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Iron in PDB 5exj: Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 A Resolution

Enzymatic activity of Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 A Resolution

All present enzymatic activity of Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 A Resolution:
2.8.1.8;

Protein crystallography data

The structure of Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 A Resolution, PDB code: 5exj 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) 50.35 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.568, 58.517, 98.772, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.7

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 A Resolution (pdb code 5exj). 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 1.64 A Resolution, PDB code: 5exj:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5exj

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Iron binding site 1 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:17.6
occ:1.00
 FE1 A:SF4401 0.0 17.6 1.0
S2 A:SF4401 2.3 17.8 1.0
S3 A:SF4401 2.3 18.8 1.0
S4 A:SF4401 2.3 16.8 1.0
SG A:CYS88 2.4 18.5 1.0
FE4 A:SF4401 2.7 19.2 1.0
FE2 A:SF4401 2.7 18.4 1.0
FE3 A:SF4401 2.7 18.5 1.0
CB A:CYS88 3.2 15.2 1.0
S1 A:SF4401 3.8 20.4 1.0
O A:HOH635 4.1 27.0 1.0
CB A:ILE90 4.3 25.7 1.0
CG1 A:ILE90 4.5 26.3 1.0
CA A:CYS88 4.6 18.9 1.0
S4 A:DTV403 4.6 33.1 0.7
CB A:CYS85 4.7 15.4 1.0
SG A:CYS85 4.8 17.9 1.0
S1 A:DTV403 4.9 22.8 1.0
SG A:CYS81 4.9 20.1 1.0
C2 A:DTV403 4.9 25.2 0.9
CG2 A:ILE90 5.0 26.2 1.0

Iron binding site 2 out of 8 in 5exj

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Iron binding site 2 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.4
occ:1.00
 FE2 A:SF4401 0.0 18.4 1.0
S1 A:SF4401 2.3 20.4 1.0
S4 A:SF4401 2.3 16.8 1.0
S3 A:SF4401 2.3 18.8 1.0
SG A:CYS85 2.4 17.9 1.0
FE1 A:SF4401 2.7 17.6 1.0
FE3 A:SF4401 2.7 18.5 1.0
FE4 A:SF4401 2.7 19.2 1.0
CB A:CYS85 3.2 15.4 1.0
S2 A:SF4401 3.9 17.8 1.0
N A:CYS85 3.9 22.0 1.0
CE2 A:PHE195 4.2 16.1 1.0
CA A:CYS85 4.2 16.7 1.0
NH2 A:ARG192 4.2 14.8 1.0
CZ A:PHE195 4.6 17.8 1.0
CB A:ARG83 4.6 20.7 1.0
CB A:CYS88 4.6 15.2 1.0
C A:ARG84 4.7 18.3 1.0
SG A:CYS88 4.7 18.5 1.0
S1 A:DTV403 4.7 22.8 1.0
SG A:CYS81 4.8 20.1 1.0
NE A:ARG192 4.9 15.1 1.0
N A:ARG84 4.9 18.2 1.0

Iron binding site 3 out of 8 in 5exj

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Iron binding site 3 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:18.5
occ:1.00
 FE3 A:SF4401 0.0 18.5 1.0
S4 A:SF4401 2.3 16.8 1.0
S1 A:SF4401 2.3 20.4 1.0
S2 A:SF4401 2.3 17.8 1.0
S1 A:DTV403 2.3 22.8 1.0
FE2 A:SF4401 2.7 18.4 1.0
FE1 A:SF4401 2.7 17.6 1.0
FE4 A:SF4401 2.7 19.2 1.0
C1 A:DTV403 3.3 24.7 1.0
C2 A:DTV403 3.6 25.2 0.9
S3 A:SF4401 3.9 18.8 1.0
O2 A:DTV403 4.3 23.5 1.0
NH2 A:ARG192 4.4 14.8 1.0
O A:HOH548 4.4 27.7 1.0
O A:HOH654 4.6 21.9 1.0
CZ A:PHE195 4.6 17.8 1.0
SG A:CYS81 4.7 20.1 1.0
C3 A:DTV403 4.8 27.1 0.7
SG A:CYS88 4.8 18.5 1.0
SG A:CYS85 4.9 17.9 1.0
N A:ALA124 4.9 20.1 1.0
C4 A:DTV403 4.9 28.9 0.7

