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Iron in PDB 6gm7: [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A

Enzymatic activity of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A

All present enzymatic activity of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A:
1.18.99.1;

Protein crystallography data

The structure of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A, PDB code: 6gm7 was solved by J.Duan, V.Engelbrecht, J.Esselborn, E.Hofmann, M.Winkler, T.Happe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.11 / 2.14
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.910, 70.910, 154.800, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 22.7

Other elements in 6gm7:

The structure of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A (pdb code 6gm7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A, PDB code: 6gm7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6gm7

Go back to Iron Binding Sites List in 6gm7
Iron binding site 1 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:21.2
occ:1.00
FE1 A:SF4601 0.0 21.2 1.0
S3 A:SF4601 2.3 19.2 1.0
S4 A:SF4601 2.3 20.9 1.0
S2 A:SF4601 2.3 14.7 1.0
SG A:CYS170 2.3 20.3 1.0
FE3 A:SF4601 2.7 22.9 1.0
FE4 A:SF4601 2.7 16.3 1.0
FE2 A:SF4601 2.7 20.3 1.0
CB A:CYS170 3.3 20.0 1.0
CA A:CYS170 3.9 21.1 1.0
S1 A:SF4601 3.9 18.1 1.0
N A:ALA416 3.9 23.5 1.0
CB A:ALA416 4.2 22.2 1.0
O A:HOH1051 4.2 48.1 1.0
CD A:PRO171 4.5 18.6 1.0
SD A:MET415 4.6 36.0 1.0
CA A:ALA416 4.6 22.6 1.0
C A:CYS170 4.6 22.3 1.0
N A:CYS417 4.6 22.5 1.0
SG A:CYS225 4.8 23.4 1.0
N A:PRO171 4.8 20.0 1.0
CA A:MET415 4.8 24.3 1.0
SG A:CYS421 4.8 19.6 1.0
SG A:CYS417 4.8 21.9 1.0
C A:MET415 4.8 20.9 1.0
N A:GLY172 4.9 18.8 1.0

Iron binding site 2 out of 4 in 6gm7

Go back to Iron Binding Sites List in 6gm7
Iron binding site 2 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:20.3
occ:1.00
FE2 A:SF4601 0.0 20.3 1.0
S4 A:SF4601 2.3 20.9 1.0
S1 A:SF4601 2.3 18.1 1.0
SG A:CYS417 2.3 21.9 1.0
S3 A:SF4601 2.3 19.2 1.0
FE3 A:SF4601 2.7 22.9 1.0
FE1 A:SF4601 2.7 21.2 1.0
FE4 A:SF4601 2.8 16.3 1.0
CB A:CYS417 3.3 27.8 1.0
N A:CYS417 3.8 22.5 1.0
S2 A:SF4601 3.9 14.7 1.0
CA A:CYS417 4.1 26.0 1.0
O A:HOH1051 4.3 48.1 1.0
CA A:GLY424 4.4 21.8 1.0
SG A:CYS225 4.6 23.4 1.0
CB A:ALA416 4.6 22.2 1.0
C A:ALA416 4.7 25.1 1.0
SG A:CYS170 4.8 20.3 1.0
O A:GLY420 4.8 22.0 1.0
CA A:CYS421 4.8 24.4 1.0
O A:HOH1007 4.8 34.2 1.0
N A:ALA416 4.8 23.5 1.0
SG A:CYS421 4.9 19.6 1.0
C A:GLY420 4.9 21.9 1.0
CA A:ALA416 4.9 22.6 1.0

Iron binding site 3 out of 4 in 6gm7

Go back to Iron Binding Sites List in 6gm7
Iron binding site 3 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:22.9
occ:1.00
FE3 A:SF4601 0.0 22.9 1.0
S4 A:SF4601 2.3 20.9 1.0
S1 A:SF4601 2.3 18.1 1.0
SG A:CYS225 2.3 23.4 1.0
S2 A:SF4601 2.3 14.7 1.0
FE2 A:SF4601 2.7 20.3 1.0
FE1 A:SF4601 2.7 21.2 1.0
FE4 A:SF4601 2.8 16.3 1.0
O A:HOH1051 3.0 48.1 1.0
CB A:CYS225 3.0 26.6 1.0
S3 A:SF4601 3.9 19.2 1.0
CA A:CYS225 4.1 19.7 1.0
SG A:CYS421 4.6 19.6 1.0
CD A:PRO171 4.7 18.6 1.0
SG A:CYS170 4.7 20.3 1.0
CE A:LYS228 4.8 12.8 1.0
CG A:PRO171 4.8 17.2 1.0
SG A:CYS417 4.9 21.9 1.0

Iron binding site 4 out of 4 in 6gm7

Go back to Iron Binding Sites List in 6gm7
Iron binding site 4 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E144A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:16.3
occ:1.00
FE4 A:SF4601 0.0 16.3 1.0
O A:HOH1051 2.1 48.1 1.0
S2 A:SF4601 2.3 14.7 1.0
S1 A:SF4601 2.3 18.1 1.0
S3 A:SF4601 2.3 19.2 1.0
SG A:CYS421 2.3 19.6 1.0
FE1 A:SF4601 2.7 21.2 1.0
FE3 A:SF4601 2.8 22.9 1.0
FE2 A:SF4601 2.8 20.3 1.0
CB A:CYS421 3.4 20.4 1.0
CA A:CYS421 3.5 24.4 1.0
N A:CYS421 3.8 26.2 1.0
S4 A:SF4601 3.9 20.9 1.0
C A:GLY420 4.4 21.9 1.0
SD A:MET415 4.6 36.0 1.0
SG A:CYS417 4.7 21.9 1.0
O A:HOH849 4.8 34.7 1.0
C A:CYS421 4.8 18.7 1.0
O A:GLY420 4.9 22.0 1.0
SG A:CYS170 4.9 20.3 1.0
CB A:CYS225 4.9 26.6 1.0
SG A:CYS225 4.9 23.4 1.0

Reference:

J.Duan, M.Senger, J.Esselborn, V.Engelbrecht, F.Wittkamp, U.P.Apfel, E.Hofmann, S.T.Stripp, T.Happe, M.Winkler. Crystallographic and Spectroscopic Assignment of the Proton Transfer Pathway in [Fefe]-Hydrogenases. Nat Commun V. 9 4726 2018.
ISSN: ESSN 2041-1723
PubMed: 30413719
DOI: 10.1038/S41467-018-07140-X
Page generated: Sun Dec 13 16:27:55 2020

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