Iron in PDB 7o25: Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
Protein crystallography data
The structure of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal), PDB code: 7o25
was solved by
R.Rohac,
L.Martin,
L.Liu,
D.Basu,
L.Tao,
R.D.Britt,
T.Rauchfuss,
Y.Nicolet,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.15 /
1.34
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.41,
81.7,
70.53,
90,
90,
90
|
R / Rfree (%)
|
14.5 /
16.6
|
Other elements in 7o25:
The structure of Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
(pdb code 7o25). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal), PDB code: 7o25:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 7o25
Go back to
Iron Binding Sites List in 7o25
Iron binding site 1 out
of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
![](/pictures/FE/pdb/o2/7o25-FE-sphere_01.jpg) Mono view
![](/pictures/FE/pdb/o2/7o25-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 Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe402
b:16.9
occ:0.53
|
N
|
A:5X8412
|
1.4
|
30.9
|
0.4
|
C
|
A:CYN405
|
1.8
|
23.8
|
0.8
|
C
|
A:CMO403
|
1.8
|
14.4
|
0.5
|
C
|
A:CMO404
|
1.8
|
19.4
|
0.8
|
N
|
A:CYS401
|
2.1
|
17.3
|
0.5
|
OXT
|
A:CYS401
|
2.1
|
19.9
|
0.5
|
CA
|
A:5X8412
|
2.1
|
30.4
|
0.4
|
SG
|
A:CYS401
|
2.4
|
29.0
|
0.5
|
SG
|
A:5X8412
|
2.6
|
21.8
|
0.4
|
CA
|
A:CYS401
|
2.8
|
18.2
|
0.5
|
C
|
A:CYS401
|
2.8
|
18.7
|
0.5
|
CB
|
A:5X8412
|
2.8
|
30.1
|
0.4
|
N
|
A:CYN405
|
3.0
|
24.2
|
0.8
|
O
|
A:CMO403
|
3.0
|
20.0
|
0.5
|
O
|
A:CMO404
|
3.1
|
23.7
|
0.8
|
CB
|
A:CYS401
|
3.1
|
18.9
|
0.5
|
C
|
A:5X8412
|
3.5
|
24.4
|
0.4
|
O
|
A:CYS401
|
4.0
|
22.5
|
0.5
|
O
|
A:5X8412
|
4.0
|
24.5
|
0.4
|
NH1
|
A:ARG159
|
4.0
|
22.9
|
0.5
|
OG1
|
A:THR269
|
4.3
|
17.6
|
0.6
|
OXT
|
A:5X8412
|
4.4
|
26.3
|
0.4
|
NH2
|
A:ARG159
|
4.4
|
34.2
|
0.5
|
C5'
|
A:5X8412
|
4.4
|
19.1
|
0.4
|
SD
|
A:MET291
|
4.4
|
31.0
|
0.7
|
O
|
A:HOH551
|
4.5
|
21.6
|
0.4
|
O
|
A:HOH553
|
4.6
|
24.7
|
1.0
|
CG2
|
A:THR268
|
4.6
|
16.4
|
1.0
|
CD1
|
A:ILE56
|
4.6
|
21.1
|
0.6
|
CE
|
A:MET291
|
4.7
|
50.8
|
0.7
|
CB
|
A:THR268
|
4.7
|
17.0
|
1.0
|
O
|
A:HOH797
|
4.8
|
19.3
|
0.3
|
CD2
|
A:LEU157
|
4.8
|
32.5
|
0.6
|
NE2
|
A:GLN107
|
4.9
|
17.3
|
1.0
|
SD
|
A:MET291
|
4.9
|
16.7
|
0.3
|
CZ
|
A:ARG159
|
4.9
|
18.7
|
0.5
|
O
|
A:HOH547
|
5.0
|
28.5
|
1.0
|
|
Iron binding site 2 out
of 5 in 7o25
Go back to
Iron Binding Sites List in 7o25
Iron binding site 2 out
of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
![](/pictures/FE/pdb/o2/7o25-FE-sphere_02.jpg) Mono view
![](/pictures/FE/pdb/o2/7o25-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 Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe415
b:14.2
occ:1.00
|
FE1
|
A:SF4415
|
0.0
|
14.2
|
1.0
|
S3
|
A:SF4415
|
2.3
|
14.1
|
1.0
|
SG
|
A:CYS70
|
2.3
|
14.1
|
1.0
|
S2
|
A:SF4415
|
2.3
|
14.8
|
1.0
|
S4
|
A:SF4415
|
2.3
|
14.5
|
1.0
|
FE2
|
A:SF4415
|
2.7
|
14.0
|
1.0
|
FE3
|
A:SF4415
|
2.7
|
14.3
|
1.0
|
FE4
|
A:SF4415
|
2.9
|
15.9
|
1.0
|
CB
|
A:CYS70
|
3.1
|
15.8
|
1.0
|
CE
|
A:SAM407
|
3.8
|
18.9
|
0.5
|
S1
|
A:SF4415
|
3.8
|
15.1
|
1.0
|
SD
|
A:MET408
|
4.2
|
23.0
|
0.5
|
CB
|
A:LEU72
|
4.2
|
12.9
|
1.0
|
SD
|
A:SAM407
|
4.5
|
20.7
|
0.5
|
CE
|
A:MET408
|
4.5
|
29.8
|
0.4
|
CA
|
A:CYS70
|
4.5
|
14.1
|
1.0
|
SG
|
A:CYS67
|
4.7
|
15.1
|
1.0
|
N
|
A:MET408
|
4.7
|
20.8
|
0.5
|
N
|
A:ARG73
|
4.7
|
13.9
|
1.0
|
CG
|
A:LEU72
|
4.8
|
15.5
|
1.0
|
CB
|
A:CYS67
|
4.8
|
14.6
|
1.0
|
CD2
|
A:LEU305
|
4.8
|
15.6
|
0.4
|
N
|
A:LEU72
|
4.8
|
12.7
|
1.0
|
SG
|
A:CYS63
|
4.8
|
14.2
|
1.0
|
OXT
|
A:SAM407
|
4.8
|
10.2
|
0.5
|
C
|
A:LEU72
|
4.8
|
14.2
|
1.0
|
CA
|
A:LEU72
|
4.9
|
13.2
|
1.0
|
O
|
A:MET408
|
4.9
|
28.7
|
0.5
|
N
|
A:SAM407
|
4.9
|
15.0
|
0.5
|
|
Iron binding site 3 out
of 5 in 7o25
Go back to
Iron Binding Sites List in 7o25
Iron binding site 3 out
of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
![](/pictures/FE/pdb/o2/7o25-FE-sphere_03.jpg) Mono view
![](/pictures/FE/pdb/o2/7o25-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 Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe415
b:14.0
occ:1.00
|
FE2
|
A:SF4415
|
0.0
|
14.0
|
1.0
|
SG
|
A:CYS63
|
2.3
|
14.2
|
1.0
|
S4
|
A:SF4415
|
2.3
|
14.5
|
1.0
|
S3
|
A:SF4415
|
2.3
|
14.1
|
1.0
|
S1
|
A:SF4415
|
2.3
|
15.1
|
1.0
|
FE1
|
A:SF4415
|
2.7
|
14.2
|
1.0
|
FE3
|
A:SF4415
|
2.7
|
14.3
|
1.0
|
FE4
|
A:SF4415
|
2.9
|
15.9
|
1.0
|
CB
|
A:CYS63
|
3.3
|
14.6
|
1.0
|
S2
|
A:SF4415
|
3.9
|
14.8
|
1.0
|
N
|
A:MET408
|
4.0
|
20.8
|
0.5
|
N
|
A:SAM407
|
4.1
|
15.0
|
0.5
|
CB
|
A:LYS65
|
4.2
|
15.2
|
1.0
|
N
|
A:GLU110
|
4.5
|
13.8
|
1.0
|
CA
|
A:GLY109
|
4.7
|
14.9
|
1.0
|
CA
|
A:CYS63
|
4.7
|
13.0
|
1.0
|
SG
|
A:CYS67
|
4.7
|
15.1
|
1.0
|
O
|
A:LYS65
|
4.8
|
15.9
|
1.0
|
SG
|
A:CYS70
|
4.8
|
14.1
|
1.0
|
N
|
A:LYS65
|
4.8
|
13.8
|
1.0
|
CA
|
A:LYS65
|
4.8
|
14.2
|
1.0
|
C
|
A:LYS65
|
4.8
|
14.5
|
1.0
|
OXT
|
A:SAM407
|
4.9
|
10.2
|
0.5
|
O
|
A:MET408
|
4.9
|
28.7
|
0.5
|
CB
|
A:LEU72
|
5.0
|
12.9
|
1.0
|
|
Iron binding site 4 out
of 5 in 7o25
Go back to
Iron Binding Sites List in 7o25
Iron binding site 4 out
of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
![](/pictures/FE/pdb/o2/7o25-FE-sphere_04.jpg) Mono view
![](/pictures/FE/pdb/o2/7o25-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 Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe415
b:14.3
occ:1.00
|
FE3
|
A:SF4415
|
0.0
|
14.3
|
1.0
|
S1
|
A:SF4415
|
2.2
|
15.1
|
1.0
|
S4
|
A:SF4415
|
2.3
|
14.5
|
1.0
|
SG
|
A:CYS67
|
2.3
|
15.1
|
1.0
|
S2
|
A:SF4415
