Atomistry » Iron » PDB 9fuh-9gyz » 9fyi
Atomistry »
  Iron »
    PDB 9fuh-9gyz »
      9fyi »

Iron in PDB 9fyi: [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis

Enzymatic activity of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis

All present enzymatic activity of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis:
4.4.1.28;

Protein crystallography data

The structure of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis, PDB code: 9fyi was solved by P.Zecchin, L.Pecqueur, B.Golinelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.62 / 2.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.121, 79.148, 156.38, 90, 90, 90
R / Rfree (%) 22.2 / 26.1

Iron Binding Sites:

The binding sites of Iron atom in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis (pdb code 9fyi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis, PDB code: 9fyi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 1 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:151.1
occ:0.65
 FE1 A:SF4401 0.0 151.1 0.7
S2 A:SF4401 2.3 151.2 0.7
SG A:CYS336 2.3 113.6 1.0
S4 A:SF4401 2.3 151.2 0.7
S3 A:SF4401 2.3 151.1 0.7
FE3 A:SF4401 2.7 151.5 0.7
FE2 A:SF4401 2.8 151.2 0.7
FE4 A:SF4401 2.8 151.2 0.7
CB A:CYS336 3.3 107.7 1.0
CA A:CYS336 3.4 106.0 1.0
S1 A:SF4401 3.9 151.1 0.7
ND2 A:ASN239 3.9 94.2 1.0
O A:CYS336 4.2 100.9 1.0
C A:CYS336 4.3 101.3 1.0
N A:CYS336 4.5 108.9 1.0
SG A:CYS329 4.5 149.4 1.0
CD A:LYS333 4.7 136.9 1.0
SG A:CYS289 4.8 116.1 1.0
CB A:LYS339 4.8 91.5 1.0
CE A:LYS333 4.9 139.2 1.0

Iron binding site 2 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 2 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:151.2
occ:0.65
 FE2 A:SF4401 0.0 151.2 0.7
S1 A:SF4401 2.3 151.1 0.7
SG A:CYS289 2.3 116.1 1.0
S3 A:SF4401 2.3 151.1 0.7
S4 A:SF4401 2.3 151.2 0.7
FE4 A:SF4401 2.7 151.2 0.7
FE1 A:SF4401 2.8 151.1 0.7
FE3 A:SF4401 2.8 151.5 0.7
CB A:CYS289 3.2 108.5 1.0
ND2 A:ASN239 3.7 94.2 1.0
S2 A:SF4401 3.9 151.2 0.7
SG A:CYS336 4.1 113.6 1.0
CA A:CYS289 4.5 106.5 1.0
CB A:ASN239 4.5 88.5 1.0
N A:CYS289 4.6 107.8 1.0
CG A:ASN239 4.6 93.1 1.0
SG A:CYS287 4.8 126.2 1.0

Iron binding site 3 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 3 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:151.5
occ:0.65
 FE3 A:SF4401 0.0 151.5 0.7
S4 A:SF4401 2.3 151.2 0.7
S1 A:SF4401 2.3 151.1 0.7
S2 A:SF4401 2.3 151.2 0.7
SG A:CYS329 2.3 149.4 1.0
FE1 A:SF4401 2.7 151.1 0.7
FE2 A:SF4401 2.8 151.2 0.7
FE4 A:SF4401 2.8 151.2 0.7
CB A:CYS329 3.1 142.5 1.0
S3 A:SF4401 3.9 151.1 0.7
CA A:CYS329 3.9 140.4 1.0
SG A:CYS287 4.5 126.2 1.0
CA A:CYS287 4.5 116.4 1.0
CB A:CYS287 4.5 118.7 1.0
O A:CYS329 4.6 139.5 1.0
C A:CYS329 4.7 139.8 1.0
SG A:CYS336 4.8 113.6 1.0
SG A:CYS289 4.9 116.1 1.0

Iron binding site 4 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 4 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:151.2
occ:0.65
 FE4 A:SF4401 0.0 151.2 0.7
S3 A:SF4401 2.3 151.1 0.7
S1 A:SF4401 2.3 151.1 0.7
S2 A:SF4401 2.3 151.2 0.7
SG A:CYS287 2.3 126.2 1.0
FE2 A:SF4401 2.7 151.2 0.7
FE3 A:SF4401 2.8 151.5 0.7
FE1 A:SF4401 2.8 151.1 0.7
CB A:CYS287 3.4 118.7 1.0
CB A:CYS289 3.8 108.5 1.0
CA A:CYS287 3.9 116.4 1.0
S4 A:SF4401 3.9 151.2 0.7
CG A:LYS339 4.1 98.8 1.0
SG A:CYS289 4.1 116.1 1.0
CB A:LYS339 4.2 91.5 1.0
CB A:CYS329 4.4 142.5 1.0
C A:CYS287 4.5 114.9 1.0
SG A:CYS329 4.6 149.4 1.0
CG1 A:VAL290 4.7 101.0 1.0
N A:CYS289 4.7 107.8 1.0
CA A:CYS329 4.7 140.4 1.0
CA A:CYS289 4.8 106.5 1.0
O A:CYS287 4.8 115.2 1.0
N A:VAL290 4.9 101.3 1.0
SG A:CYS336 4.9 113.6 1.0

