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
Go back to
Iron Binding Sites List in 5exi
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 Sites List in 5exi
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 Sites List in 5exi
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 Sites List in 5exi
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 Sites List in 5exi
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 Sites List in 5exi
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
Go back to
Iron Binding Sites List in 5exi
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
Go back to
Iron Binding Sites List in 5exi
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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