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Iron in PDB 5exi: Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution

Enzymatic activity of Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution

All present enzymatic activity of Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution:
2.8.1.8;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution, PDB code: 5exi was solved by M.I.Mclaughlin, N.D.Lanz, P.J.Goldman, K.-H.Lee, S.J.Booker, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.28 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.663, 57.815, 116.568, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution (pdb code 5exi). 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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution, PDB code: 5exi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5exi

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Iron binding site 1 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:28.2
occ:1.00
 FE1 A:SF4401 0.0 28.2 1.0
S2 A:SF4401 2.3 30.3 1.0
S4 A:SF4401 2.3 30.9 1.0
S3 A:SF4401 2.3 30.1 1.0
SG A:CYS88 2.4 25.7 1.0
FE4 A:SF4401 2.7 30.5 1.0
FE2 A:SF4401 2.7 30.5 1.0
FE3 A:SF4401 2.7 31.9 1.0
CB A:CYS88 3.1 32.0 1.0
S1 A:SF4401 3.8 31.8 1.0
CB A:ILE90 4.2 33.3 1.0
CG1 A:ILE90 4.3 34.1 1.0
CA A:CYS88 4.6 29.3 1.0
C3 A:DTV403 4.7 36.6 1.0
CB A:CYS85 4.7 30.1 1.0
SG A:CYS85 4.9 32.3 1.0
O A:HOH502 5.0 34.4 0.7

Iron binding site 2 out of 8 in 5exi

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Iron binding site 2 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:30.5
occ:1.00
 FE2 A:SF4401 0.0 30.5 1.0
S1 A:SF4401 2.3 31.8 1.0
S4 A:SF4401 2.3 30.9 1.0
S3 A:SF4401 2.3 30.1 1.0
SG A:CYS85 2.5 32.3 1.0
FE4 A:SF4401 2.7 30.5 1.0
FE1 A:SF4401 2.7 28.2 1.0
FE3 A:SF4401 2.7 31.9 1.0
CB A:CYS85 3.3 30.1 1.0
S2 A:SF4401 3.9 30.3 1.0
N A:CYS85 4.0 33.3 1.0
NH2 A:ARG192 4.1 25.9 1.0
CE2 A:PHE195 4.2 28.3 1.0
CA A:CYS85 4.3 31.2 1.0
C A:ARG84 4.6 35.0 1.0
CB A:CYS88 4.6 32.0 1.0
CZ A:PHE195 4.6 29.4 1.0
CB A:ARG83 4.7 30.0 1.0
N A:ARG84 4.8 32.6 1.0
SG A:CYS88 4.8 25.7 1.0
SG A:CYS81 4.8 35.0 1.0
O A:HOH645 4.9 31.1 1.0
S4 A:DTV403 4.9 37.6 1.0
NE A:ARG192 4.9 30.9 1.0
C A:ARG83 5.0 32.9 1.0

Iron binding site 3 out of 8 in 5exi

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Iron binding site 3 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:31.9
occ:1.00
 FE3 A:SF4401 0.0 31.9 1.0
S4 A:SF4401 2.3 30.9 1.0
S2 A:SF4401 2.3 30.3 1.0
S1 A:SF4401 2.3 31.8 1.0
S4 A:DTV403 2.5 37.6 1.0
FE1 A:SF4401 2.7 28.2 1.0
FE2 A:SF4401 2.7 30.5 1.0
FE4 A:SF4401 2.7 30.5 1.0
C4 A:DTV403 3.4 35.2 1.0
C3 A:DTV403 3.4 36.6 1.0
S3 A:SF4401 3.9 30.1 1.0
O3 A:DTV403 4.1 36.6 1.0
O A:HOH502 4.3 34.4 0.7
NH2 A:ARG192 4.4 25.9 1.0
O A:HOH619 4.5 27.3 1.0
C1 A:DTV403 4.7 37.6 1.0
C2 A:DTV403 4.7 38.5 1.0
CZ A:PHE195 4.7 29.4 1.0
SG A:CYS81 4.8 35.0 1.0
N A:ALA124 4.9 35.6 1.0
SG A:CYS88 4.9 25.7 1.0
O A:GLY122 5.0 41.0 1.0
SG A:CYS85 5.0 32.3 1.0