Iron binding site 5 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 5 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:153.5
occ:0.65
 FE1 B:SF4401 0.0 153.5 0.7
S2 B:SF4401 2.3 153.4 0.7
S3 B:SF4401 2.3 153.5 0.7
S4 B:SF4401 2.3 153.4 0.7
SG B:CYS287 2.3 142.8 1.0
FE3 B:SF4401 2.7 153.5 0.7
FE2 B:SF4401 2.8 153.7 0.7
FE4 B:SF4401 2.8 153.5 0.7
CB B:CYS287 3.5 136.7 1.0
CA B:CYS287 3.8 134.9 1.0
S1 B:SF4401 3.9 153.6 0.7
N B:GLY288 4.1 132.5 1.0
N B:CYS289 4.1 128.3 1.0
CB B:CYS289 4.1 128.8 1.0
CG B:LYS339 4.2 107.5 1.0
SG B:CYS289 4.4 134.9 1.0
CB B:LYS339 4.5 101.7 1.0
C B:CYS287 4.5 134.1 1.0
CA B:CYS289 4.7 127.2 1.0
CG1 B:VAL290 4.7 123.3 1.0
N B:VAL290 4.7 123.4 1.0
SG B:CYS329 4.7 160.0 1.0
CA B:CYS329 4.8 153.7 1.0
SG B:CYS336 4.9 124.9 1.0
CB B:CYS329 5.0 155.1 1.0

Iron binding site 6 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 6 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:153.7
occ:0.65
 FE2 B:SF4401 0.0 153.7 0.7
S4 B:SF4401 2.3 153.4 0.7
S1 B:SF4401 2.3 153.6 0.7
S3 B:SF4401 2.3 153.5 0.7
SG B:CYS329 2.3 160.0 1.0
FE1 B:SF4401 2.8 153.5 0.7
FE3 B:SF4401 2.8 153.5 0.7
FE4 B:SF4401 2.8 153.5 0.7
CB B:CYS329 3.3 155.1 1.0
CA B:CYS329 3.8 153.7 1.0
S2 B:SF4401 3.9 153.4 0.7
SG B:CYS336 4.1 124.9 1.0
CA B:CYS287 4.2 134.9 1.0
SG B:CYS287 4.4 142.8 1.0
CB B:CYS287 4.5 136.7 1.0
C B:CYS329 4.6 153.7 1.0
N B:ASP330 4.7 153.2 1.0
N B:CYS287 4.8 134.4 1.0
SG B:CYS289 4.9 134.9 1.0
N B:GLY288 5.0 132.5 1.0

Iron binding site 7 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 7 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:153.5
occ:0.65
 FE3 B:SF4401 0.0 153.5 0.7
SG B:CYS289 2.3 134.9 1.0
S4 B:SF4401 2.3 153.4 0.7
S1 B:SF4401 2.3 153.6 0.7
S2 B:SF4401 2.3 153.4 0.7
FE1 B:SF4401 2.7 153.5 0.7
FE2 B:SF4401 2.8 153.7 0.7
FE4 B:SF4401 2.8 153.5 0.7
CB B:CYS289 3.1 128.8 1.0
S3 B:SF4401 3.9 153.5 0.7
N B:CYS289 3.9 128.3 1.0
ND2 B:ASN239 4.1 110.9 1.0
CA B:CYS289 4.1 127.2 1.0
CB B:ASN239 4.6 105.4 1.0
N B:GLY288 4.8 132.5 1.0
SG B:CYS336 4.8 124.9 1.0
SG B:CYS287 4.8 142.8 1.0
CG B:ASN239 4.9 109.8 1.0

Iron binding site 8 out of 8 in 9fyi

Go back to Iron Binding Sites List in 9fyi
Iron binding site 8 out of 8 in the [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of [4FE-4S] Cluster-Containing L-Cysteine Desulfidase Cyua From Methanococcus Maripaludis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:153.5
occ:0.65
 FE4 B:SF4401 0.0 153.5 0.7
S2 B:SF4401 2.3 153.4 0.7
S3 B:SF4401 2.3 153.5 0.7
SG B:CYS336 2.3 124.9 1.0
S1 B:SF4401 2.3 153.6 0.7
FE2 B:SF4401 2.8 153.7 0.7
FE3 B:SF4401 2.8 153.5 0.7
FE1 B:SF4401 2.8 153.5 0.7
CB B:CYS336 3.1 119.0 1.0
CA B:CYS336 3.8 117.6 1.0
S4 B:SF4401 3.9 153.4 0.7
ND2 B:ASN239 3.9 110.9 1.0
SG B:CYS329 4.4 160.0 1.0
O B:CYS336 4.6 114.1 1.0
C B:CYS336 4.7 114.2 1.0
CB B:LYS339 4.7 101.7 1.0
SG B:CYS289 4.8 134.9 1.0
N B:CYS336 4.8 119.7 1.0
CG B:ASN239 4.9 109.8 1.0
SG B:CYS287 5.0 142.8 1.0

Reference:

P.Zecchin, B.Golinelli. Insights Into the Phylogenetic Distribution, Structure and Function of [4FE-4S]-Dependent L-Cysteine Desulfidase, An Enzyme That Supplies Sulfide to the Archaeon Methanococcus Maripaludis To Be Published.
Page generated: Fri Aug 8 06:05:22 2025

Last articles

Hg in 1BNT
Hg in 1BNQ
Hg in 1BNN
Hg in 1ARO
Hg in 1BNM
Hg in 1BN4
Hg in 1BN3
Hg in 1BN1
Hg in 1BH9
Hg in 1BIC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy