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Iron in PDB 4rqo: Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila

Enzymatic activity of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila

All present enzymatic activity of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila:
4.3.1.17;

Protein crystallography data

The structure of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila, PDB code: 4rqo was solved by J.B.Thoden, H.M.Holden, G.A.Grant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.45 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 81.390, 81.390, 267.521, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 25.8

Other elements in 4rqo:

The structure of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila (pdb code 4rqo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila, PDB code: 4rqo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4rqo

Go back to Iron Binding Sites List in 4rqo
Iron binding site 1 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:33.6
occ:1.00
 FE1 A:SF4500 0.0 33.6 1.0
S3 A:SF4500 2.1 34.0 1.0
S2 A:SF4500 2.1 36.6 1.0
S4 A:SF4500 2.1 33.4 1.0
SG A:CYS458 2.2 36.8 1.0
FE4 A:SF4500 3.0 32.0 1.0
FE3 A:SF4500 3.0 31.5 1.0
FE2 A:SF4500 3.0 30.9 1.0
CB A:CYS458 3.1 36.1 1.0
S1 A:SF4500 3.7 33.0 1.0
N A:CYS458 4.1 34.9 1.0
CA A:CYS458 4.2 33.9 1.0
CA A:GLY292 4.3 31.4 1.0
CG2 A:THR290 4.6 39.1 1.0
C A:GLY292 4.7 28.1 1.0
CB A:PRO456 4.8 36.8 1.0
SG A:CYS385 4.8 27.2 1.0
N A:GLU457 4.8 36.2 1.0
CB A:GLU346 4.8 33.0 1.0
SG A:CYS396 4.9 28.2 1.0
SG A:CYS343 5.0 28.5 1.0

Iron binding site 2 out of 8 in 4rqo

Go back to Iron Binding Sites List in 4rqo
Iron binding site 2 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:30.9
occ:1.00
 FE2 A:SF4500 0.0 30.9 1.0
S1 A:SF4500 2.1 33.0 1.0
S4 A:SF4500 2.1 33.4 1.0
S3 A:SF4500 2.1 34.0 1.0
SG A:CYS396 2.2 28.2 1.0
FE4 A:SF4500 3.0 32.0 1.0
FE3 A:SF4500 3.0 31.5 1.0
FE1 A:SF4500 3.0 33.6 1.0
CB A:CYS396 3.1 24.9 1.0
S2 A:SF4500 3.7 36.6 1.0
CA A:CYS396 3.8 26.6 1.0
N A:CYS396 4.3 29.4 1.0
CG A:PRO387 4.4 28.1 1.0
CB A:PRO387 4.4 30.0 1.0
CG1 A:VAL392 4.5 28.9 1.0
CA A:VAL392 4.9 29.5 1.0
SG A:CYS385 4.9 27.2 1.0
SG A:CYS458 5.0 36.8 1.0
CB A:CYS458 5.0 36.1 1.0

Iron binding site 3 out of 8 in 4rqo

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Iron binding site 3 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:31.5
occ:1.00
 FE3 A:SF4500 0.0 31.5 1.0
S1 A:SF4500 2.1 33.0 1.0
S4 A:SF4500 2.1 33.4 1.0
S2 A:SF4500 2.1 36.6 1.0
SG A:CYS343 2.2 28.5 1.0
CB A:CYS343 3.0 30.0 1.0
FE2 A:SF4500 3.0 30.9 1.0
FE1 A:SF4500 3.0 33.6 1.0
FE4 A:SF4500 3.0 32.0 1.0
S3 A:SF4500 3.7 34.0 1.0
CA A:CYS343 3.8 28.5 1.0
NH1 A:ARG399 4.0 28.3 1.0
CG2 A:VAL347 4.2 26.0 1.0
C A:CYS343 4.7 31.2 1.0
O A:CYS343 4.7 38.3 1.0
CD A:ARG399 4.8 33.3 1.0
CB A:VAL347 4.8 26.7 1.0
N A:CYS343 4.8 31.6 1.0
O A:THR384 4.9 29.0 1.0
SG A:CYS385 4.9 27.2 1.0
SG A:CYS396 5.0 28.2 1.0
CB A:CYS385 5.0 27.8 1.0

