Iron in PDB 6gl6: Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
Enzymatic activity of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
All present enzymatic activity of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H:
1.18.99.1;
Protein crystallography data
The structure of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H, PDB code: 6gl6
was solved by
L.Kertess,
T.Happe,
E.Hofmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.91 /
1.80
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.730,
70.730,
155.900,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.9 /
19.7
|
Other elements in 6gl6:
The structure of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
(pdb code 6gl6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H, PDB code: 6gl6:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 6gl6
Go back to
Iron Binding Sites List in 6gl6
Iron binding site 1 out
of 4 in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:24.4
occ:1.00
|
FE1
|
A:SF4501
|
0.0
|
24.4
|
1.0
|
S2
|
A:SF4501
|
2.3
|
25.8
|
1.0
|
S3
|
A:SF4501
|
2.3
|
29.6
|
1.0
|
S4
|
A:SF4501
|
2.3
|
26.4
|
1.0
|
SG
|
A:CYS130
|
2.4
|
25.7
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
25.2
|
1.0
|
FE4
|
A:SF4501
|
2.7
|
25.7
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
26.0
|
1.0
|
H
|
A:ALA376
|
3.2
|
28.9
|
1.0
|
HB2
|
A:CYS130
|
3.3
|
29.4
|
1.0
|
HD2
|
A:PRO131
|
3.4
|
32.4
|
1.0
|
HA
|
A:CYS130
|
3.4
|
28.3
|
1.0
|
CB
|
A:CYS130
|
3.4
|
24.5
|
1.0
|
HB3
|
A:ALA376
|
3.5
|
35.1
|
1.0
|
HE3
|
A:MET375
|
3.6
|
34.4
|
1.0
|
H
|
A:GLY132
|
3.8
|
28.4
|
1.0
|
S1
|
A:SF4501
|
3.9
|
28.3
|
1.0
|
CA
|
A:CYS130
|
3.9
|
23.6
|
1.0
|
N
|
A:ALA376
|
4.1
|
24.1
|
1.0
|
CB
|
A:ALA376
|
4.2
|
29.2
|
1.0
|
HB3
|
A:CYS130
|
4.2
|
29.4
|
1.0
|
HB2
|
A:ALA376
|
4.3
|
35.1
|
1.0
|
HE1
|
A:MET375
|
4.3
|
34.4
|
1.0
|
CD
|
A:PRO131
|
4.3
|
27.0
|
1.0
|
H
|
A:HIS377
|
4.3
|
33.2
|
1.0
|
CE
|
A:MET375
|
4.4
|
28.7
|
1.0
|
HB3
|
A:MET375
|
4.4
|
28.2
|
1.0
|
HA
|
A:MET375
|
4.4
|
28.9
|
1.0
|
C
|
A:CYS130
|
4.5
|
23.2
|
1.0
|
N
|
A:PRO131
|
4.6
|
22.2
|
1.0
|
ND1
|
A:HIS377
|
4.6
|
26.3
|
1.0
|
HG2
|
A:PRO131
|
4.6
|
36.3
|
1.0
|
N
|
A:GLY132
|
4.7
|
23.7
|
1.0
|
HA3
|
A:GLY132
|
4.7
|
30.6
|
1.0
|
CA
|
A:ALA376
|
4.7
|
29.1
|
1.0
|
HD2
|
A:ARG187
|
4.8
|
53.4
|
1.0
|
HD3
|
A:PRO131
|
4.9
|
32.4
|
1.0
|
SG
|
A:CYS381
|
5.0
|
31.0
|
1.0
|
N
|
A:HIS377
|
5.0
|
27.6
|
1.0
|
HE2
|
A:LYS188
|
5.0
|
26.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 6gl6
Go back to
Iron Binding Sites List in 6gl6