Iron binding site 4 out of 8 in 5exj

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Iron binding site 4 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:19.2
occ:1.00
 FE4 A:SF4401 0.0 19.2 1.0
S3 A:SF4401 2.3 18.8 1.0
S2 A:SF4401 2.3 17.8 1.0
S1 A:SF4401 2.3 20.4 1.0
SG A:CYS81 2.3 20.1 1.0
FE1 A:SF4401 2.7 17.6 1.0
FE2 A:SF4401 2.7 18.4 1.0
FE3 A:SF4401 2.7 18.5 1.0
CB A:CYS81 3.3 23.2 1.0
S4 A:SF4401 3.9 16.8 1.0
O A:ARG83 4.2 23.2 1.0
CB A:ARG83 4.3 20.7 1.0
N A:ALA124 4.4 20.1 1.0
C A:ARG83 4.5 24.7 1.0
CA A:CYS81 4.7 22.3 1.0
CB A:ALA124 4.8 20.4 1.0
S1 A:DTV403 4.8 22.8 1.0
CA A:ARG83 4.8 20.2 1.0
N A:ARG83 4.8 19.5 1.0
SG A:CYS88 4.9 18.5 1.0
CB A:VAL123 4.9 20.0 1.0
CA A:VAL123 5.0 18.2 1.0
CG2 A:ILE90 5.0 26.2 1.0
SG A:CYS85 5.0 17.9 1.0

Iron binding site 5 out of 8 in 5exj

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Iron binding site 5 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:14.3
occ:1.00
 FE1 A:SF4402 0.0 14.3 1.0
S2 A:SF4402 2.3 13.8 1.0
S3 A:SF4402 2.3 13.7 1.0
S4 A:SF4402 2.3 13.5 1.0
SG A:CYS60 2.3 14.3 1.0
FE4 A:SF4402 2.7 15.7 1.0
FE2 A:SF4402 2.7 14.3 1.0
FE3 A:SF4402 2.7 13.9 1.0
CB A:CYS60 3.1 15.8 1.0
S1 A:SF4402 3.9 13.8 1.0
CB A:ASN62 4.1 10.7 1.0
CD A:ARG290 4.3 17.8 1.0
ND2 A:ASN62 4.3 16.1 1.0
CB A:ARG290 4.4 17.3 1.0
OG A:SER292 4.5 15.8 1.0
CA A:CYS60 4.5 12.3 1.0
CG A:ARG290 4.6 20.3 1.0
SG A:CYS66 4.7 14.8 1.0
CG A:ASN62 4.7 15.8 1.0
CA A:CYS55 4.8 14.8 1.0
N A:ASN62 4.8 14.4 1.0
SG A:CYS55 4.8 13.9 1.0
CA A:ASN62 4.8 16.5 1.0
NE A:ARG290 4.9 25.7 1.0
C A:ASN62 4.9 14.3 1.0
C A:CYS60 5.0 14.6 1.0
CB A:CYS55 5.0 13.2 1.0

