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Iron in PDB 6gm5: [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A

Enzymatic activity of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A

All present enzymatic activity of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A:
1.18.99.1;

Protein crystallography data

The structure of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A, PDB code: 6gm5 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) 48.00 / 1.45
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.620, 70.620, 154.910, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 19.7

Other elements in 6gm5:

The structure of [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A (pdb code 6gm5). 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 E141A, PDB code: 6gm5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6gm5

Go back to Iron Binding Sites List in 6gm5
Iron binding site 1 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A


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 E141A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:15.1
occ:1.00
FE1 A:SF4601 0.0 15.1 1.0
S4 A:SF4601 2.2 17.1 1.0
S2 A:SF4601 2.3 14.1 1.0
S3 A:SF4601 2.3 16.0 1.0
SG A:CYS170 2.3 14.7 1.0
FE3 A:SF4601 2.7 15.7 1.0
FE4 A:SF4601 2.7 14.8 1.0
FE2 A:SF4601 2.7 16.0 1.0
CB A:CYS170 3.3 13.9 1.0
S1 A:SF4601 3.9 14.3 1.0
CA A:CYS170 3.9 12.5 1.0
N A:ALA416 4.0 13.4 1.0
CE A:MET415 4.2 22.9 1.0
CB A:ALA416 4.3 17.3 1.0
CD A:PRO171 4.4 14.7 1.0
C A:CYS170 4.6 13.2 1.0
N A:PRO171 4.6 13.3 1.0
N A:CYS417 4.7 15.8 1.0
CA A:ALA416 4.7 16.8 1.0
SG A:CYS225 4.7 18.1 1.0
SG A:CYS417 4.8 18.0 1.0
SG A:CYS421 4.8 16.8 1.0
N A:GLY172 4.8 14.5 1.0
CA A:MET415 4.8 15.4 1.0
C A:MET415 4.9 15.4 1.0

Iron binding site 2 out of 4 in 6gm5

Go back to Iron Binding Sites List in 6gm5
Iron binding site 2 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A


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 E141A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:16.0
occ:1.00
FE2 A:SF4601 0.0 16.0 1.0
S3 A:SF4601 2.3 16.0 1.0
S1 A:SF4601 2.3 14.3 1.0
SG A:CYS417 2.3 18.0 1.0
S4 A:SF4601 2.3 17.1 1.0
FE3 A:SF4601 2.7 15.7 1.0
FE4 A:SF4601 2.7 14.8 1.0
FE1 A:SF4601 2.7 15.1 1.0
CB A:CYS417 3.2 20.4 1.0
N A:CYS417 3.8 15.8 1.0
S2 A:SF4601 3.9 14.1 1.0
O A:HOH991 3.9 23.1 1.0
CA A:CYS417 4.1 19.6 1.0
CA A:GLY424 4.4 14.9 1.0
SG A:CYS225 4.6 18.1 1.0
CA A:CYS421 4.7 14.1 1.0
C A:ALA416 4.8 20.6 1.0
O A:HOH1027 4.8 44.8 1.0
SG A:CYS170 4.8 14.7 1.0
CB A:ALA416 4.8 17.3 1.0
O A:GLY420 4.8 16.9 1.0
O A:HOH951 4.8 36.6 1.0
SG A:CYS421 4.8 16.8 1.0
N A:ALA416 4.8 13.4 1.0
C A:GLY420 4.9 17.1 1.0
N A:CYS421 4.9 15.0 1.0

Iron binding site 3 out of 4 in 6gm5

Go back to Iron Binding Sites List in 6gm5
Iron binding site 3 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A


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 E141A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:15.7
occ:1.00
FE3 A:SF4601 0.0 15.7 1.0
SG A:CYS225 2.2 18.1 1.0
S4 A:SF4601 2.3 17.1 1.0
S1 A:SF4601 2.3 14.3 1.0
S2 A:SF4601 2.3 14.1 1.0
FE1 A:SF4601 2.7 15.1 1.0
FE2 A:SF4601 2.7 16.0 1.0
FE4 A:SF4601 2.7 14.8 1.0
CB A:CYS225 3.0 15.0 1.0
S3 A:SF4601 3.8 16.0 1.0
O A:HOH991 4.0 23.1 1.0
CA A:CYS225 4.0 18.6 1.0
O A:HOH1229 4.1 28.1 1.0
CD A:PRO171 4.6 14.7 1.0
SG A:CYS170 4.7 14.7 1.0
SG A:CYS421 4.7 16.8 1.0
SG A:CYS417 4.7 18.0 1.0
CE A:LYS228 4.9 14.9 1.0
CG A:PRO171 4.9 16.9 1.0
CB A:ARG227 4.9 15.4 1.0
C A:CYS225 5.0 17.5 1.0
CG A:LYS228 5.0 14.1 1.0

Iron binding site 4 out of 4 in 6gm5

Go back to Iron Binding Sites List in 6gm5
Iron binding site 4 out of 4 in the [Fefe]-Hydrogenase HYDA1 From Chlamydomonas Reinhardtii,Variant E141A


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 E141A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:14.8
occ:1.00
FE4 A:SF4601 0.0 14.8 1.0
S2 A:SF4601 2.3 14.1 1.0
S1 A:SF4601 2.3 14.3 1.0
SG A:CYS421 2.3 16.8 1.0
S3 A:SF4601 2.3 16.0 1.0
FE3 A:SF4601 2.7 15.7 1.0
FE1 A:SF4601 2.7 15.1 1.0
FE2 A:SF4601 2.7 16.0 1.0
CB A:CYS421 3.4 14.0 1.0
CA A:CYS421 3.6 14.1 1.0
O A:HOH1229 3.8 28.1 1.0
CE A:MET415 3.8 22.9 1.0
S4 A:SF4601 3.9 17.1 1.0
N A:CYS421 3.9 15.0 1.0
C A:GLY420 4.5 17.1 1.0
O A:HOH1106 4.8 41.2 1.0
SG A:CYS225 4.8 18.1 1.0
SG A:CYS417 4.8 18.0 1.0
SG A:CYS170 4.9 14.7 1.0
CB A:CYS225 4.9 15.0 1.0
C A:CYS421 4.9 13.4 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 16:27:52 2020

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