Iron in PDB 6n2n: Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
Protein crystallography data
The structure of Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus, PDB code: 6n2n
was solved by
P.Y.-T.Chen,
C.L.Drennan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
98.15 /
1.94
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.282,
123.161,
162.487,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.8 /
20.5
|
Other elements in 6n2n:
The structure of Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
(pdb code 6n2n). 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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus, PDB code: 6n2n:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 1 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:25.6
occ:1.00
|
FE1
|
B:SF4401
|
0.0
|
25.6
|
1.0
|
SG
|
B:CYS209
|
2.3
|
24.8
|
1.0
|
S4
|
B:SF4401
|
2.3
|
24.4
|
1.0
|
S2
|
B:SF4401
|
2.3
|
25.9
|
1.0
|
S3
|
B:SF4401
|
2.3
|
27.1
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
22.7
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
27.2
|
1.0
|
FE4
|
B:SF4401
|
2.8
|
23.6
|
1.0
|
CB
|
B:CYS209
|
3.3
|
24.4
|
1.0
|
CA
|
B:CYS209
|
3.8
|
27.2
|
1.0
|
S1
|
B:SF4401
|
3.9
|
23.1
|
1.0
|
O
|
B:HOH604
|
4.4
|
25.1
|
1.0
|
C
|
B:CYS209
|
4.4
|
27.5
|
1.0
|
CD2
|
B:PHE212
|
4.4
|
25.3
|
1.0
|
CB
|
B:THR211
|
4.5
|
27.4
|
1.0
|
CA
|
B:GLY134
|
4.5
|
22.8
|
1.0
|
OG1
|
B:THR211
|
4.7
|
25.9
|
1.0
|
SG
|
B:CYS29
|
4.8
|
24.9
|
1.0
|
N
|
B:THR211
|
4.8
|
27.7
|
1.0
|
ND2
|
B:ASN130
|
4.8
|
22.4
|
1.0
|
SG
|
B:CYS60
|
4.8
|
24.8
|
1.0
|
SG
|
B:CYS26
|
4.9
|
25.1
|
1.0
|
N
|
B:PRO210
|
4.9
|
27.4
|
1.0
|
O
|
B:CYS209
|
4.9
|
24.5
|
1.0
|
CE2
|
B:PHE212
|
5.0
|
26.8
|
1.0
|
|
Iron binding site 2 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 2 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:27.2
occ:1.00
|
FE2
|
B:SF4401
|
0.0
|
27.2
|
1.0
|
SG
|
B:CYS29
|
2.3
|
24.9
|
1.0
|
S3
|
B:SF4401
|
2.3
|
27.1
|
1.0
|
S1
|
B:SF4401
|
2.3
|
23.1
|
1.0
|
S4
|
B:SF4401
|
2.3
|
24.4
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
23.6
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
22.7
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
25.6
|
1.0
|
CB
|
B:CYS29
|
3.1
|
25.9
|
1.0
|
O
|
B:HOH604
|
3.8
|
25.1
|
1.0
|
S2
|
B:SF4401
|
3.9
|
25.9
|
1.0
|
CA
|
B:CYS29
|
4.2
|
28.4