Iron binding site 4 out of 8 in 4rqo

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Iron binding site 4 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe500

b:32.0
occ:1.00
 FE4 A:SF4500 0.0 32.0 1.0
SG A:CYS385 2.1 27.2 1.0
S1 A:SF4500 2.1 33.0 1.0
S3 A:SF4500 2.1 34.0 1.0
S2 A:SF4500 2.1 36.6 1.0
CB A:CYS385 3.0 27.8 1.0
FE2 A:SF4500 3.0 30.9 1.0
FE1 A:SF4500 3.0 33.6 1.0
FE3 A:SF4500 3.0 31.5 1.0
CA A:CYS385 3.6 30.6 1.0
S4 A:SF4500 3.7 33.4 1.0
N A:GLU457 4.1 36.2 1.0
CG A:PRO387 4.2 28.1 1.0
CD A:PRO387 4.2 26.4 1.0
C A:CYS385 4.3 30.5 1.0
N A:ASP386 4.5 32.7 1.0
CB A:GLU457 4.6 36.4 1.0
CA A:PRO456 4.6 35.0 1.0
CB A:CYS343 4.7 30.0 1.0
N A:CYS385 4.8 31.8 1.0
SG A:CYS343 4.9 28.5 1.0
C A:PRO456 4.9 36.8 1.0
CA A:GLU457 4.9 36.0 1.0
O A:HOH629 4.9 27.6 1.0
SG A:CYS458 4.9 36.8 1.0
SG A:CYS396 4.9 28.2 1.0
CB A:PRO387 5.0 30.0 1.0

Iron binding site 5 out of 8 in 4rqo

Go back to Iron Binding Sites List in 4rqo
Iron binding site 5 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:31.9
occ:1.00
 FE1 B:SF4501 0.0 31.9 1.0
S3 B:SF4501 2.1 32.2 1.0
S2 B:SF4501 2.1 35.9 1.0
S4 B:SF4501 2.1 34.4 1.0
SG B:CYS458 2.2 30.5 1.0
CB B:CYS458 2.9 26.8 1.0
FE3 B:SF4501 3.0 29.4 1.0
FE4 B:SF4501 3.0 28.1 1.0
FE2 B:SF4501 3.0 30.2 1.0
S1 B:SF4501 3.7 32.3 1.0
N B:CYS458 4.0 27.6 1.0
CA B:GLY292 4.1 26.4 1.0
CA B:CYS458 4.1 28.4 1.0
C B:GLY292 4.6 24.5 1.0
CB B:PRO456 4.7 28.6 1.0
CB B:GLU346 4.8 31.0 1.0
CG2 B:THR290 4.8 29.4 1.0
SG B:CYS396 4.8 27.7 1.0
CG1 B:VAL392 4.9 31.2 1.0
CG B:GLU346 4.9 30.5 1.0
N B:GLY292 4.9 27.8 1.0
SG B:CYS385 4.9 26.1 1.0
O B:GLY292 4.9 23.7 1.0
SG B:CYS343 4.9 26.5 1.0
N B:GLU457 4.9 28.0 1.0
C B:CYS458 5.0 31.2 1.0

Iron binding site 6 out of 8 in 4rqo

Go back to Iron Binding Sites List in 4rqo
Iron binding site 6 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:30.2
occ:1.00
 FE2 B:SF4501 0.0 30.2 1.0
SG B:CYS396 2.0 27.7 1.0
S1 B:SF4501 2.1 32.3 1.0
S3 B:SF4501 2.1 32.2 1.0
S4 B:SF4501 2.1 34.4 1.0
CB B:CYS396 3.0 23.7 1.0
FE1 B:SF4501 3.0 31.9 1.0
FE3 B:SF4501 3.0 29.4 1.0
FE4 B:SF4501 3.0 28.1 1.0
S2 B:SF4501 3.7 35.9 1.0
CA B:CYS396 3.8 25.8 1.0
N B:CYS396 4.2 29.4 1.0
CB B:PRO387 4.3 29.5 1.0
CG1 B:VAL392 4.4 31.2 1.0
CG B:PRO387 4.5 28.4 1.0
CA B:VAL392 4.8 29.6 1.0
CB B:CYS458 4.9 26.8 1.0
SG B:CYS385 5.0 26.1 1.0