|
2.3
|
14.8
|
1.0
|
FE2
|
A:SF4415
|
2.7
|
14.0
|
1.0
|
FE1
|
A:SF4415
|
2.7
|
14.2
|
1.0
|
FE4
|
A:SF4415
|
2.9
|
15.9
|
1.0
|
CB
|
A:CYS67
|
3.2
|
14.6
|
1.0
|
S3
|
A:SF4415
|
3.9
|
14.1
|
1.0
|
O
|
A:HOH631
|
3.9
|
22.3
|
1.0
|
N
|
A:CYS67
|
4.2
|
15.0
|
1.0
|
O
|
A:MET408
|
4.2
|
28.7
|
0.5
|
OXT
|
A:SAM407
|
4.2
|
10.2
|
0.5
|
CA
|
A:CYS67
|
4.3
|
13.8
|
1.0
|
NH2
|
A:ARG172
|
4.4
|
16.3
|
1.0
|
CB
|
A:LYS65
|
4.4
|
15.2
|
1.0
|
CB
|
A:CYS70
|
4.4
|
15.8
|
1.0
|
SG
|
A:CYS70
|
4.6
|
14.1
|
1.0
|
OH
|
A:TYR69
|
4.7
|
18.5
|
1.0
|
SG
|
A:CYS63
|
4.7
|
14.2
|
1.0
|
CE1
|
A:TYR69
|
4.9
|
13.8
|
1.0
|
N
|
A:MET408
|
4.9
|
20.8
|
0.5
|
NE
|
A:ARG172
|
4.9
|
16.1
|
1.0
|
O
|
A:HOH580
|
4.9
|
18.6
|
1.0
|
CD
|
A:LYS65
|
4.9
|
16.7
|
1.0
|
N
|
A:SAM407
|
5.0
|
15.0
|
0.5
|
|
Iron binding site 5 out
of 5 in 7o25
Go back to
Iron Binding Sites List in 7o25
Iron binding site 5 out
of 5 in the Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal)
![](/pictures/FE/pdb/o2/7o25-FE-sphere_05.jpg) Mono view
![](/pictures/FE/pdb/o2/7o25-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 Complex-B Bound [Fefe]-Hydrogenase Maturase Hyde From T. Maritima (Reaction Triggered in the Crystal) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe415
b:15.9
occ:1.00
|
FE4
|
A:SF4415
|
0.0
|
15.9
|
1.0
|
OXT
|
A:SAM407
|
2.2
|
10.2
|
0.5
|
N
|
A:MET408
|
2.2
|
20.8
|
0.5
|
O
|
A:MET408
|
2.2
|
28.7
|
0.5
|
S2
|
A:SF4415
|
2.3
|
14.8
|
1.0
|
N
|
A:SAM407
|
2.3
|
15.0
|
0.5
|
S1
|
A:SF4415
|
2.4
|
15.1
|
1.0
|
S3
|
A:SF4415
|
2.4
|
14.1
|
1.0
|
SD
|
A:MET408
|
2.9
|
23.0
|
0.5
|
FE2
|
A:SF4415
|
2.9
|
14.0
|
1.0
|
FE1
|
A:SF4415
|
2.9
|
14.2
|
1.0
|
FE3
|
A:SF4415
|
2.9
|
14.3
|
1.0
|
C
|
A:MET408
|
3.0
|
26.4
|
0.4
|
C
|
A:SAM407
|
3.1
|
9.5
|
0.5
|
SD
|
A:SAM407
|
3.1
|
20.7
|
0.5
|
CA
|
A:MET408
|
3.1
|
23.7
|
0.4
|
CA
|
A:SAM407
|
3.3
|
11.6
|
0.5
|
CG
|
A:SAM407
|
3.6
|
16.5
|
0.5
|
CE
|
A:SAM407
|
3.7
|
18.9
|
0.5
|
CE
|
A:MET408
|
3.9
|
29.8
|
0.4
|
CG
|
A:MET408
|
3.9
|
25.1
|
0.4
|
CB
|
A:MET408
|
4.0
|
24.1
|
0.5
|
CB
|
A:SAM407
|
4.0
|
17.0
|
0.5
|
O
|
A:HOH631
|
4.0
|
22.3
|
1.0
|
O
|
A:HOH580
|
4.1
|
18.6
|
1.0
|
S4
|
A:SF4415
|
4.1
|
14.5
|
1.0
|
OXT
|
A:MET408
|
4.2
|
29.7
|
0.5
|
O
|
A:SAM407
|
4.3
|
11.4
|
0.5
|
SG
|
A:CYS63
|
4.7
|
14.2
|
1.0
|
C5'
|
A:SAM407
|
4.8
|
19.6
|
0.5
|
SG
|
A:CYS70
|
4.9
|
14.1
|
1.0
|
C3'
|
A:SAM407
|
5.0
|
18.1
|
0.5
|
SG
|
A:CYS67
|
5.0
|
15.1
|
1.0
|
|
Reference:
Y.Nicolet,
J.K.Rubach,
M.C.Posewitz,
P.Amara,
C.Mathevon,
M.Atta,
M.Fontecave,
J.C.Fontecilla-Camps.
X-Ray Structure of the [Fefe]-Hydrogenase Maturase Hyde From Thermotoga Maritima* Journal of Biological V. 283 18861 2008CHEMISTRY.
DOI: 10.1074/JBC.M801161200
Page generated: Thu Aug 8 10:20:22 2024
|