|
F:HIS65
|
4.8
|
23.2
|
1.0
|
H21
|
F:GOA202
|
4.8
|
43.1
|
1.0
|
HB3
|
F:GLU32
|
4.9
|
21.1
|
1.0
|
HG3
|
F:GLU62
|
4.9
|
28.4
|
1.0
|
HB3
|
F:ALA35
|
4.9
|
24.2
|
1.0
|
CE1
|
H:HIS65
|
4.9
|
22.5
|
1.0
|
CB
|
F:GLU32
|
5.0
|
17.5
|
1.0
|
|
Iron binding site 8 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 8 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
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 Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe204
b:21.8
occ:1.00
|
OE1
|
H:GLU62
|
2.3
|
21.4
|
1.0
|
OE2
|
F:GLU62
|
2.3
|
30.9
|
1.0
|
OE1
|
H:GLU32
|
2.3
|
26.6
|
1.0
|
ND1
|
H:HIS65
|
2.4
|
21.9
|
1.0
|
OE2
|
H:GLU32
|
2.5
|
22.6
|
1.0
|
O11
|
F:GOA202
|
2.5
|
30.4
|
1.0
|
OE1
|
F:GLU62
|
2.6
|
19.1
|
1.0
|
CD
|
H:GLU32
|
2.8
|
26.0
|
1.0
|
CD
|
F:GLU62
|
2.8
|
24.5
|
1.0
|
HE1
|
H:HIS65
|
3.2
|
27.0
|
1.0
|
CE1
|
H:HIS65
|
3.2
|
22.5
|
1.0
|
CD
|
H:GLU62
|
3.4
|
27.6
|
1.0
|
C1
|
F:GOA202
|
3.4
|
30.9
|
1.0
|
O12
|
F:GOA202
|
3.4
|
48.2
|
1.0
|
HA
|
H:GLU62
|
3.5
|
21.2
|
1.0
|
FE
|
F:FE201
|
3.6
|
21.2
|
1.0
|
CG
|
H:HIS65
|
3.6
|
24.0
|
1.0
|
HE2
|
F:TYR39
|
3.7
|
21.3
|
1.0
|
HB2
|
H:HIS65
|
3.7
|
25.8
|
1.0
|
HB3
|
H:GLU62
|
3.8
|
21.5
|
1.0
|
HH
|
F:TYR39
|
4.0
|
28.3
|
1.0
|
HB3
|
H:HIS65
|
4.0
|
25.8
|
1.0
|
CB
|
H:HIS65
|
4.0
|
21.5
|
1.0
|
OE2
|
H:GLU62
|
4.1
|
29.7
|
1.0
|
HB3
|
F:ASN58
|
4.2
|
20.1
|
1.0
|
CG
|
H:GLU32
|
4.2
|
22.4
|
1.0
|
HE1
|
F:HIS65
|
4.3
|
30.3
|
1.0
|
CA
|
H:GLU62
|
4.3
|
17.7
|
1.0
|
CG
|
F:GLU62
|
4.3
|
23.7
|
1.0
|
HA
|
H:GLU32
|
4.3
|
21.5
|
1.0
|
CB
|
H:GLU62
|
4.3
|
17.9
|
1.0
|
CG
|
H:GLU62
|
4.4
|
23.6
|
1.0
|
NE2
|
H:HIS65
|
4.4
|
21.9
|
1.0
|
CE2
|
F:TYR39
|
4.6
|
17.7
|
1.0
|
HG3
|
H:GLU32
|
4.6
|
26.8
|
1.0
|
HG3
|
F:GLU62
|
4.6
|
28.4
|
1.0
|
CD2
|
H:HIS65
|
4.6
|
19.3
|
1.0
|
HG2
|
F:GLU62
|
4.7
|
28.4
|
1.0
|
HG2
|
H:GLU32
|
4.7
|
26.8
|
1.0
|
HB1
|
F:ALA35
|
4.7
|
24.2
|
1.0
|
OH
|
F:TYR39
|
4.8
|
23.6
|
1.0
|
C2
|
F:GOA202
|
4.8
|
36.0
|
1.0
|
HB3
|
H:GLU32
|
4.8
|
24.4
|
1.0
|
HG3
|
H:GLU62
|
4.9
|
28.3
|
1.0
|
CE1
|
F:HIS65
|
4.9
|
25.2
|
1.0
|
CB
|
H:GLU32
|
5.0
