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Iron in PDB 4r0v: [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster

Enzymatic activity of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster

All present enzymatic activity of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster:
1.18.99.1;

Protein crystallography data

The structure of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster, PDB code: 4r0v was solved by S.D.Swanson, M.W.Ratzloff, D.W.Mulder, J.H.Artz, S.Ghose, A.Hoffman, S.White, O.A.Zadvornyy, J.B.Broderick, B.Bothner, P.W.King, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.645, 70.964, 94.686, 90.00, 91.91, 90.00
R / Rfree (%) 20.6 / 25.2

Other elements in 4r0v:

The structure of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster also contains other interesting chemical elements:

Arsenic (As) 2 atoms
Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster (pdb code 4r0v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster, PDB code: 4r0v:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 1 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:38.9
occ:1.00
 FE1 A:SF4601 0.0 38.9 1.0
S4 A:SF4601 2.1 25.2 1.0
S2 A:SF4601 2.1 27.9 1.0
S3 A:SF4601 2.1 24.9 1.0
SG A:CYS417 2.3 40.0 1.0
CB A:CYS417 3.0 39.2 1.0
FE4 A:SF4601 3.0 41.5 1.0
FE3 A:SF4601 3.0 39.8 1.0
FE2 A:SF4601 3.0 40.1 1.0
S1 A:SF4601 3.7 25.6 1.0
N A:CYS417 3.9 41.4 1.0
CA A:CYS417 4.0 40.8 1.0
O A:GLY420 4.2 39.1 1.0
C A:GLY420 4.2 34.3 1.0
CA A:CYS421 4.2 33.1 1.0
CA A:GLY424 4.3 34.2 1.0
N A:CYS421 4.3 34.1 1.0
O A:HOH701 4.5 47.5 1.0
SG A:CYS421 4.5 35.9 1.0
N A:GLY424 4.7 35.2 1.0
CA A:GLY420 4.8 37.1 1.0
C A:ALA416 4.9 41.8 1.0
CB A:CYS421 5.0 32.9 1.0

Iron binding site 2 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 2 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:40.1
occ:1.00
 FE2 A:SF4601 0.0 40.1 1.0
S3 A:SF4601 2.1 24.9 1.0
S4 A:SF4601 2.1 25.2 1.0
S1 A:SF4601 2.1 25.6 1.0
SG A:CYS421 2.2 35.9 1.0
FE4 A:SF4601 3.0 41.5 1.0
FE1 A:SF4601 3.0 38.9 1.0
FE3 A:SF4601 3.1 39.8 1.0
CB A:CYS421 3.3 32.9 1.0
CA A:CYS421 3.6 33.1 1.0
S2 A:SF4601 3.7 27.9 1.0
N A:CYS421 4.1 34.1 1.0
CB A:CYS225 4.4 39.1 1.0
SG A:CYS225 4.4 38.0 1.0
O A:HOH716 4.5 50.1 1.0
C A:GLY420 4.8 34.3 1.0
CG A:PRO224 4.9 33.0 1.0
C A:CYS421 4.9 32.3 1.0

Iron binding site 3 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 3 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:39.8
occ:1.00
 FE3 A:SF4601 0.0 39.8 1.0
S2 A:SF4601 2.1 27.9 1.0
S4 A:SF4601 2.1 25.2 1.0
S1 A:SF4601 2.1 25.6 1.0
SG A:CYS170 2.4 36.3 1.0
FE1 A:SF4601 3.0 38.9 1.0
FE4 A:SF4601 3.1 41.5 1.0
FE2 A:SF4601 3.1 40.1 1.0
CB A:CYS170 3.3 33.6 1.0
S3 A:SF4601 3.7 24.9 1.0
N A:ALA416 3.9 35.5 1.0
CA A:CYS170 4.0 32.3 1.0
CB A:MET415 4.3 38.3 0.5
SG A:CYS421 4.4 35.9 1.0
CA A:MET415 4.5 38.5 0.5
CA A:MET415 4.5 39.7 0.5
SD A:MET415 4.6 41.8 0.5
CB A:ALA416 4.6 38.2 1.0
C A:MET415 4.6 37.4 1.0
CB A:MET415 4.7 41.9 0.5
N A:CYS417 4.7 41.4 1.0
CA A:ALA416 4.7 36.7 1.0
CD A:PRO171 4.8 39.8 1.0
C A:CYS170 4.9 35.4 1.0
OD A:CSO169 4.9 25.0 0.3
SG A:CYS417 4.9 40.0 1.0
CG A:MET415 5.0 39.7 0.5
N A:PRO171 5.0 36.8 1.0

Iron binding site 4 out of 8 in 4r0v

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Iron binding site 4 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:41.5
occ:1.00
 FE4 A:SF4601 0.0 41.5 1.0
S3 A:SF4601 2.1 24.9 1.0
S1 A:SF4601 2.1 25.6 1.0
S2 A:SF4601 2.2 27.9 1.0
SG A:CYS225 2.4 38.0 1.0
FE1 A:SF4601 3.0 38.9 1.0
FE2 A:SF4601 3.0 40.1 1.0
FE3 A:SF4601 3.1 39.8 1.0
CB A:CYS225 3.4 39.1 1.0
S4 A:SF4601 3.7 25.2 1.0
O A:HOH701 3.8 47.5 1.0
SG A:CYS170 4.4 36.3 1.0
CA A:CYS225 4.4 38.0 1.0
SG A:CYS417 4.5 40.0 1.0
CD A:PRO171 4.6 39.8 1.0
CB A:ARG227 4.7 39.5 1.0
CD A:ARG227 4.8 55.7 1.0
CG A:ARG227 4.9 46.3 1.0
NE A:ARG227 4.9 60.9 1.0