|
1.0
|
CD2
|
B:HIS31
|
4.3
|
26.2
|
1.0
|
N
|
B:CYS26
|
4.5
|
28.9
|
1.0
|
NE2
|
B:HIS31
|
4.6
|
25.1
|
1.0
|
CB
|
B:CYS26
|
4.6
|
27.1
|
1.0
|
SG
|
B:CYS26
|
4.7
|
25.1
|
1.0
|
CB
|
B:TRP25
|
4.7
|
27.3
|
1.0
|
CB
|
B:CYS60
|
4.7
|
23.7
|
1.0
|
SG
|
B:CYS209
|
4.7
|
24.8
|
1.0
|
SG
|
B:CYS60
|
4.7
|
24.8
|
1.0
|
CD1
|
B:TRP25
|
4.8
|
26.0
|
1.0
|
O
|
B:GLN208
|
4.8
|
26.5
|
1.0
|
CG
|
B:HIS31
|
4.8
|
26.0
|
1.0
|
CG
|
B:TRP25
|
4.9
|
26.8
|
1.0
|
CA
|
B:CYS209
|
4.9
|
27.2
|
1.0
|
CB
|
B:CYS209
|
4.9
|
24.4
|
1.0
|
|
Iron binding site 3 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 3 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:22.7
occ:1.00
|
FE3
|
B:SF4401
|
0.0
|
22.7
|
1.0
|
S2
|
B:SF4401
|
2.3
|
25.9
|
1.0
|
S4
|
B:SF4401
|
2.3
|
24.4
|
1.0
|
S1
|
B:SF4401
|
2.3
|
23.1
|
1.0
|
SG
|
B:CYS60
|
2.3
|
24.8
|
1.0
|
FE4
|
B:SF4401
|
2.7
|
23.6
|
1.0
|
FE1
|
B:SF4401
|
2.7
|
25.6
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
27.2
|
1.0
|
CB
|
B:CYS60
|
3.1
|
23.7
|
1.0
|
S3
|
B:SF4401
|
3.9
|
27.1
|
1.0
|
O
|
B:HOH528
|
3.9
|
28.6
|
1.0
|
CA
|
B:GLY134
|
4.4
|
22.8
|
1.0
|
C
|
B:GLY134
|
4.5
|
25.2
|
1.0
|
CA
|
B:CYS60
|
4.6
|
23.2
|
1.0
|
CD1
|
A:ILE46
|
4.6
|
28.1
|
1.0
|
SG
|
B:CYS29
|
4.8
|
24.9
|
1.0
|
N
|
B:LEU135
|
4.8
|
23.7
|
1.0
|
O
|
B:GLY134
|
4.8
|
26.5
|
1.0
|
SG
|
B:CYS26
|
4.8
|
25.1
|
1.0
|
SG
|
B:CYS209
|
4.8
|
24.8
|
1.0
|
O3B
|
B:TPP402
|
4.9
|
23.5
|
1.0
|
CD1
|
B:TRP25
|
5.0
|
26.0
|
1.0
|
|
Iron binding site 4 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 4 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe401
b:23.6
occ:1.00
|
FE4
|
B:SF4401
|
0.0
|
23.6
|
1.0
|
S1
|
B:SF4401
|
2.3
|
23.1
|
1.0
|
S3
|
B:SF4401
|
2.3
|
27.1
|
1.0
|
SG
|
B:CYS26
|
2.3
|
25.1
|
1.0
|
S2
|
B:SF4401
|
2.3
|
25.9
|
1.0
|
FE2
|
B:SF4401
|
2.7
|
27.2
|
1.0
|
FE3
|
B:SF4401
|
2.7
|
22.7
|
1.0
|
FE1
|
B:SF4401
|
2.8
|
25.6
|
1.0
|
CB
|
B:CYS26
|
3.1
|
27.1
|
1.0
|
OG1
|
B:THR211
|
3.7
|
25.9
|
1.0
|
N
|
B:CYS26
|
3.8
|
28.9
|
1.0
|
S4
|
B:SF4401
|
3.9
|
24.4
|
1.0
|
CA
|
B:CYS26
|
4.1
|
30.2
|
1.0
|
CB
|
B:THR211
|
4.2
|
27.4
|
1.0
|
CG2
|
A:ILE46
|
4.4
|
28.2
|
1.0
|
O
|
B:HOH610
|
4.5
|
30.9
|
1.0
|
CB
|
B:CYS29
|
4.7
|
25.9
|
1.0
|
SG
|
B:CYS29
|
4.8
|
24.9
|
1.0
|
SG
|
B:CYS209
|
4.8
|
24.8
|
1.0
|
SG
|
B:CYS60
|
4.8
|
24.8
|
1.0
|
CB
|
A:ILE46
|
4.9
|
29.7
|
1.0
