Iron in PDB 1rgv: Crystal Structure of the Ferredoxin From Thauera Aromatica
Protein crystallography data
The structure of Crystal Structure of the Ferredoxin From Thauera Aromatica, PDB code: 1rgv
was solved by
M.Unciuleac,
M.Boll,
E.Warkentin,
U.Ermler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.86 /
2.90
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.000,
79.000,
49.300,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.7 /
21.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Ferredoxin From Thauera Aromatica
(pdb code 1rgv). 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 the Ferredoxin From Thauera Aromatica, PDB code: 1rgv:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 1 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:43.1
occ:1.00
|
FE1
|
A:SF4101
|
0.0
|
43.1
|
1.0
|
S2
|
A:SF4101
|
2.2
|
43.6
|
1.0
|
S4
|
A:SF4101
|
2.3
|
43.0
|
1.0
|
S3
|
A:SF4101
|
2.4
|
43.2
|
1.0
|
SG
|
A:CYS53
|
2.5
|
43.1
|
1.0
|
FE3
|
A:SF4101
|
2.7
|
43.3
|
1.0
|
FE4
|
A:SF4101
|
2.7
|
44.8
|
1.0
|
FE2
|
A:SF4101
|
2.8
|
42.7
|
1.0
|
CB
|
A:CYS53
|
3.2
|
41.3
|
1.0
|
SG
|
A:CYS57
|
3.6
|
39.0
|
1.0
|
CA
|
A:CYS53
|
3.8
|
40.8
|
1.0
|
S1
|
A:SF4101
|
3.9
|
42.9
|
1.0
|
CD
|
A:PRO54
|
4.1
|
41.0
|
1.0
|
C
|
A:CYS53
|
4.4
|
40.7
|
1.0
|
N
|
A:PRO54
|
4.4
|
41.2
|
1.0
|
N
|
A:ALA55
|
4.6
|
43.1
|
1.0
|
CD1
|
A:ILE58
|
4.6
|
39.9
|
1.0
|
SG
|
A:CYS11
|
4.7
|
39.6
|
1.0
|
CB
|
A:ALA55
|
4.7
|
44.0
|
1.0
|
CG1
|
A:ILE58
|
4.9
|
38.7
|
1.0
|
CG
|
A:PRO54
|
4.9
|
40.6
|
1.0
|
N
|
A:CYS53
|
5.0
|
39.6
|
1.0
|
|
Iron binding site 2 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 2 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:42.7
occ:1.00
|
FE2
|
A:SF4101
|
0.0
|
42.7
|
1.0
|
S3
|
A:SF4101
|
2.2
|
43.2
|
1.0
|
S1
|
A:SF4101
|
2.2
|
42.9
|
1.0
|
S4
|
A:SF4101
|
2.3
|
43.0
|
1.0
|
SG
|
A:CYS14
|
2.5
|
37.0
|
1.0
|
FE4
|
A:SF4101
|
2.7
|
44.8
|
1.0
|
FE3
|
A:SF4101
|
2.7
|
43.3
|
1.0
|
FE1
|
A:SF4101
|
2.8
|
43.1
|
1.0
|
CB
|
A:CYS14
|
3.3
|
41.4
|
1.0
|
S2
|
A:SF4101
|
3.7
|
43.6
|
1.0
|
N
|
A:CYS14
|
4.1
|
42.2
|
1.0