Iron binding site 2 out
of 4 in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:25.2
occ:1.00
|
FE2
|
A:SF4501
|
0.0
|
25.2
|
1.0
|
ND1
|
A:HIS377
|
2.2
|
26.3
|
1.0
|
S1
|
A:SF4501
|
2.3
|
28.3
|
1.0
|
S3
|
A:SF4501
|
2.3
|
29.6
|
1.0
|
S4
|
A:SF4501
|
2.3
|
26.4
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
24.4
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
26.0
|
1.0
|
FE4
|
A:SF4501
|
2.7
|
25.7
|
1.0
|
CE1
|
A:HIS377
|
3.0
|
28.7
|
1.0
|
HE1
|
A:HIS377
|
3.0
|
34.4
|
1.0
|
HB2
|
A:HIS377
|
3.2
|
34.1
|
1.0
|
CG
|
A:HIS377
|
3.3
|
28.6
|
1.0
|
H
|
A:HIS377
|
3.4
|
33.2
|
1.0
|
HB3
|
A:ALA376
|
3.6
|
35.1
|
1.0
|
HA2
|
A:GLY384
|
3.7
|
30.0
|
1.0
|
CB
|
A:HIS377
|
3.7
|
28.4
|
1.0
|
HA
|
A:CYS381
|
3.9
|
30.2
|
1.0
|
S2
|
A:SF4501
|
3.9
|
25.8
|
1.0
|
HB3
|
A:CYS185
|
3.9
|
31.7
|
1.0
|
N
|
A:HIS377
|
4.0
|
27.6
|
1.0
|
NE2
|
A:HIS377
|
4.2
|
25.5
|
1.0
|
H
|
A:ALA376
|
4.2
|
28.9
|
1.0
|
CD2
|
A:HIS377
|
4.3
|
23.6
|
1.0
|
HA3
|
A:GLY384
|
4.4
|
30.0
|
1.0
|
CA
|
A:GLY384
|
4.4
|
25.0
|
1.0
|
CA
|
A:HIS377
|
4.5
|
27.5
|
1.0
|
CB
|
A:ALA376
|
4.5
|
29.2
|
1.0
|
HB3
|
A:HIS377
|
4.5
|
34.1
|
1.0
|
CB
|
A:CYS185
|
4.6
|
26.4
|
1.0
|
HB2
|
A:CYS185
|
4.6
|
31.7
|
1.0
|
C
|
A:ALA376
|
4.8
|
31.3
|
1.0
|
SG
|
A:CYS130
|
4.8
|
25.7
|
1.0
|
SG
|
A:CYS185
|
4.8
|
28.4
|
1.0
|
N
|
A:ALA376
|
4.8
|
24.1
|
1.0
|
HE3
|
A:MET375
|
4.8
|
34.4
|
1.0
|
CA
|
A:CYS381
|
4.8
|
25.1
|
1.0
|
O
|
A:GLY380
|
4.9
|
24.9
|
1.0
|
H
|
A:GLY385
|
4.9
|
25.2
|
1.0
|
HE2
|
A:HIS377
|
4.9
|
30.6
|
1.0
|
CA
|
A:ALA376
|
4.9
|
29.1
|
1.0
|
HB1
|
A:ALA376
|
5.0
|
35.1
|
1.0
|
|
Iron binding site 3 out
of 4 in 6gl6
Go back to
Iron Binding Sites List in 6gl6
Iron binding site 3 out
of 4 in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:26.0
occ:1.00
|
FE3
|
A:SF4501
|
0.0
|
26.0
|
1.0
|
S4
|
A:SF4501
|
2.3
|
26.4
|
1.0
|
S2
|
A:SF4501
|
2.3
|
25.8
|
1.0
|
S1
|
A:SF4501
|
2.3
|
28.3
|
1.0
|
SG
|
A:CYS185
|
2.4
|
28.4
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
25.2
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
24.4
|
1.0
|
FE4
|
A:SF4501
|
2.7
|
25.7
|
1.0
|
HB3
|
A:CYS185
|
3.0
|
31.7
|
1.0
|
CB
|
A:CYS185
|
3.2
|
26.4
|
1.0
|
HB2
|
A:CYS185
|
3.5
|
31.7
|
1.0
|
HD2
|
A:PRO131
|
3.8
|
32.4
|
1.0
|
S3
|
A:SF4501
|
3.9
|
29.6
|
1.0
|
HG2
|
A:ARG187
|
4.0
|
54.1
|
1.0
|
HG2
|
A:LYS188
|
4.0
|
28.7
|
1.0
|
HG2
|
A:PRO184
|
4.1
|
27.3
|
1.0
|
HE2
|
A:LYS188
|
4.2
|
26.7
|
1.0
|
HE1
|
A:HIS377
|
4.2
|
34.4
|
1.0
|
HG2
|
A:PRO131
|
4.3
|
36.3
|
1.0
|
ND1
|
A:HIS377
|
4.6
|
26.3
|
1.0
|
CA