Iron binding site 4 out of 8 in 5exi

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Iron binding site 4 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:30.5
occ:1.00
 FE4 A:SF4401 0.0 30.5 1.0
S3 A:SF4401 2.2 30.1 1.0
S1 A:SF4401 2.3 31.8 1.0
S2 A:SF4401 2.3 30.3 1.0
SG A:CYS81 2.5 35.0 1.0
FE1 A:SF4401 2.7 28.2 1.0
FE2 A:SF4401 2.7 30.5 1.0
FE3 A:SF4401 2.7 31.9 1.0
CB A:CYS81 3.2 31.2 1.0
S4 A:SF4401 3.9 30.9 1.0
O A:ARG83 4.3 32.6 1.0
N A:ALA124 4.4 35.6 1.0
CB A:ARG83 4.5 30.0 1.0
C A:ARG83 4.5 32.9 1.0
CA A:CYS81 4.7 34.5 1.0
CB A:ALA124 4.8 30.1 1.0
N A:ARG83 4.8 34.3 1.0
CA A:ARG83 4.9 35.8 1.0
S4 A:DTV403 4.9 37.6 1.0
CA A:VAL123 4.9 29.1 1.0
CB A:ILE90 4.9 33.3 1.0
SG A:CYS88 4.9 25.7 1.0
CB A:VAL123 5.0 34.6 1.0
CG2 A:ILE90 5.0 31.6 1.0

Iron binding site 5 out of 8 in 5exi

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Iron binding site 5 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:22.7
occ:1.00
 FE1 A:SF4402 0.0 22.7 1.0
S3 A:SF4402 2.3 23.0 1.0
S2 A:SF4402 2.3 22.3 1.0
S4 A:SF4402 2.3 21.7 1.0
SG A:CYS60 2.4 25.2 1.0
FE2 A:SF4402 2.7 24.0 1.0
FE4 A:SF4402 2.7 25.2 1.0
FE3 A:SF4402 2.7 23.9 1.0
CB A:CYS60 3.2 27.0 1.0
S1 A:SF4402 3.9 22.0 1.0
CB A:ASN62 4.1 23.2 1.0
CD A:ARG290 4.3 26.6 1.0
ND2 A:ASN62 4.3 22.3 1.0
CB A:ARG290 4.4 24.6 1.0
CG A:ARG290 4.6 28.5 1.0
CA A:CYS60 4.6 26.3 1.0
CA A:CYS55 4.8 24.4 1.0
CG A:ASN62 4.8 23.8 1.0
SG A:CYS66 4.8 25.8 1.0
OG A:SER292 4.8 28.8 1.0
CB A:CYS55 4.8 27.0 1.0
N A:ASN62 4.9 24.4 1.0
CA A:ASN62 4.9 24.3 1.0
NE A:ARG290 4.9 36.3 1.0
N A:ILE63 4.9 25.2 1.0
SG A:CYS55 5.0 26.3 1.0
C A:ASN62 5.0 29.2 1.0

Iron binding site 6 out of 8 in 5exi

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Iron binding site 6 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:24.0
occ:1.00
 FE2 A:SF4402 0.0 24.0 1.0
S3 A:SF4402 2.3 23.0 1.0
S1 A:SF4402 2.3 22.0 1.0
S4 A:SF4402 2.3 21.7 1.0
SG A:CYS66 2.4 25.8 1.0
FE1 A:SF4402 2.7 22.7 1.0
FE4 A:SF4402 2.7 25.2 1.0
FE3 A:SF4402 2.7 23.9 1.0
CB A:CYS66 3.1 24.1 1.0
S2 A:SF4402 3.9 22.3 1.0
CB A:ASN62 4.2 23.2 1.0
CA A:CYS66 4.6 25.1 1.0
CA A:TYR293 4.7 23.8 1.0
O A:SER292 4.7 26.5 1.0
O A:HOH575 4.7 29.1 1.0
O A:HOH538 4.7 27.2 1.0
O A:ASN62 4.7 28.2 1.0
N A:TYR293 4.8 23.0 1.0
C A:ASN62 4.8 29.2 1.0
C A:SER292 4.8 26.2 1.0
SG A:CYS60 4.8 25.2 1.0
OG A:SER292 4.9 28.8 1.0
CD1 A:TYR293 4.9 25.2 1.0
SG A:CYS55 5.0 26.3 1.0

Iron binding site 7 out of 8 in 5exi

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Iron binding site 7 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:23.9
occ:1.00
 FE3 A:SF4402 0.0 23.9 1.0
S4 A:SF4402 2.3 21.7 1.0
S1 A:SF4402 2.3 22.0 1.0
S2 A:SF4402 2.3 22.3 1.0
SG A:CYS55 2.5 26.3 1.0
FE1 A:SF4402 2.7 22.7 1.0
FE2 A:SF4402 2.7 24.0 1.0
FE4 A:SF4402 2.7 25.2 1.0
CB A:CYS55 3.2 27.0 1.0
CA A:CYS55 3.7 24.4 1.0
S3 A:SF4402 3.9 23.0 1.0
OG1 A:THR73 4.1 24.0 1.0
N A:CYS55 4.1 24.3 1.0
CB A:THR73 4.2 25.5 1.0
N A:THR73 4.3 23.4 1.0
CA A:ALA72 4.6 24.6 1.0
OG A:SER292 4.7 28.8 1.0
C A:ALA72 4.8 23.7 1.0
CB A:CYS66 4.8 24.1 1.0
NE1 A:TRP67 4.9 23.9 1.0
CA A:THR73 4.9 23.3 1.0
SG A:CYS66 4.9 25.8 1.0
SG A:CYS60 4.9 25.2 1.0
CB A:CYS60 5.0 27.0 1.0

Iron binding site 8 out of 8 in 5exi

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Iron binding site 8 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution


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 M. Tuberculosis Lipoyl Synthase at 2.28 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:25.2
occ:1.00
 FE4 A:SF4402 0.0 25.2 1.0
S3 A:SF4402 2.3 23.0 1.0
S2 A:SF4402 2.3 22.3 1.0
S1 A:SF4402 2.3 22.0 1.0
OG A:SER292 2.3 28.8 1.0
FE1 A:SF4402 2.7 22.7 1.0
FE2 A:SF4402 2.7 24.0 1.0
FE3 A:SF4402 2.7 23.9 1.0
CB A:SER292 3.1 29.9 1.0
OG1 A:THR73 3.5 24.0 1.0
C A:SER292 3.8 26.2 1.0
S4 A:SF4402 3.9 21.7 1.0
CA A:SER292 3.9 26.1 1.0
O A:HOH533 4.0 34.6 1.0
N A:TYR293 4.0 23.0 1.0
O A:SER292 4.1 26.5 1.0
N A:SER292 4.2 24.1 1.0
CB A:THR73 4.3 25.5 1.0
CB A:ARG290 4.5 24.6 1.0
CA A:TYR293 4.7 23.8 1.0
NE A:ARG290 4.9 36.3 1.0
SG A:CYS60 4.9 25.2 1.0
SG A:CYS66 4.9 25.8 1.0
CD A:ARG290 5.0 26.6 1.0
O A:HOH538 5.0 27.2 1.0

Reference:

M.I.Mclaughlin, N.D.Lanz, P.J.Goldman, K.H.Lee, S.J.Booker, C.L.Drennan. Crystallographic Snapshots of Sulfur Insertion By Lipoyl Synthase. Proc.Natl.Acad.Sci.Usa V. 113 9446 2016.
ISSN: ESSN 1091-6490
PubMed: 27506792
DOI: 10.1073/PNAS.1602486113
Page generated: Tue Aug 6 00:37:01 2024

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