|
CA
|
A:CYS14
|
4.4
|
41.8
|
1.0
|
SG
|
A:CYS11
|
4.8
|
39.6
|
1.0
|
SG
|
A:CYS8
|
4.8
|
43.8
|
1.0
|
CD2
|
A:TYR30
|
4.8
|
37.0
|
1.0
|
N
|
A:ASP12
|
4.9
|
44.0
|
1.0
|
N
|
A:ALA13
|
4.9
|
43.2
|
1.0
|
CD1
|
A:ILE4
|
5.0
|
28.8
|
1.0
|
|
Iron binding site 3 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 3 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:43.3
occ:1.00
|
FE3
|
A:SF4101
|
0.0
|
43.3
|
1.0
|
S2
|
A:SF4101
|
2.1
|
43.6
|
1.0
|
S4
|
A:SF4101
|
2.1
|
43.0
|
1.0
|
S1
|
A:SF4101
|
2.3
|
42.9
|
1.0
|
SG
|
A:CYS8
|
2.5
|
43.8
|
1.0
|
FE1
|
A:SF4101
|
2.7
|
43.1
|
1.0
|
FE2
|
A:SF4101
|
2.7
|
42.7
|
1.0
|
FE4
|
A:SF4101
|
2.8
|
44.8
|
1.0
|
CB
|
A:CYS8
|
3.4
|
45.4
|
1.0
|
CA
|
A:CYS8
|
3.7
|
45.4
|
1.0
|
SG
|
A:CYS57
|
3.8
|
39.0
|
1.0
|
S3
|
A:SF4101
|
3.8
|
43.2
|
1.0
|
N
|
A:THR9
|
3.9
|
44.8
|
1.0
|
N
|
A:ALA10
|
4.0
|
42.7
|
1.0
|
C
|
A:CYS8
|
4.3
|
45.0
|
1.0
|
CG2
|
A:ILE4
|
4.5
|
33.8
|
1.0
|
CA
|
A:ALA10
|
4.6
|
41.7
|
1.0
|
N
|
A:CYS11
|
4.9
|
42.0
|
1.0
|
CB
|
A:TYR30
|
4.9
|
37.4
|
1.0
|
SG
|
A:CYS53
|
4.9
|
43.1
|
1.0
|
|
Iron binding site 4 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 4 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe101
b:44.8
occ:1.00
|
FE4
|
A:SF4101
|
0.0
|
44.8
|
1.0
|
S2
|
A:SF4101
|
2.1
|
43.6
|
1.0
|
S3
|
A:SF4101
|
2.2
|
43.2
|
1.0
|
S1
|
A:SF4101
|
2.4
|
42.9
|
1.0
|
SG
|
A:CYS11
|
2.5
|
39.6
|
1.0
|
FE2
|
A:SF4101
|
2.7
|
42.7
|
1.0
|
FE1
|
A:SF4101
|
2.7
|
43.1
|
1.0
|
FE3
|
A:SF4101
|
2.8
|
43.3
|
1.0
|
N
|
A:CYS11
|
3.4
|
42.0
|
1.0
|
CB
|
A:CYS11
|
3.7
|
41.1
|
1.0
|
S4
|
A:SF4101
|
3.8
|
43.0
|
1.0
|
N
|
A:ASP12
|
3.9
|
44.0
|
1.0
|
CA
|
A:CYS11
|
3.9
|
42.0
|
1.0
|
C
|
A:CYS11
|
4.2
|
43.0
|
1.0
|
CD
|
A:PRO54
|
4.3
|
41.0
|
1.0
|
N
|
A:ALA10
|
4.3
|
42.7
|
1.0
|
N
|
A:ALA13
|
4.4
|
43.2
|
1.0
|
C
|
A:ALA10
|
4.4
|
41.6
|
1.0
|
CA
|
A:ALA10
|
4.6
|
41.7
|
1.0
|
CG
|
A:PRO54
|
4.7
|
40.6
|
1.0
|
SG
|
A:CYS8
|
4.8
|
43.8
|
1.0
|
CA
|
A:ASP12
|
4.8
|
45.0
|
1.0
|
N
|
A:THR9
|
4.9
|
44.8
|
1.0
|
CB
|
A:ALA13
|
4.9
|
41.6
|
1.0
|
SG
|
A:CYS14
|
4.9
|
37.0
|
1.0
|
C
|
