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Iron in PDB 3lx4: Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)

Enzymatic activity of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)

All present enzymatic activity of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg):
1.18.99.1;

Protein crystallography data

The structure of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg), PDB code: 3lx4 was solved by D.W.Mulder, E.S.Boyd, R.Sarma, R.K.Lange, J.A.Endrizzi, J.B.Broderick, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.97
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 70.895, 70.895, 155.429, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 21.6

Other elements in 3lx4:

The structure of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) (pdb code 3lx4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg), PDB code: 3lx4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 3lx4

Go back to Iron Binding Sites List in 3lx4
Iron binding site 1 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe458

b:18.9
occ:1.00
 FE1 A:SF4458 0.0 18.9 1.0
SG A:CYS130 2.3 18.2 1.0
S2 A:SF4458 2.3 19.9 1.0
S3 A:SF4458 2.3 20.7 1.0
S4 A:SF4458 2.3 24.3 1.0
FE3 A:SF4458 2.7 21.3 1.0
FE4 A:SF4458 2.8 21.6 1.0
FE2 A:SF4458 2.8 20.7 1.0
CB A:CYS130 3.3 14.7 1.0
CA A:CYS130 3.9 15.7 1.0
N A:ALA376 3.9 16.1 1.0
S1 A:SF4458 3.9 20.3 1.0
CB A:ALA376 4.2 18.2 1.0
CH3 A:ACT460 4.3 39.4 1.0
CD A:PRO131 4.4 15.5 1.0
C A:CYS130 4.5 19.6 1.0
CA A:ALA376 4.6 26.8 1.0
N A:CYS377 4.6 16.2 1.0
N A:PRO131 4.7 17.2 1.0
SG A:CYS185 4.8 20.1 1.0
SG A:CYS377 4.8 21.2 1.0
SG A:CYS381 4.8 22.4 1.0
SD A:MET375 4.8 45.6 1.0
N A:GLY132 4.8 16.2 1.0
CA A:MET375 4.8 18.9 1.0
C A:MET375 4.8 24.4 1.0

Iron binding site 2 out of 8 in 3lx4

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Iron binding site 2 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe458

b:20.7
occ:1.00
 FE2 A:SF4458 0.0 20.7 1.0
SG A:CYS377 2.3 21.2 1.0
S4 A:SF4458 2.3 24.3 1.0
S3 A:SF4458 2.3 20.7 1.0
S1 A:SF4458 2.3 20.3 1.0
FE3 A:SF4458 2.7 21.3 1.0
FE4 A:SF4458 2.8 21.6 1.0
FE1 A:SF4458 2.8 18.9 1.0
CB A:CYS377 3.2 17.4 1.0
N A:CYS377 3.8 16.2 1.0
S2 A:SF4458 3.9 19.9 1.0
O A:HOH830 4.0 25.1 1.0
CA A:CYS377 4.1 20.9 1.0
CA A:GLY384 4.4 16.6 1.0
SG A:CYS185 4.5 20.1 1.0
CB A:ALA376 4.7 18.2 1.0
C A:ALA376 4.7 23.7 1.0
O A:GLY380 4.7 18.5 1.0
SG A:CYS130 4.8 18.2 1.0
CA A:CYS381 4.8 20.8 1.0
O A:HOH572 4.8 36.5 1.0
SG A:CYS381 4.8 22.4 1.0
N A:ALA376 4.9 16.1 1.0
C A:GLY380 4.9 21.5 1.0
CA A:ALA376 5.0 26.8 1.0

Iron binding site 3 out of 8 in 3lx4

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Iron binding site 3 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe458

b:21.3
occ:1.00
 FE3 A:SF4458 0.0 21.3 1.0
SG A:CYS185 2.2 20.1 1.0
S4 A:SF4458 2.3 24.3 1.0
S1 A:SF4458 2.3 20.3 1.0
S2 A:SF4458 2.3 19.9 1.0
FE2 A:SF4458 2.7 20.7 1.0
FE1 A:SF4458 2.7 18.9 1.0
FE4 A:SF4458 2.7 21.6 1.0
CB A:CYS185 3.1 24.7 1.0
S3 A:SF4458 3.8 20.7 1.0
O A:HOH1025 4.1 33.1 1.0
O A:HOH830 4.1 25.1 1.0
CA A:CYS185 4.2 22.5 1.0
CD A:PRO131 4.6 15.5 1.0
SG A:CYS130 4.7 18.2 1.0
SG A:CYS381 4.7 22.4 1.0
SG A:CYS377 4.7 21.2 1.0
CE A:LYS188 4.8 20.1 1.0
CG A:PRO131 4.8 17.9 1.0