|
A:CYS185
|
4.6
|
33.7
|
1.0
|
CD
|
A:PRO131
|
4.6
|
27.0
|
1.0
|
CE1
|
A:HIS377
|
4.7
|
28.7
|
1.0
|
HE
|
A:ARG187
|
4.8
|
52.6
|
1.0
|
HE3
|
A:LYS188
|
4.8
|
26.7
|
1.0
|
HA
|
A:CYS381
|
4.8
|
30.2
|
1.0
|
CG
|
A:ARG187
|
4.8
|
45.1
|
1.0
|
CG
|
A:LYS188
|
4.9
|
23.9
|
1.0
|
CG
|
A:PRO131
|
4.9
|
30.2
|
1.0
|
SG
|
A:CYS381
|
4.9
|
31.0
|
1.0
|
SG
|
A:CYS130
|
4.9
|
25.7
|
1.0
|
CE
|
A:LYS188
|
4.9
|
22.3
|
1.0
|
HA
|
A:CYS130
|
4.9
|
28.3
|
1.0
|
HG3
|
A:LYS188
|
4.9
|
28.7
|
1.0
|
N
|
A:CYS185
|
4.9
|
26.5
|
1.0
|
HD2
|
A:ARG187
|
5.0
|
53.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 6gl6
Go back to
Iron Binding Sites List in 6gl6
Iron binding site 4 out
of 4 in the Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Apo [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii, Variant C377H within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe501
b:25.7
occ:1.00
|
FE4
|
A:SF4501
|
0.0
|
25.7
|
1.0
|
S3
|
A:SF4501
|
2.3
|
29.6
|
1.0
|
S1
|
A:SF4501
|
2.3
|
28.3
|
1.0
|
S2
|
A:SF4501
|
2.3
|
25.8
|
1.0
|
SG
|
A:CYS381
|
2.5
|
31.0
|
1.0
|
FE1
|
A:SF4501
|
2.7
|
24.4
|
1.0
|
FE2
|
A:SF4501
|
2.7
|
25.2
|
1.0
|
FE3
|
A:SF4501
|
2.7
|
26.0
|
1.0
|
HA
|
A:CYS381
|
2.9
|
30.2
|
1.0
|
HE3
|
A:MET375
|
3.2
|
34.4
|
1.0
|
CB
|
A:CYS381
|
3.4
|
26.6
|
1.0
|
CA
|
A:CYS381
|
3.5
|
25.1
|
1.0
|
HE1
|
A:MET375
|
3.6
|
34.4
|
1.0
|
HB3
|
A:CYS381
|
3.7
|
31.9
|
1.0
|
CE
|
A:MET375
|
3.8
|
28.7
|
1.0
|
S4
|
A:SF4501
|
3.9
|
26.4
|
1.0
|
N
|
A:CYS381
|
4.0
|
28.0
|
1.0
|
HE2
|
A:MET375
|
4.1
|
34.4
|
1.0
|
H
|
A:CYS381
|
4.2
|
33.6
|
1.0
|
HG2
|
A:PRO184
|
4.2
|
27.3
|
1.0
|
HB2
|
A:CYS381
|
4.3
|
31.9
|
1.0
|
C
|
A:GLY380
|
4.5
|
30.3
|
1.0
|
HB3
|
A:MET375
|
4.6
|
28.2
|
1.0
|
HB2
|
A:HIS377
|
4.8
|
34.1
|
1.0
|
HB2
|
A:CYS130
|
4.8
|
29.4
|
1.0
|
HB3
|
A:CYS185
|
4.8
|
31.7
|
1.0
|
ND1
|
A:HIS377
|
4.8
|
26.3
|
1.0
|
HG3
|
A:PRO184
|
4.8
|
27.3
|
1.0
|
C
|
A:CYS381
|
4.8
|
23.3
|
1.0
|
HA2
|
A:GLY380
|
4.8
|
38.2
|
1.0
|
SG
|
A:CYS185
|
4.9
|
28.4
|
1.0
|
SG
|
A:CYS130
|
4.9
|
25.7
|
1.0
|
O
|
A:GLY380
|
4.9
|
24.9
|
1.0
|
H
|
A:HIS377
|
4.9
|
33.2
|
1.0
|
HA
|
A:CYS130
|
4.9
|
28.3
|
1.0
|
HD2
|
A:PRO131
|
5.0
|
32.4
|
1.0
|
CG
|
A:PRO184
|
5.0
|
22.7
|
1.0
|
|
Reference:
P.Rodriguez-Macia,
L.Kertess,
J.Burnik,
J.A.Birrell,
E.Hofmann,
W.Lubitz,
T.Happe,
O.Rudiger.
His-Ligation to the [4FE-4S] Subcluster Tunes the Catalytic Bias of [Fefe] Hydrogenase. J.Am.Chem.Soc. V. 141 472 2019.
ISSN: ESSN 1520-5126
PubMed: 30545220
DOI: 10.1021/JACS.8B11149
Page generated: Tue Aug 6 20:03:11 2024
|