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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:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

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: Sun Dec 13 16:27:44 2020

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