Iron binding site 4 out of 8 in 3lx4

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Iron binding site 4 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe458

b:21.6
occ:1.00
 FE4 A:SF4458 0.0 21.6 1.0
SG A:CYS381 2.3 22.4 1.0
S1 A:SF4458 2.3 20.3 1.0
S3 A:SF4458 2.3 20.7 1.0
S2 A:SF4458 2.3 19.9 1.0
FE3 A:SF4458 2.7 21.3 1.0
FE2 A:SF4458 2.8 20.7 1.0
FE1 A:SF4458 2.8 18.9 1.0
CB A:CYS381 3.4 20.2 1.0
CA A:CYS381 3.6 20.8 1.0
O A:HOH1025 3.8 33.1 1.0
CH3 A:ACT460 3.9 39.4 1.0
N A:CYS381 3.9 17.4 1.0
S4 A:SF4458 3.9 24.3 1.0
C A:ACT460 4.5 49.0 1.0
O A:ACT460 4.5 45.9 1.0
C A:GLY380 4.5 21.5 1.0
SD A:MET375 4.7 45.6 1.0
SG A:CYS185 4.8 20.1 1.0
SG A:CYS377 4.8 21.2 1.0
SG A:CYS130 4.9 18.2 1.0
C A:CYS381 4.9 15.2 1.0
CB A:CYS185 4.9 24.7 1.0
O A:GLY380 4.9 18.5 1.0

Iron binding site 5 out of 8 in 3lx4

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Iron binding site 5 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe458

b:21.5
occ:1.00
 FE1 B:SF4458 0.0 21.5 1.0
SG B:CYS185 2.2 19.8 1.0
S4 B:SF4458 2.3 24.8 1.0
S2 B:SF4458 2.3 19.4 1.0
S3 B:SF4458 2.3 20.6 1.0
FE3 B:SF4458 2.7 20.1 1.0
FE2 B:SF4458 2.7 19.4 1.0
FE4 B:SF4458 2.7 21.3 1.0
CB B:CYS185 3.2 24.4 1.0
S1 B:SF4458 3.9 21.9 1.0
O B:HOH598 4.2 25.2 1.0
O B:HOH649 4.2 36.8 1.0
CA B:CYS185 4.2 23.4 1.0
CD B:PRO131 4.6 14.2 1.0
SG B:CYS130 4.7 18.1 1.0
SG B:CYS381 4.7 21.3 1.0
SG B:CYS377 4.8 21.5 1.0
CE B:LYS188 4.9 21.0 1.0
CG B:PRO131 4.9 18.3 1.0
CB B:ARG187 5.0 17.6 1.0

Iron binding site 6 out of 8 in 3lx4

Go back to Iron Binding Sites List in 3lx4
Iron binding site 6 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe458

b:19.4
occ:1.00
 FE2 B:SF4458 0.0 19.4 1.0
SG B:CYS130 2.3 18.1 1.0
S3 B:SF4458 2.3 20.6 1.0
S4 B:SF4458 2.3 24.8 1.0
S1 B:SF4458 2.3 21.9 1.0
FE1 B:SF4458 2.7 21.5 1.0
FE4 B:SF4458 2.7 21.3 1.0
FE3 B:SF4458 2.8 20.1 1.0
CB B:CYS130 3.3 14.3 1.0
CA B:CYS130 3.9 15.4 1.0
S2 B:SF4458 3.9 19.4 1.0
N B:ALA376 4.0 16.9 1.0
CB B:ALA376 4.2 18.0 1.0
CH3 B:ACT460 4.4 33.4 1.0
CD B:PRO131 4.4 14.2 1.0
C B:CYS130 4.6 19.3 1.0
CA B:ALA376 4.6 26.5 1.0
N B:CYS377 4.6 17.8 1.0
N B:PRO131 4.7 17.4 1.0
SG B:CYS185 4.8 19.8 1.0
SD B:MET375 4.8 45.9 1.0
N B:GLY132 4.8 17.4 1.0
SG B:CYS381 4.8 21.3 1.0
SG B:CYS377 4.8 21.5 1.0
C B:MET375 4.9 23.7 1.0
CA B:MET375 4.9 18.7 1.0