|
20.3
|
1.0
|
|
Iron binding site 9 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 9 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:23.1
occ:1.00
|
OE2
|
I:GLU62
|
2.3
|
38.2
|
1.0
|
OE1
|
G:GLU32
|
2.3
|
25.3
|
1.0
|
OE1
|
G:GLU62
|
2.3
|
22.9
|
1.0
|
O12
|
G:GOA202
|
2.4
|
31.6
|
1.0
|
OE2
|
G:GLU32
|
2.5
|
24.9
|
1.0
|
ND1
|
G:HIS65
|
2.5
|
21.3
|
1.0
|
OE1
|
I:GLU62
|
2.6
|
23.3
|
1.0
|
CD
|
G:GLU32
|
2.7
|
22.4
|
1.0
|
CD
|
I:GLU62
|
2.8
|
30.6
|
1.0
|
HE1
|
G:HIS65
|
3.2
|
29.5
|
1.0
|
CE1
|
G:HIS65
|
3.3
|
24.6
|
1.0
|
CD
|
G:GLU62
|
3.4
|
29.1
|
1.0
|
HA
|
G:GLU62
|
3.5
|
24.4
|
1.0
|
FE
|
G:FE204
|
3.6
|
20.8
|
1.0
|
C1
|
G:GOA202
|
3.6
|
30.5
|
1.0
|
CG
|
G:HIS65
|
3.6
|
23.3
|
1.0
|
HB2
|
G:HIS65
|
3.7
|
22.7
|
1.0
|
O2
|
G:GOA202
|
3.7
|
49.1
|
1.0
|
HE2
|
I:TYR39
|
3.8
|
23.9
|
1.0
|
HB3
|
G:GLU62
|
3.9
|
25.2
|
1.0
|
HH
|
I:TYR39
|
4.0
|
25.7
|
1.0
|
HB3
|
G:HIS65
|
4.0
|
22.7
|
1.0
|
CB
|
G:HIS65
|
4.0
|
18.9
|
1.0
|
OE2
|
G:GLU62
|
4.1
|
30.6
|
1.0
|
C2
|
G:GOA202
|
4.2
|
36.5
|
1.0
|
CG
|
G:GLU32
|
4.2
|
23.2
|
1.0
|
HB3
|
I:ASN58
|
4.3
|
26.1
|
1.0
|
HA
|
G:GLU32
|
4.3
|
20.9
|
1.0
|
CA
|
G:GLU62
|
4.3
|
20.3
|
1.0
|
CG
|
I:GLU62
|
4.4
|
26.9
|
1.0
|
CB
|
G:GLU62
|
4.4
|
21.0
|
1.0
|
HE1
|
I:HIS65
|
4.4
|
24.7
|
1.0
|
CG
|
G:GLU62
|
4.5
|
24.6
|
1.0
|
NE2
|
G:HIS65
|
4.5
|
21.7
|
1.0
|
H2
|
G:GOA202
|
4.5
|
58.9
|
1.0
|
H22
|
G:GOA202
|
4.5
|
43.8
|
1.0
|
HG3
|
G:GLU32
|
4.6
|
27.8
|
1.0
|
O11
|
G:GOA202
|
4.6
|
44.2
|
1.0
|
HG3
|
I:GLU62
|
4.6
|
32.2
|
1.0
|
CE2
|
I:TYR39
|
4.6
|
19.9
|
1.0
|
HG2
|
G:GLU32
|
4.7
|
27.8
|
1.0
|
CD2
|
G:HIS65
|
4.7
|
25.4
|
1.0
|
HG2
|
I:GLU62
|
4.7
|
32.2
|
1.0
|
OH
|
I:TYR39
|
4.8
|
21.4
|
1.0
|
HB1
|
I:ALA35
|
4.8
|
23.2
|
1.0
|
HB3
|
G:GLU32
|
4.9
|
18.5
|
1.0
|
HG3
|
G:GLU62
|
4.9
|
29.5
|
1.0
|
CB
|
G:GLU32
|
5.0
|
15.4
|
1.0
|
|
Iron binding site 10 out
of 30 in 5da5
Go back to
Iron Binding Sites List in 5da5
Iron binding site 10 out
of 30 in the Crystal Structure of Rhodospirillum Rubrum RRU_A0973
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Crystal Structure of Rhodospirillum Rubrum RRU_A0973 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe204
b:20.8
occ:1.00
|
OE2
|
G:GLU62
|
2.3
|
30.6
|
1.0
|
OE1
|
I:GLU62
|
2.4
|
23.3
|
1.0
|
OE1
|
I:GLU32
|
2.4
|
25.2
|
1.0
|
OE2
|
I:GLU32
|
2.5
|
18.9
|
1.0
|
ND1
|
I:HIS65
|
2.6
|
21.5
|
1.0
|
O12
|
G:GOA202
|
2.7
|
31.6
|
1.0
|
OE1
|
G:GLU62
|
2.7
|
22.9
|
1.0
|
CD
|
I:GLU32
|
2.8
|
24.2
|
1.0
|
CD
|
G:GLU62
|
2.9
|
29.1
|
1.0
|
O11
|
G:GOA202
|
3.3
|
44.2
|
1.0
|
C1
|
G:GOA202
|
3.4
|
30.5
|
1.0
|
CD
|
I:GLU62
|
3.5
|
30.6
|
1.0
|
CE1
|
I:HIS65
|
3.5
|
20.6
|
1.0
|
HA
|
I:GLU62
|
3.5
|
24.8
|
1.0
|
HE1
|
I:HIS65
|
3.5
|
24.7
|
1.0
|
FE
|
G:FE201
|
3.6
|
23.1
|
1.0
|
HE2
|
G:TYR39
|
3.6
|
31.1
|
1.0
|
HB2
|
I:HIS65
|
3.6
|
24.5
|
1.0
|
CG
|
I:HIS65
|
3.7
|
14.1
|
1.0
|
HB3
|
I:GLU62
|
3.8
|
26.3
|
1.0
|
HH
|
G:TYR39
|
3.9
|
25.4
|
1.0
|
HB3
|
I:HIS65
|
3.9
|
24.5
|
1.0
|
CB
|
I:HIS65
|
4.0
|
20.4
|
1.0
|
OE2
|
I:GLU62
|
4.2
|
38.2
|
1.0
|
CG
|
I:GLU32
|
4.3
|
21.2
|
1.0
|
HE1
|
G:HIS65
|
4.3
|
29.5
|
1.0
|
HA
|
I:GLU32
|
4.3
|
22.7
|
1.0
|
CA
|
I:GLU62
|
4.3
|
20.7
|
1.0
|
HB3
|
G:ASN58
|
4.4
|
25.7
|
1.0
|
CB
|
I:GLU62
|
4.4
|
21.9
|
1.0
|
CG
|
G:GLU62
|
4.4
|
24.6
|
1.0
|
CG
|
I:GLU62
|
4.5
|
26.9
|
1.0
|
CE2
|
G:TYR39
|
4.5
|
25.9
|
1.0
|
HG3
|
I:GLU32
|
4.6
|
25.4
|
1.0
|
HG3
|
G:GLU62
|
4.7
|
29.5
|
1.0
|
HG2
|
I:GLU32
|
4.7
|
25.4
|
1.0
|
NE2
|
I:HIS65
|
4.7
|
23.4
|
1.0
|
OH
|
G:TYR39
|
4.7
|
21.1
|
1.0
|
HB1
|
G:ALA35
|
4.7
|
24.7
|
1.0
|
HG2
|
G:GLU62
|
4.7
|
29.5
|
1.0
|
CD2
|
I:HIS65
|
4.8
|
18.9
|
1.0
|
C2
|
G:GOA202
|
4.8
|
36.5
|
1.0
|
HG3
|
I:GLU62
|
4.9
|
32.2
|
1.0
|
HB3
|
I:GLU32
|
4.9
|
28.2
|
1.0
|
CE1
|
G:HIS65
|
5.0
|
24.6
|
1.0
|
HB3
|
I:ALA35
|
5.0
|
23.2
|
1.0
|
|
Reference:
D.He,
S.Hughes,
S.Vanden-Hehir,
A.Georgiev,
K.Altenbach,
E.J.Tarrant,
C.L.Mackay,
K.J.Waldron,
D.J.Clarke,
J.Marles-Wright.
Structural Characterization of Encapsulated Ferritin Provides Insight Into Iron Storage in Bacterial Nanocompartments. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27529188
DOI: 10.7554/ELIFE.18972
Page generated: Mon Aug 5 23:18:19 2024
|