A:ASP12
|
5.0
|
44.6
|
1.0
|
N
|
A:CYS14
|
5.0
|
42.2
|
1.0
|
|
Iron binding site 5 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 5 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe102
b:38.5
occ:1.00
|
FE1
|
A:SF4102
|
0.0
|
38.5
|
1.0
|
S2
|
A:SF4102
|
2.2
|
38.6
|
1.0
|
S4
|
A:SF4102
|
2.3
|
37.4
|
1.0
|
S3
|
A:SF4102
|
2.4
|
37.1
|
1.0
|
SG
|
A:CYS18
|
2.4
|
47.7
|
1.0
|
FE3
|
A:SF4102
|
2.7
|
38.5
|
1.0
|
FE4
|
A:SF4102
|
2.7
|
38.8
|
1.0
|
FE2
|
A:SF4102
|
2.8
|
38.5
|
1.0
|
CB
|
A:CYS18
|
3.3
|
45.2
|
1.0
|
CA
|
A:CYS18
|
3.8
|
43.9
|
1.0
|
S1
|
A:SF4102
|
3.9
|
37.0
|
1.0
|
CD
|
A:PRO19
|
4.0
|
43.5
|
1.0
|
CB
|
A:ALA22
|
4.1
|
43.2
|
1.0
|
C
|
A:CYS18
|
4.5
|
43.3
|
1.0
|
N
|
A:PRO19
|
4.5
|
43.4
|
1.0
|
N
|
A:ASN20
|
4.8
|
45.8
|
1.0
|
N
|
A:ALA22
|
4.8
|
44.4
|
1.0
|
CG
|
A:PRO19
|
4.8
|
42.8
|
1.0
|
N
|
A:CYS18
|
4.9
|
43.5
|
1.0
|
SG
|
A:CYS40
|
4.9
|
48.3
|
1.0
|
CB
|
A:ASN20
|
5.0
|
45.5
|
1.0
|
CG1
|
A:ILE23
|
5.0
|
38.2
|
1.0
|
|
Iron binding site 6 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 6 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe102
b:38.5
occ:1.00
|
FE2
|
A:SF4102
|
0.0
|
38.5
|
1.0
|
S3
|
A:SF4102
|
2.2
|
37.1
|
1.0
|
S1
|
A:SF4102
|
2.3
|
37.0
|
1.0
|
S4
|
A:SF4102
|
2.3
|
37.4
|
1.0
|
SG
|
A:CYS49
|
2.6
|
33.0
|
1.0
|
FE4
|
A:SF4102
|
2.7
|
38.8
|
1.0
|
FE3
|
A:SF4102
|
2.7
|
38.5
|
1.0
|
FE1
|
A:SF4102
|
2.8
|
38.5
|
1.0
|
CB
|
A:CYS49
|
3.3
|
34.1
|
1.0
|
S2
|
A:SF4102
|
3.7
|
38.6
|
1.0
|
N
|
A:CYS49
|
4.0
|
34.6
|
1.0
|
CA
|
A:CYS49
|
4.3
|
34.5
|
1.0
|
CD1
|
A:ILE23
|
4.6
|
37.5
|
1.0
|
SG
|
A:CYS40
|
4.7
|
48.3
|
1.0
|
CB
|
A:PRO47
|
4.7
|
37.6
|
1.0
|
N
|
A:GLN48
|
4.9
|
35.1
|
1.0
|
SG
|
A:CYS37
|
4.9
|
37.2
|
1.0
|
SG
|
A:CYS18
|
4.9
|
47.7
|
1.0
|
CB
|
A:CYS18
|
4.9
|
45.2
|
1.0
|
CD1
|
A:LEU2
|
4.9
|
32.0
|
1.0
|
|
Iron binding site 7 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 7 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe102
b:38.5
occ:1.00
|
FE3
|
A:SF4102
|
0.0
|
38.5
|
1.0
|
S2
|
A:SF4102
|
2.1
|
38.6
|
1.0
|
S4
|
A:SF4102
|
2.1
|
37.4
|
1.0
|
S1
