Iron in PDB 5ksw: Dhodb-I74D Mutant

Enzymatic activity of Dhodb-I74D Mutant

All present enzymatic activity of Dhodb-I74D Mutant:
1.3.1.14;

Protein crystallography data

The structure of Dhodb-I74D Mutant, PDB code: 5ksw was solved by Y.A.Pompeu, J.D.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.92 / 2.47
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.990, 151.720, 214.310, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.4

Other elements in 5ksw:

The structure of Dhodb-I74D Mutant also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Dhodb-I74D Mutant (pdb code 5ksw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dhodb-I74D Mutant, PDB code: 5ksw:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5ksw

Go back to Iron Binding Sites List in 5ksw
Iron binding site 1 out of 4 in the Dhodb-I74D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dhodb-I74D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:38.7
occ:1.00
FE1 B:FES302 0.0 38.7 1.0
S1 B:FES302 2.2 41.1 1.0
S2 B:FES302 2.2 40.3 1.0
SG B:CYS231 2.4 39.1 1.0
SG B:CYS226 2.5 44.9 1.0
FE2 B:FES302 3.0 39.5 1.0
N B:CYS231 3.4 42.4 1.0
CB B:CYS231 3.4 38.3 1.0
N B:CYS226 3.5 31.8 1.0
CB B:CYS226 3.6 34.9 1.0
N B:GLY227 3.7 37.6 1.0
CA B:CYS231 3.8 41.3 1.0
N B:TYR232 3.8 39.5 1.0
CA B:CYS226 4.0 36.7 1.0
N B:ALA233 4.1 37.0 1.0
C B:CYS231 4.1 35.7 1.0
N B:GLY229 4.2 47.0 1.0
N B:ALA230 4.2 47.4 1.0
C B:CYS226 4.3 40.9 1.0
SG B:CYS249 4.5 44.2 1.0
CB B:ALA233 4.5 26.6 1.0
N B:ALA225 4.5 36.2 1.0
N B:ILE228 4.5 34.4 1.0
CA B:GLY229 4.6 31.9 1.0
C B:ALA225 4.6 41.0 1.0
C B:ALA230 4.6 37.4 1.0
C B:GLY229 4.6 45.6 1.0
CA B:GLY227 4.7 28.2 1.0
CA B:TYR232 4.8 32.7 1.0
CA B:ALA225 4.9 35.5 1.0
CB B:ALA225 4.9 35.0 1.0
CA B:ALA233 4.9 42.2 1.0
CA B:ALA230 4.9 39.4 1.0
C B:TYR232 4.9 46.2 1.0

Iron binding site 2 out of 4 in 5ksw

Go back to Iron Binding Sites List in 5ksw
Iron binding site 2 out of 4 in the Dhodb-I74D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dhodb-I74D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:39.5
occ:1.00
FE2 B:FES302 0.0 39.5 1.0
S2 B:FES302 2.2 40.3 1.0
S1 B:FES302 2.2 41.1 1.0
SG B:CYS234 2.3 44.1 1.0
SG B:CYS249 2.5 44.2 1.0
FE1 B:FES302 3.0 38.7 1.0
CB B:CYS249 3.2 42.4 1.0
CB B:CYS234 3.6 41.1 1.0
N B:CYS249 4.1 38.9 1.0
N B:CYS234 4.1 35.7 1.0
N B:GLY229 4.2 47.0 1.0
CA B:CYS249 4.3 34.0 1.0
CA B:GLY229 4.4 31.9 1.0
CA B:CYS234 4.5 34.7 1.0
CB B:LYS247 4.6 39.6 1.0
N B:ALA233 4.7 37.0 1.0
N B:GLY227 4.7 37.6 1.0
SG B:CYS226 4.7 44.9 1.0
CA B:GLY227 4.8 28.2 1.0
N B:ILE228 4.9 34.4 1.0
CG B:MET224 4.9 32.5 1.0
SG B:CYS231 5.0 39.1 1.0

Iron binding site 3 out of 4 in 5ksw

Go back to Iron Binding Sites List in 5ksw
Iron binding site 3 out of 4 in the Dhodb-I74D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dhodb-I74D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:34.3
occ:1.00
FE1 D:FES302 0.0 34.3 1.0
S1 D:FES302 2.2 37.0 1.0
S2 D:FES302 2.2 37.1 1.0
SG D:CYS231 2.5 29.6 1.0
SG D:CYS226 2.5 29.6 1.0
FE2 D:FES302 2.7 32.9 1.0
N D:CYS226 3.5 29.6 1.0
CB D:CYS231 3.5 29.6 1.0
CB D:CYS226 3.6 29.6 1.0
N D:GLY227 3.6 30.6 1.0
N D:CYS231 3.6 29.6 1.0
N D:TYR232 3.9 37.5 1.0
CA D:CYS226 3.9 29.6 1.0
CA D:CYS231 3.9 29.6 1.0
N D:ALA233 4.1 38.2 1.0
C D:CYS226 4.2 29.6 1.0
C D:CYS231 4.2 29.6 1.0
N D:GLY229 4.3 42.1 1.0
N D:ALA225 4.4 33.2 1.0
CB D:ALA233 4.4 36.3 1.0
SG D:CYS249 4.4 37.9 1.0
N D:ALA230 4.4 34.5 1.0
C D:ALA225 4.5 29.6 1.0
N D:ILE228 4.6 33.5 1.0
CA D:GLY227 4.6 28.2 1.0
CA D:GLY229 4.7 29.6 1.0
C D:ALA230 4.8 45.4 1.0
C D:GLY229 4.8 37.0 1.0
CA D:ALA225 4.8 24.0 1.0
CA D:TYR232 4.9 39.7 1.0
CA D:ALA233 4.9 38.1 1.0
SG D:CYS234 4.9 41.2 1.0
CB D:ALA225 5.0 35.7 1.0

Iron binding site 4 out of 4 in 5ksw

Go back to Iron Binding Sites List in 5ksw
Iron binding site 4 out of 4 in the Dhodb-I74D Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dhodb-I74D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe302

b:32.9
occ:1.00
FE2 D:FES302 0.0 32.9 1.0
S2 D:FES302 2.2 37.1 1.0
S1 D:FES302 2.2 37.0 1.0
SG D:CYS234 2.5 41.2 1.0
SG D:CYS249 2.5 37.9 1.0
FE1 D:FES302 2.7 34.3 1.0
CB D:CYS249 3.4 17.7 1.0
CB D:CYS234 3.8 45.5 1.0
N D:GLY229 4.1 42.1 1.0
N D:CYS249 4.2 48.9 1.0
N D:CYS234 4.2 34.6 1.0
CA D:GLY229 4.3 29.6 1.0
CB D:LYS247 4.4 29.6 1.0
CA D:CYS249 4.4 42.0 1.0
SG D:CYS226 4.5 29.6 1.0
N D:ALA233 4.6 38.2 1.0
CA D:CYS234 4.7 29.3 1.0
N D:GLY227 4.7 30.6 1.0
CG D:LYS247 4.8 42.6 1.0
N D:ILE228 4.8 33.5 1.0
SG D:CYS231 4.9 29.6 1.0
N D:TYR232 4.9 37.5 1.0
CA D:GLY227 4.9 28.2 1.0
CD D:LYS247 4.9 38.1 1.0

Reference:

Y.A.Pompeu, J.D.Stewart. Isoleucine 74 Plays A Key Role in Controlling Electron Transfer Between Lactococcus Lactis Dihydroorotate Dehydrogenase 1B Subunits To Be Published.
Page generated: Sun Dec 13 16:06:19 2020

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