Iron in PDB 1g3o: Crystal Structure of V19E Mutant of Ferredoxin I
Protein crystallography data
The structure of Crystal Structure of V19E Mutant of Ferredoxin I, PDB code: 1g3o
was solved by
C.D.Stout,
B.K.Burgess,
C.A.Bonagura,
Y.S.Jung,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.65
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.930,
54.930,
92.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.9 /
26.5
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of V19E Mutant of Ferredoxin I
(pdb code 1g3o). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 7 binding sites of Iron where determined in the
Crystal Structure of V19E Mutant of Ferredoxin I, PDB code: 1g3o:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
Iron binding site 1 out
of 7 in 1g3o
Go back to
Iron Binding Sites List in 1g3o
Iron binding site 1 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe107
b:18.9
occ:1.00
|
FE1
|
A:SF4107
|
0.0
|
18.9
|
1.0
|
S2
|
A:SF4107
|
2.2
|
18.8
|
1.0
|
S3
|
A:SF4107
|
2.3
|
18.6
|
1.0
|
S4
|
A:SF4107
|
2.3
|
18.6
|
1.0
|
SG
|
A:CYS39
|
2.4
|
19.0
|
1.0
|
FE2
|
A:SF4107
|
2.7
|
18.9
|
1.0
|
FE4
|
A:SF4107
|
2.7
|
19.0
|
1.0
|
FE3
|
A:SF4107
|
2.8
|
18.6
|
1.0
|
CB
|
A:CYS39
|
3.3
|
19.0
|
1.0
|
CA
|
A:CYS39
|
3.6
|
19.6
|
1.0
|
S1
|
A:SF4107
|
3.9
|
18.8
|
1.0
|
SG
|
A:CYS24
|
4.0
|
19.1
|
1.0
|
N
|
A:ILE40
|
4.0
|
18.8
|
1.0
|
C
|
A:CYS39
|
4.1
|
19.5
|
1.0
|
N
|
A:ASP41
|
4.2
|
18.7
|
1.0
|
CG2
|
A:ILE34
|
4.3
|
16.0
|
1.0
|
CB
|
A:PHE2
|
4.6
|
16.6
|
1.0
|
CA
|
A:ASP41
|
4.8
|
19.1
|
1.0
|
SG
|
A:CYS45
|
4.8
|
18.4
|
1.0
|
N
|
A:CYS42
|
4.8
|
18.4
|
1.0
|
SG
|
A:CYS20
|
4.9
|
19.6
|
1.0
|
SG
|
A:CYS42
|
4.9
|
17.9
|
1.0
|
N
|
A:PHE2
|
4.9
|
16.8
|
1.0
|
N
|
A:CYS39
|
4.9
|
20.0
|
1.0
|
|
Iron binding site 2 out
of 7 in 1g3o
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Iron Binding Sites List in 1g3o
Iron binding site 2 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe107
b:18.9
occ:1.00
|
FE2
|
A:SF4107
|
0.0
|
18.9
|
1.0
|
S1
|
A:SF4107
|
2.2
|
18.8
|
1.0
|
S4
|
A:SF4107
|
2.2
|
18.6
|
1.0
|
SG
|
A:CYS42
|
2.2
|
17.9
|
1.0
|
S3
|
A:SF4107
|
2.2
|
18.6
|
1.0
|
FE3
|
A:SF4107
|
2.7
|
18.6
|
1.0
|
FE1
|
A:SF4107
|
2.7
|
18.9
|
1.0
|
FE4
|
A:SF4107
|
2.7
|
19.0
|
1.0
|
CB
|
A:CYS42
|
3.5
|
18.3
|
1.0
|
N
|
A:CYS42
|
3.6
|
18.4
|
1.0
|
S2
|
A:SF4107
|
3.9
|
18.8
|
1.0
|
CA
|
A:CYS42
|
4.0
|
18.3
|
1.0
|
N
|
A:ALA43
|
4.0
|
18.4
|
1.0
|
CD
|
A:PRO21
|
4.3
|
19.8
|
1.0
|
C
|
A:CYS42
|
4.4
|
18.5
|
1.0
|
N
|
A:LEU44
|
4.5
|
18.5
|
1.0
|
SG
|
A:CYS45
|
4.7
|
18.4
|
1.0
|
N
|
A:ASP41
|
4.7
|
18.7
|
1.0
|
C
|
A:ASP41
|
4.7
|
18.5
|
1.0
|
SG
|
A:CYS20
|
4.7
|
19.6
|
1.0
|
CG1
|
A:ILE40
|
4.8
|
17.1
|
1.0
|
SG
|
A:CYS39
|
4.8
|
19.0
|
1.0
|
N
|
A:ILE40
|
4.9
|
18.8
|
1.0
|
CA
|
A:ALA43
|
4.9
|
18.5
|
1.0
|
CA
|
A:ASP41
|
4.9
|
19.1
|
1.0
|
CA
|
A:CYS20
|
5.0
|
20.4
|
1.0
|
|
Iron binding site 3 out
of 7 in 1g3o
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Iron Binding Sites List in 1g3o
Iron binding site 3 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe107
b:18.6
occ:1.00
|
FE3
|
A:SF4107
|
0.0
|
18.6
|
1.0
|
SG
|
A:CYS45
|
2.3
|
18.4
|
1.0
|
S2
|
A:SF4107
|
2.3
|
18.8
|
1.0
|
S1
|
A:SF4107
|
2.3
|
18.8
|
1.0
|
S4
|
A:SF4107
|
2.3
|
18.6
|
1.0
|
FE2
|
A:SF4107
|
2.7
|
18.9
|
1.0
|
FE4
|
A:SF4107
|
2.7
|
19.0
|
1.0
|
FE1
|
A:SF4107
|
2.8
|
18.9
|
1.0
|
CB
|
A:CYS45
|
3.3
|
19.1
|
1.0
|
S3
|
A:SF4107
|
3.9
|
18.6
|
1.0
|
CE2
|
A:PHE25
|
4.1
|
17.7
|
1.0
|
CZ
|
A:PHE25
|
4.2
|
17.9
|
1.0
|
N
|
A:CYS45
|
4.3
|
19.7
|
1.0
|
CA
|
A:CYS45
|
4.4
|
20.0
|
1.0
|
CD1
|
A:ILE34
|
4.5
|
16.1
|
1.0
|
SG
|
A:CYS42
|
4.5
|
17.9
|
1.0
|
CB
|
A:PHE2
|
4.6
|
16.6
|
1.0
|
SG
|
A:CYS20
|
4.8
|
19.6
|
1.0
|
SG
|
A:CYS39
|
4.8
|
19.0
|
1.0
|
|
Iron binding site 4 out
of 7 in 1g3o
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Iron Binding Sites List in 1g3o
Iron binding site 4 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe107
b:19.0
occ:1.00
|
FE4
|
A:SF4107
|
0.0
|
19.0
|
1.0
|
S1
|
A:SF4107
|
2.3
|
18.8
|
1.0
|
SG
|
A:CYS20
|
2.3
|
19.6
|
1.0
|
S2
|
A:SF4107
|
2.3
|
18.8
|
1.0
|
S3
|
A:SF4107
|
2.4
|
18.6
|
1.0
|
FE2
|
A:SF4107
|
2.7
|
18.9
|
1.0
|
FE1
|
A:SF4107
|
2.7
|
18.9
|
1.0
|
FE3
|
A:SF4107
|
2.7
|
18.6
|
1.0
|
CB
|
A:CYS20
|
3.3
|
19.6
|
1.0
|
SG
|
A:CYS24
|
3.5
|
19.1
|
1.0
|
CA
|
A:CYS20
|
3.8
|
20.4
|
1.0
|
S4
|
A:SF4107
|
3.9
|
18.6
|
1.0
|
CE2
|
A:PHE25
|
4.0
|
17.7
|
1.0
|
CG2
|
A:VAL22
|
4.4
|
20.6
|
1.0
|
CD2
|
A:PHE25
|
4.5
|
17.0
|
1.0
|
CD
|
A:PRO21
|
4.5
|
19.8
|
1.0
|
SG
|
A:CYS42
|
4.6
|
17.9
|
1.0
|
C
|
A:CYS20
|
4.6
|
20.0
|
1.0
|
SG
|
A:CYS45
|
4.8
|
18.4
|
1.0
|
CZ
|
A:PHE25
|
4.8
|
17.9
|
1.0
|
N
|
A:CYS20
|
4.9
|
21.3
|
1.0
|
N
|
A:CYS24
|
4.9
|
19.2
|
1.0
|
N
|
A:PRO21
|
5.0
|
20.0
|
1.0
|
SG
|
A:CYS39
|
5.0
|
19.0
|
1.0
|
|
Iron binding site 5 out
of 7 in 1g3o
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Iron Binding Sites List in 1g3o
Iron binding site 5 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_05.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe108
b:18.9
occ:1.00
|
FE1
|
A:F3S108
|
0.0
|
18.9
|
1.0
|
SG
|
A:CYS16
|
2.2
|
17.9
|
1.0
|
S2
|
A:F3S108
|
2.3
|
18.4
|
1.0
|
S1
|
A:F3S108
|
2.3
|
18.0
|
1.0
|
S3
|
A:F3S108
|
2.3
|
18.1
|
1.0
|
FE4
|
A:F3S108
|
2.8
|
17.7
|
1.0
|
FE3
|
A:F3S108
|
2.8
|
18.2
|
1.0
|
CB
|
A:CYS16
|
3.1
|
18.8
|
1.0
|
N
|
A:THR14
|
3.9
|
16.4
|
1.0
|
CA
|
A:THR14
|
3.9
|
17.3
|
1.0
|
S4
|
A:F3S108
|
3.9
|
18.2
|
1.0
|
CD1
|
A:LEU32
|
4.1
|
17.2
|
1.0
|
N
|
A:CYS16
|
4.1
|
19.7
|
1.0
|
CA
|
A:CYS16
|
4.3
|
19.5
|
1.0
|
CG
|
A:LEU32
|
4.5
|
17.5
|
1.0
|
C
|
A:THR14
|
4.5
|
17.9
|
1.0
|
N
|
A:ASP15
|
4.6
|
18.9
|
1.0
|
SG
|
A:CYS49
|
4.7
|
18.8
|
1.0
|
CB
|
A:LEU32
|
4.7
|
15.9
|
1.0
|
CD1
|
A:ILE54
|
4.8
|
17.2
|
1.0
|
CE1
|
A:PHE25
|
4.8
|
17.9
|
1.0
|
SG
|
A:CYS8
|
4.8
|
16.8
|
1.0
|
|
Iron binding site 6 out
of 7 in 1g3o
Go back to
Iron Binding Sites List in 1g3o
Iron binding site 6 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_06.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe108
b:18.2
occ:1.00
|
FE3
|
A:F3S108
|
0.0
|
18.2
|
1.0
|
SG
|
A:CYS8
|
2.2
|
16.8
|
1.0
|
S1
|
A:F3S108
|
2.3
|
18.0
|
1.0
|
S4
|
A:F3S108
|
2.3
|
18.2
|
1.0
|
S3
|
A:F3S108
|
2.4
|
18.1
|
1.0
|
FE4
|
A:F3S108
|
2.8
|
17.7
|
1.0
|
FE1
|
A:F3S108
|
2.8
|
18.9
|
1.0
|
CB
|
A:CYS8
|
3.1
|
15.0
|
1.0
|
CA
|
A:LYS12
|
3.9
|
15.6
|
1.0
|
S2
|
A:F3S108
|
3.9
|
18.4
|
1.0
|
CA
|
A:CYS8
|
4.0
|
15.2
|
1.0
|
N
|
A:LYS12
|
4.4
|
15.4
|
1.0
|
N
|
A:TYR13
|
4.4
|
15.3
|
1.0
|
CB
|
A:LEU32
|
4.4
|
15.9
|
1.0
|
CG1
|
A:VAL4
|
4.5
|
15.0
|
1.0
|
O
|
A:CYS8
|
4.5
|
15.4
|
1.0
|
CG
|
A:LEU32
|
4.5
|
17.5
|
1.0
|
C
|
A:LYS12
|
4.5
|
15.2
|
1.0
|
C
|
A:CYS8
|
4.6
|
15.2
|
1.0
|
SG
|
A:CYS49
|
4.6
|
18.8
|
1.0
|
N
|
A:LEU32
|
4.7
|
15.3
|
1.0
|
SG
|
A:CYS16
|
4.8
|
17.9
|
1.0
|
CB
|
A:LYS12
|
4.9
|
15.7
|
1.0
|
N
|
A:THR14
|
4.9
|
16.4
|
1.0
|
|
Iron binding site 7 out
of 7 in 1g3o
Go back to
Iron Binding Sites List in 1g3o
Iron binding site 7 out
of 7 in the Crystal Structure of V19E Mutant of Ferredoxin I
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_07.jpg) Mono view
![](/pictures/FE/pdb/g3/1g3o-FE-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of V19E Mutant of Ferredoxin I within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe108
b:17.7
occ:1.00
|
FE4
|
A:F3S108
|
0.0
|
17.7
|
1.0
|
SG
|
A:CYS49
|
2.1
|
18.8
|
1.0
|
S4
|
A:F3S108
|
2.2
|
18.2
|
1.0
|
S2
|
A:F3S108
|
2.3
|
18.4
|
1.0
|
S3
|
A:F3S108
|
2.3
|
18.1
|
1.0
|
FE1
|
A:F3S108
|
2.8
|
18.9
|
1.0
|
FE3
|
A:F3S108
|
2.8
|
18.2
|
1.0
|
CB
|
A:CYS49
|
3.2
|
18.8
|
1.0
|
S1
|
A:F3S108
|
3.9
|
18.0
|
1.0
|
CA
|
A:CYS49
|
4.1
|
19.8
|
1.0
|
CD
|
A:PRO50
|
4.5
|
18.9
|
1.0
|
C
|
A:CYS49
|
4.6
|
19.4
|
1.0
|
CD2
|
A:TYR13
|
4.7
|
16.0
|
1.0
|
SG
|
A:CYS8
|
4.7
|
16.8
|
1.0
|
CB
|
A:ALA51
|
4.7
|
18.0
|
1.0
|
SG
|
A:CYS16
|
4.7
|
17.9
|
1.0
|
CB
|
A:TYR13
|
4.7
|
15.3
|
1.0
|
N
|
A:PRO50
|
4.8
|
19.2
|
1.0
|
N
|
A:TYR13
|
4.8
|
15.3
|
1.0
|
CB
|
A:CYS16
|
4.8
|
18.8
|
1.0
|
CB
|
A:ALA53
|
4.8
|
18.1
|
1.0
|
CB
|
A:CYS8
|
4.8
|
15.0
|
1.0
|
N
|
A:ALA51
|
4.9
|
18.7
|
1.0
|
CD1
|
A:ILE54
|
4.9
|
17.2
|
1.0
|
N
|
A:THR14
|
5.0
|
16.4
|
1.0
|
|
Reference:
K.Chen,
Y.S.Jung,
C.A.Bonagura,
G.J.Tilley,
G.S.Prasad,
V.Sridhar,
F.A.Armstrong,
C.D.Stout,
B.K.Burgess.
Azotobacter Vinelandii Ferredoxin I: A Sequence and Structure Comparison Approach to Alteration of [4FE-4S]2+/+ Reduction Potential J.Biol.Chem. V. 277 5603 2002.
ISSN: ISSN 0021-9258
PubMed: 11704670
DOI: 10.1074/JBC.M108916200
Page generated: Sat Aug 3 05:44:44 2024
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