Iron binding site 6 out of 8 in 5exj

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Iron binding site 6 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:14.3
occ:1.00
 FE2 A:SF4402 0.0 14.3 1.0
S1 A:SF4402 2.3 13.8 1.0
S4 A:SF4402 2.3 13.5 1.0
S3 A:SF4402 2.3 13.7 1.0
SG A:CYS66 2.3 14.8 1.0
FE4 A:SF4402 2.7 15.7 1.0
FE3 A:SF4402 2.7 13.9 1.0
FE1 A:SF4402 2.7 14.3 1.0
CB A:CYS66 3.1 10.7 1.0
S2 A:SF4402 3.8 13.8 1.0
CB A:ASN62 4.1 10.7 1.0
OG A:SER292 4.5 15.8 1.0
O A:ASN62 4.6 14.7 1.0
CA A:CYS66 4.6 14.0 1.0
O A:SER292 4.6 12.9 1.0
SG A:CYS60 4.7 14.3 1.0
CA A:TYR293 4.7 11.2 1.0
C A:ASN62 4.7 14.3 1.0
O A:HOH620 4.8 18.2 1.0
SG A:CYS55 4.8 13.9 1.0
C A:SER292 4.8 15.2 1.0
N A:TYR293 4.8 12.5 1.0
O A:HOH599 4.9 18.1 1.0
CD1 A:TYR293 4.9 13.9 1.0
CB A:SER292 5.0 16.9 1.0
ND2 A:ASN62 5.0 16.1 1.0

Iron binding site 7 out of 8 in 5exj

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Iron binding site 7 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:13.9
occ:1.00
 FE3 A:SF4402 0.0 13.9 1.0
S4 A:SF4402 2.3 13.5 1.0
S1 A:SF4402 2.3 13.8 1.0
S2 A:SF4402 2.3 13.8 1.0
SG A:CYS55 2.4 13.9 1.0
FE4 A:SF4402 2.7 15.7 1.0
FE2 A:SF4402 2.7 14.3 1.0
FE1 A:SF4402 2.7 14.3 1.0
CB A:CYS55 3.3 13.2 1.0
CA A:CYS55 3.7 14.8 1.0
S3 A:SF4402 3.9 13.7 1.0
N A:CYS55 4.2 14.2 1.0
OG1 A:THR73 4.2 13.9 1.0
N A:THR73 4.3 12.5 1.0
CB A:THR73 4.4 12.6 1.0
OG A:SER292 4.5 15.8 1.0
CA A:ALA72 4.6 11.7 1.0
CB A:CYS66 4.7 10.7 1.0
SG A:CYS66 4.8 14.8 1.0
NE1 A:TRP67 4.8 14.2 1.0
SG A:CYS60 4.8 14.3 1.0
C A:ALA72 4.8 11.0 1.0
CB A:CYS60 4.9 15.8 1.0

Iron binding site 8 out of 8 in 5exj

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Iron binding site 8 out of 8 in the Crystal Structure of M. Tuberculosis Lipoyl Synthase at 1.64 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 1.64 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:15.7
occ:1.00
 FE4 A:SF4402 0.0 15.7 1.0
OG A:SER292 2.1 15.8 1.0
S3 A:SF4402 2.3 13.7 1.0
S2 A:SF4402 2.3 13.8 1.0
S1 A:SF4402 2.3 13.8 1.0
FE2 A:SF4402 2.7 14.3 1.0
FE1 A:SF4402 2.7 14.3 1.0
FE3 A:SF4402 2.7 13.9 1.0
CB A:SER292 3.0 16.9 1.0
OG1 A:THR73 3.6 13.9 1.0
CA A:SER292 3.8 11.6 1.0
S4 A:SF4402 3.8 13.5 1.0
C A:SER292 3.8 15.2 1.0
O A:HOH544 4.0 21.2 1.0
N A:SER292 4.1 14.6 1.0
N A:TYR293 4.2 12.5 1.0
O A:SER292 4.2 12.9 1.0
CB A:THR73 4.4 12.6 1.0
CB A:ARG290 4.4 17.3 1.0
SG A:CYS60 4.8 14.3 1.0
SG A:CYS66 4.8 14.8 1.0
CA A:TYR293 4.8 11.2 1.0
SG A:CYS55 4.8 13.9 1.0
NE A:ARG290 4.9 25.7 1.0
O A:HOH599 5.0 18.1 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: Sun Dec 13 16:01:02 2020

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