Iron binding site 7 out of 8 in 3lx4

Go back to Iron Binding Sites List in 3lx4
Iron binding site 7 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe458

b:20.1
occ:1.00
 FE3 B:SF4458 0.0 20.1 1.0
S4 B:SF4458 2.3 24.8 1.0
S2 B:SF4458 2.3 19.4 1.0
SG B:CYS377 2.3 21.5 1.0
S1 B:SF4458 2.3 21.9 1.0
FE1 B:SF4458 2.7 21.5 1.0
FE4 B:SF4458 2.8 21.3 1.0
FE2 B:SF4458 2.8 19.4 1.0
CB B:CYS377 3.2 17.9 1.0
N B:CYS377 3.7 17.8 1.0
S3 B:SF4458 3.9 20.6 1.0
CA B:CYS377 4.1 21.3 1.0
O B:HOH598 4.2 25.2 1.0
CA B:GLY384 4.4 16.8 1.0
SG B:CYS185 4.6 19.8 1.0
C B:ALA376 4.7 23.9 1.0
CB B:ALA376 4.7 18.0 1.0
SG B:CYS130 4.7 18.1 1.0
O B:HOH1082 4.8 45.3 1.0
O B:GLY380 4.8 17.7 1.0
CA B:CYS381 4.8 21.0 1.0
O B:HOH651 4.9 37.8 1.0
N B:ALA376 4.9 16.9 1.0
SG B:CYS381 4.9 21.3 1.0
C B:GLY380 4.9 22.7 1.0
CA B:ALA376 5.0 26.5 1.0

Iron binding site 8 out of 8 in 3lx4

Go back to Iron Binding Sites List in 3lx4
Iron binding site 8 out of 8 in the Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe458

b:21.3
occ:1.00
 FE4 B:SF4458 0.0 21.3 1.0
S1 B:SF4458 2.3 21.9 1.0
S2 B:SF4458 2.3 19.4 1.0
S3 B:SF4458 2.3 20.6 1.0
SG B:CYS381 2.3 21.3 1.0
FE1 B:SF4458 2.7 21.5 1.0
FE2 B:SF4458 2.7 19.4 1.0
FE3 B:SF4458 2.8 20.1 1.0
CB B:CYS381 3.5 18.4 1.0
CA B:CYS381 3.6 21.0 1.0
O B:HOH649 3.9 36.8 1.0
CH3 B:ACT460 3.9 33.4 1.0
N B:CYS381 3.9 17.1 1.0
S4 B:SF4458 3.9 24.8 1.0
C B:GLY380 4.5 22.7 1.0
C B:ACT460 4.6 51.9 1.0
OXT B:ACT460 4.6 51.5 1.0
SD B:MET375 4.7 45.9 1.0
SG B:CYS185 4.8 19.8 1.0
SG B:CYS377 4.8 21.5 1.0
SG B:CYS130 4.9 18.1 1.0
C B:CYS381 4.9 15.8 1.0
O B:GLY380 4.9 17.7 1.0
CB B:CYS185 5.0 24.4 1.0

Reference:

D.W.Mulder, E.S.Boyd, R.Sarma, R.K.Lange, J.A.Endrizzi, J.B.Broderick, J.W.Peters. Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed in the Structure of Hyda(Deltaefg). Nature V. 465 248 2010.
ISSN: ISSN 0028-0836
PubMed: 20418861
DOI: 10.1038/NATURE08993
Page generated: Sun Aug 4 14:33:50 2024

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