|
A:SF4102
|
2.3
|
37.0
|
1.0
|
SG
|
A:CYS37
|
2.5
|
37.2
|
1.0
|
FE1
|
A:SF4102
|
2.7
|
38.5
|
1.0
|
FE2
|
A:SF4102
|
2.7
|
38.5
|
1.0
|
FE4
|
A:SF4102
|
2.8
|
38.8
|
1.0
|
CB
|
A:CYS37
|
3.4
|
42.2
|
1.0
|
CA
|
A:CYS37
|
3.8
|
42.9
|
1.0
|
S3
|
A:SF4102
|
3.8
|
37.1
|
1.0
|
N
|
A:GLU39
|
3.9
|
48.2
|
1.0
|
CA
|
A:GLU39
|
4.1
|
48.9
|
1.0
|
N
|
A:SER38
|
4.3
|
45.2
|
1.0
|
C
|
A:CYS37
|
4.3
|
43.8
|
1.0
|
N
|
A:CYS40
|
4.5
|
48.8
|
1.0
|
C
|
A:GLU39
|
4.7
|
49.1
|
1.0
|
CB
|
A:ALA22
|
4.8
|
43.2
|
1.0
|
SG
|
A:CYS18
|
5.0
|
47.7
|
1.0
|
|
Iron binding site 8 out
of 8 in 1rgv
Go back to
Iron Binding Sites List in 1rgv
Iron binding site 8 out
of 8 in the Crystal Structure of the Ferredoxin From Thauera Aromatica
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 the Ferredoxin From Thauera Aromatica within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe102
b:38.8
occ:1.00
|
FE4
|
A:SF4102
|
0.0
|
38.8
|
1.0
|
S2
|
A:SF4102
|
2.1
|
38.6
|
1.0
|
S3
|
A:SF4102
|
2.2
|
37.1
|
1.0
|
S1
|
A:SF4102
|
2.4
|
37.0
|
1.0
|
SG
|
A:CYS40
|
2.5
|
48.3
|
1.0
|
FE2
|
A:SF4102
|
2.7
|
38.5
|
1.0
|
FE1
|
A:SF4102
|
2.7
|
38.5
|
1.0
|
FE3
|
A:SF4102
|
2.8
|
38.5
|
1.0
|
N
|
A:CYS40
|
3.3
|
48.8
|
1.0
|
CB
|
A:CYS40
|
3.5
|
48.7
|
1.0
|
CA
|
A:CYS40
|
3.7
|
48.7
|
1.0
|
S4
|
A:SF4102
|
3.8
|
37.4
|
1.0
|
C
|
A:GLU39
|
3.9
|
49.1
|
1.0
|
CD
|
A:PRO19
|
4.1
|
43.5
|
1.0
|
CA
|
A:GLU39
|
4.3
|
48.9
|
1.0
|
N
|
A:GLN48
|
4.4
|
35.1
|
1.0
|
CA
|
A:PRO47
|
4.4
|
38.4
|
1.0
|
N
|
A:GLU39
|
4.5
|
48.2
|
1.0
|
CB
|
A:PRO47
|
4.6
|
37.6
|
1.0
|
CG
|
A:PRO19
|
4.6
|
42.8
|
1.0
|
O
|
A:GLU39
|
4.7
|
49.9
|
1.0
|
C
|
A:PRO47
|
4.9
|
36.9
|
1.0
|
SG
|
A:CYS18
|
4.9
|
47.7
|
1.0
|
SG
|
A:CYS49
|
4.9
|
33.0
|
1.0
|
|
Reference:
M.Unciuleac,
M.Boll,
E.Warkentin,
U.Ermler.
Crystallization of 4-Hydroxybenzoyl-Coa Reductase and the Structure of Its Electron Donor Ferredoxin. Acta Crystallogr.,Sect.D V. 60 388 2004.
ISSN: ISSN 0907-4449
PubMed: 14747735
DOI: 10.1107/S0907444903028506
Page generated: Sat Aug 3 14:15:50 2024
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