Iron binding site 5 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 5 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:39.2
occ:1.00
 FE1 B:SF4601 0.0 39.2 1.0
S2 B:SF4601 2.1 27.6 1.0
S4 B:SF4601 2.1 25.3 1.0
S3 B:SF4601 2.1 24.8 1.0
SG B:CYS417 2.4 40.0 1.0
FE4 B:SF4601 3.0 41.4 1.0
FE3 B:SF4601 3.0 39.9 1.0
FE2 B:SF4601 3.0 40.4 1.0
CB B:CYS417 3.0 38.7 1.0
N B:CYS417 3.7 41.5 1.0
S1 B:SF4601 3.7 25.8 1.0
CA B:CYS417 4.0 40.5 1.0
O B:HOH701 4.1 47.3 1.0
CA B:GLY424 4.4 33.9 1.0
C B:ALA416 4.6 41.8 1.0
O B:GLY420 4.6 38.4 1.0
C B:GLY420 4.7 34.4 1.0
CB B:ALA416 4.8 38.1 1.0
N B:CYS421 4.8 34.1 1.0
N B:ALA416 4.9 35.2 1.0
CA B:CYS421 4.9 33.1 1.0
SG B:CYS225 4.9 38.1 1.0
N B:GLY424 5.0 35.2 1.0
CA B:ALA416 5.0 36.6 1.0

Iron binding site 6 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 6 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:40.4
occ:1.00
 FE2 B:SF4601 0.0 40.4 1.0
S4 B:SF4601 2.1 25.3 1.0
S1 B:SF4601 2.1 25.8 1.0
S3 B:SF4601 2.1 24.8 1.0
SG B:CYS225 2.3 38.1 1.0
FE3 B:SF4601 3.0 39.9 1.0
FE1 B:SF4601 3.0 39.2 1.0
FE4 B:SF4601 3.0 41.4 1.0
CB B:CYS225 3.0 39.4 1.0
S2 B:SF4601 3.7 27.6 1.0
O B:HOH701 4.1 47.3 1.0
CA B:CYS225 4.2 38.1 1.0
CD B:PRO171 4.7 39.2 1.0
CE B:LYS228 4.8 36.3 1.0
CG B:LYS228 4.9 33.8 1.0

Iron binding site 7 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 7 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:39.9
occ:1.00
 FE3 B:SF4601 0.0 39.9 1.0
S2 B:SF4601 2.1 27.6 1.0
S1 B:SF4601 2.1 25.8 1.0
S4 B:SF4601 2.1 25.3 1.0
SG B:CYS421 2.8 35.8 1.0
FE1 B:SF4601 3.0 39.2 1.0
FE4 B:SF4601 3.0 41.4 1.0
FE2 B:SF4601 3.0 40.4 1.0
CA B:CYS421 3.4 33.1 1.0
N B:CYS421 3.5 34.1 1.0
CB B:CYS421 3.7 33.4 1.0
S3 B:SF4601 3.7 24.8 1.0
C B:GLY420 4.2 34.4 1.0
O B:GLY420 4.7 38.4 1.0
C B:CYS421 4.7 32.6 1.0
CA B:GLY420 4.8 37.4 1.0
SD B:MET415 4.9 45.6 0.5
OD B:CSO169 5.0 22.0 0.3

Iron binding site 8 out of 8 in 4r0v

Go back to Iron Binding Sites List in 4r0v
Iron binding site 8 out of 8 in the [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated By the Modification and Degradation of the H Cluster 2FE Subcluster within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe601

b:41.4
occ:1.00
 FE4 B:SF4601 0.0 41.4 1.0
S1 B:SF4601 2.1 25.8 1.0
S2 B:SF4601 2.1 27.6 1.0
S3 B:SF4601 2.1 24.8 1.0
SG B:CYS170 2.4 36.8 1.0
FE1 B:SF4601 3.0 39.2 1.0
FE3 B:SF4601 3.0 39.9 1.0
FE2 B:SF4601 3.0 40.4 1.0
CB B:CYS170 3.1 33.1 1.0
CA B:CYS170 3.7 32.2 1.0
S4 B:SF4601 3.7 25.3 1.0
N B:ALA416 3.9 35.2 1.0
CB B:ALA416 4.3 38.1 1.0
CD B:PRO171 4.5 39.2 1.0
C B:CYS170 4.5 34.9 1.0
CA B:ALA416 4.6 36.6 1.0
N B:PRO171 4.6 36.2 1.0
CA B:MET415 4.7 38.6 0.5
N B:CYS417 4.7 41.5 1.0
CB B:MET415 4.7 39.8 0.5
C B:MET415 4.7 37.5 1.0
CA B:MET415 4.7 39.3 0.5
N B:GLY172 4.8 38.9 1.0
N B:CYS170 4.8 34.2 1.0
SD B:MET415 5.0 45.6 0.5

Reference:

K.D.Swanson, M.W.Ratzloff, D.W.Mulder, J.H.Artz, S.Ghose, A.Hoffman, S.White, O.A.Zadvornyy, J.B.Broderick, B.Bothner, P.W.King, J.W.Peters. [Fefe]-Hydrogenase Oxygen Inactivation Is Initiated at the H Cluster 2FE Subcluster. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25579778
DOI: 10.1021/JA510169S
Page generated: Mon Aug 5 09:03:19 2024

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