Iron binding site 7 out of 8 in 4rqo

Go back to Iron Binding Sites List in 4rqo
Iron binding site 7 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:29.4
occ:1.00
 FE3 B:SF4501 0.0 29.4 1.0
S2 B:SF4501 2.1 35.9 1.0
S1 B:SF4501 2.1 32.3 1.0
S4 B:SF4501 2.1 34.4 1.0
SG B:CYS343 2.2 26.5 1.0
FE1 B:SF4501 3.0 31.9 1.0
FE4 B:SF4501 3.0 28.1 1.0
FE2 B:SF4501 3.0 30.2 1.0
CB B:CYS343 3.0 30.1 1.0
S3 B:SF4501 3.7 32.2 1.0
CA B:CYS343 3.8 25.9 1.0
CG2 B:VAL347 4.0 26.8 1.0
NH1 B:ARG399 4.1 23.8 1.0
CD B:ARG399 4.7 27.3 1.0
SG B:CYS396 4.7 27.7 1.0
O B:CYS343 4.7 29.0 1.0
C B:CYS343 4.8 27.3 1.0
N B:CYS343 4.8 23.9 1.0
CB B:VAL347 4.9 29.1 1.0
SG B:CYS385 5.0 26.1 1.0
CB B:CYS385 5.0 24.2 1.0

Iron binding site 8 out of 8 in 4rqo

Go back to Iron Binding Sites List in 4rqo
Iron binding site 8 out of 8 in the Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of L-Serine Dehydratase From Legionella Pneumophila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:28.1
occ:1.00
 FE4 B:SF4501 0.0 28.1 1.0
S3 B:SF4501 2.1 32.2 1.0
S1 B:SF4501 2.1 32.3 1.0
S2 B:SF4501 2.1 35.9 1.0
SG B:CYS385 2.2 26.1 1.0
FE3 B:SF4501 3.0 29.4 1.0
FE1 B:SF4501 3.0 31.9 1.0
FE2 B:SF4501 3.0 30.2 1.0
CB B:CYS385 3.1 24.2 1.0
S4 B:SF4501 3.7 34.4 1.0
CA B:CYS385 3.8 28.9 1.0
N B:GLU457 4.1 28.0 1.0
CG B:PRO387 4.2 28.4 1.0
CD B:PRO387 4.3 27.7 1.0
CA B:PRO456 4.5 27.6 1.0
CB B:GLU457 4.5 32.2 1.0
C B:CYS385 4.5 31.9 1.0
SG B:CYS396 4.8 27.7 1.0
CB B:PRO456 4.8 28.6 1.0
CB B:CYS343 4.8 30.1 1.0
SG B:CYS458 4.8 30.5 1.0
C B:PRO456 4.8 26.5 1.0
CA B:GLU457 4.8 28.4 1.0
CB B:PRO387 4.9 29.5 1.0
SG B:CYS343 4.9 26.5 1.0
N B:ASP386 4.9 31.4 1.0
CG B:GLU457 4.9 35.9 1.0
N B:CYS458 4.9 27.6 1.0
N B:CYS385 4.9 27.8 1.0

Reference:

J.B.Thoden, H.M.Holden, G.A.Grant. Structure of L-Serine Dehydratase From Legionella Pneumophila: Novel Use of the C-Terminal Cysteine As An Intrinsic Competitive Inhibitor. Biochemistry 2014.
ISSN: ISSN 0006-2960
PubMed: 25380533
DOI: 10.1021/BI501253W
Page generated: Mon Aug 5 09:22:57 2024

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