|
O
|
B:HOH528
|
5.0
|
28.6
|
1.0
|
CG2
|
B:THR211
|
5.0
|
28.3
|
1.0
|
|
Iron binding site 5 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 5 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:22.8
occ:1.00
|
FE1
|
D:SF4401
|
0.0
|
22.8
|
1.0
|
S3
|
D:SF4401
|
2.3
|
21.8
|
1.0
|
SG
|
D:CYS209
|
2.3
|
22.6
|
1.0
|
S4
|
D:SF4401
|
2.3
|
23.8
|
1.0
|
S2
|
D:SF4401
|
2.3
|
23.9
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
22.6
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
20.6
|
1.0
|
FE4
|
D:SF4401
|
2.8
|
22.6
|
1.0
|
CB
|
D:CYS209
|
3.3
|
21.8
|
1.0
|
CA
|
D:CYS209
|
3.8
|
24.6
|
1.0
|
S1
|
D:SF4401
|
3.9
|
22.8
|
1.0
|
O
|
D:HOH571
|
4.3
|
22.0
|
1.0
|
C
|
D:CYS209
|
4.4
|
23.0
|
1.0
|
CB
|
D:THR211
|
4.4
|
23.4
|
1.0
|
CA
|
D:GLY134
|
4.5
|
18.7
|
1.0
|
CD2
|
D:PHE212
|
4.5
|
21.2
|
1.0
|
OG1
|
D:THR211
|
4.7
|
28.5
|
1.0
|
N
|
D:THR211
|
4.7
|
22.9
|
1.0
|
SG
|
D:CYS29
|
4.7
|
23.4
|
1.0
|
ND2
|
D:ASN130
|
4.8
|
22.1
|
1.0
|
SG
|
D:CYS60
|
4.8
|
21.1
|
1.0
|
SG
|
D:CYS26
|
4.8
|
24.9
|
1.0
|
O
|
D:CYS209
|
4.9
|
22.9
|
1.0
|
N
|
D:PRO210
|
4.9
|
24.4
|
1.0
|
|
Iron binding site 6 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 6 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:22.6
occ:1.00
|
FE2
|
D:SF4401
|
0.0
|
22.6
|
1.0
|
SG
|
D:CYS29
|
2.3
|
23.4
|
1.0
|
S4
|
D:SF4401
|
2.3
|
23.8
|
1.0
|
S1
|
D:SF4401
|
2.3
|
22.8
|
1.0
|
S3
|
D:SF4401
|
2.3
|
21.8
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
22.6
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
20.6
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
22.8
|
1.0
|
CB
|
D:CYS29
|
3.1
|
23.4
|
1.0
|
O
|
D:HOH571
|
3.8
|
22.0
|
1.0
|
S2
|
D:SF4401
|
3.9
|
23.9
|
1.0
|
CA
|
D:CYS29
|
4.2
|
23.9
|
1.0
|
CD2
|
D:HIS31
|
4.2
|
22.4
|
1.0
|
N
|
D:CYS26
|
4.5
|
27.0
|
1.0
|
NE2
|
D:HIS31
|
4.6
|
24.1
|
1.0
|
CB
|
D:CYS26
|
4.6
|
26.2
|
1.0
|
CB
|
D:TRP25
|
4.7
|
24.7
|
1.0
|
CB
|
D:CYS60
|
4.7
|
21.5
|
1.0
|
SG
|
D:CYS26
|
4.7
|
24.9
|
1.0
|
SG
|
D:CYS60
|
4.7
|
21.1
|
1.0
|
CG
|
D:HIS31
|
4.7
|
22.5
|
1.0
|
SG
|
D:CYS209
|
4.8
|
22.6
|
1.0
|
CD1
|
D:TRP25
|
4.8
|
25.9
|
1.0
|
CG
|
D:TRP25
|
4.8
|
23.9
|
1.0
|
O
|
D:GLN208
|
4.9
|
24.1
|
1.0
|
CA
|
D:CYS209
|
4.9
|
24.6
|
1.0
|
CB
|
D:CYS209
|
4.9
|
21.8
|
1.0
|
|
Iron binding site 7 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 7 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:20.6
occ:1.00
|
FE3
|
D:SF4401
|
0.0
|
20.6
|
1.0
|
S4
|
D:SF4401
|
2.3
|
23.8
|
1.0
|
S1
|
D:SF4401
|
2.3
|
22.8
|
1.0
|
S2
|
D:SF4401
|
2.3
|
23.9
|
1.0
|
SG
|
D:CYS60
|
2.3
|
21.1
|
1.0
|
FE4
|
D:SF4401
|
2.7
|
22.6
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
22.6
|
1.0
|
FE1
|
D:SF4401
|
2.7
|
22.8
|
1.0
|
CB
|
D:CYS60
|
3.1
|
21.5
|
1.0
|
S3
|
D:SF4401
|
3.9
|
21.8
|
1.0
|
O
|
D:HOH659
|
3.9
|
25.2
|
1.0
|
CA
|
D:GLY134
|
4.4
|
18.7
|
1.0
|
C
|
D:GLY134
|
4.5
|
21.6
|
1.0
|
CA
|
D:CYS60
|
4.5
|
23.3
|
1.0
|
CD1
|
C:ILE46
|
4.7
|
28.5
|
1.0
|
N
|
D:LEU135
|
4.7
|
19.6
|
1.0
|
O
|
D:GLY134
|
4.8
|
22.0
|
1.0
|
SG
|
D:CYS26
|
4.8
|
24.9
|
1.0
|
SG
|
D:CYS29
|
4.8
|
23.4
|
1.0
|
O2B
|
D:TPP402
|
4.8
|
19.1
|
1.0
|
SG
|
D:CYS209
|
4.8
|
22.6
|
1.0
|
CD1
|
D:TRP25
|
5.0
|
25.9
|
1.0
|
|
Iron binding site 8 out
of 8 in 6n2n
Go back to
Iron Binding Sites List in 6n2n
Iron binding site 8 out
of 8 in the Crystal Structure of 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus
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 2-Oxoglutarate:Ferredoxin Oxidoreductase From Magnetococcus Marinus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:22.6
occ:1.00
|
FE4
|
D:SF4401
|
0.0
|
22.6
|
1.0
|
S1
|
D:SF4401
|
2.3
|
22.8
|
1.0
|
S2
|
D:SF4401
|
2.3
|
23.9
|
1.0
|
S3
|
D:SF4401
|
2.3
|
21.8
|
1.0
|
SG
|
D:CYS26
|
2.3
|
24.9
|
1.0
|
FE3
|
D:SF4401
|
2.7
|
20.6
|
1.0
|
FE2
|
D:SF4401
|
2.7
|
22.6
|
1.0
|
FE1
|
D:SF4401
|
2.8
|
22.8
|
1.0
|
CB
|
D:CYS26
|
3.1
|
26.2
|
1.0
|
OG1
|
D:THR211
|
3.7
|
28.5
|
1.0
|
N
|
D:CYS26
|
3.8
|
27.0
|
1.0
|
S4
|
D:SF4401
|
3.9
|
23.8
|
1.0
|
CA
|
D:CYS26
|
4.0
|
26.4
|
1.0
|
CB
|
D:THR211
|
4.1
|
23.4
|
1.0
|
O
|
D:HOH597
|
4.4
|
30.0
|
1.0
|
CG2
|
C:ILE46
|
4.4
|
27.1
|
1.0
|
CB
|
D:CYS29
|
4.7
|
23.4
|
1.0
|
SG
|
D:CYS29
|
4.8
|
23.4
|
1.0
|
CB
|
C:ILE46
|
4.8
|
30.4
|
1.0
|
SG
|
D:CYS209
|
4.8
|
22.6
|
1.0
|
SG
|
D:CYS60
|
4.8
|
21.1
|
1.0
|
CG2
|
D:THR211
|
4.9
|
27.5
|
1.0
|
C
|
D:TRP25
|
5.0
|
28.4
|
1.0
|
O
|
D:HOH659
|
5.0
|
25.2
|
1.0
|
|
Reference:
P.Y.Chen,
B.Li,
C.L.Drennan,
S.J.Elliott.
A Reverse Tca Cycle 2-Oxoacid:Ferredoxin Oxidoreductase That Makes C-C Bonds From CO2. Joule V. 3 595 2019.
ISSN: ESSN 2542-4351
PubMed: 31080943
DOI: 10.1016/J.JOULE.2018.12.006
Page generated: Wed Aug 7 02:47:45 2024
|