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: Tue Aug 6 20:03:11 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy