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Iron in PDB 4u0o: Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt

Enzymatic activity of Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt

All present enzymatic activity of Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt:
2.8.1.8;

Protein crystallography data

The structure of Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt, PDB code: 4u0o was solved by J.E.Harmer, M.J.Hiscox, P.C.Dinis, J.Sandy, P.L.Roach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.99 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 70.880, 162.800, 58.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.2

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt (pdb code 4u0o). 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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt, PDB code: 4u0o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4u0o

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Iron binding site 1 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:34.9
occ:1.00
 FE1 B:SF4301 0.0 34.9 1.0
S4 B:SF4301 2.2 30.3 1.0
S2 B:SF4301 2.2 33.5 1.0
H2 B:DTT303 2.2 38.0 1.0
S3 B:SF4301 2.2 30.9 1.0
S4 B:DTT303 2.6 42.2 1.0
FE3 B:SF4301 2.8 31.4 1.0
FE2 B:SF4301 2.9 30.3 1.0
FE4 B:SF4301 3.0 32.8 1.0
HS2 B:DTT303 3.0 50.6 1.0
H41 B:DTT303 3.2 42.1 1.0
C2 B:DTT303 3.2 31.7 1.0
C4 B:DTT303 3.3 35.1 1.0
H12 B:DTT303 3.5 51.6 1.0
C3 B:DTT303 3.8 37.3 1.0
C1 B:DTT303 3.9 43.0 1.0
S1 B:SF4301 3.9 32.6 1.0
HA B:VAL106 4.1 35.7 1.0
HO3 B:DTT303 4.2 44.7 1.0
O2 B:DTT303 4.2 41.0 1.0
O3 B:DTT303 4.3 37.3 1.0
O B:HOH483 4.3 40.0 1.0
HS1 B:DTT303 4.3 56.8 1.0
H B:ALA107 4.3 34.9 1.0
H42 B:DTT303 4.3 42.1 1.0
S1 B:DTT303 4.5 47.3 1.0
O B:HOH569 4.6 32.9 1.0
O B:SER105 4.6 26.4 1.0
H3 B:DTT303 4.7 44.7 1.0
HB2 B:ALA107 4.8 35.9 1.0
HO2 B:DTT303 4.8 49.3 1.0
SG B:CYS67 4.8 36.9 1.0
H11 B:DTT303 4.8 51.6 1.0
N B:ALA107 4.9 29.1 1.0
SG B:CYS70 4.9 32.4 1.0
HZ B:PHE69 5.0 34.4 1.0

Iron binding site 2 out of 8 in 4u0o

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Iron binding site 2 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.3
occ:1.00
 FE2 B:SF4301 0.0 30.3 1.0
S3 B:SF4301 2.2 30.9 1.0
S4 B:SF4301 2.2 30.3 1.0
S1 B:SF4301 2.2 32.6 1.0
SG B:CYS70 2.3 32.4 1.0
FE4 B:SF4301 2.7 32.8 1.0
FE3 B:SF4301 2.7 31.4 1.0
FE1 B:SF4301 2.9 34.9 1.0
CB B:CYS70 3.2 29.9 1.0
HB3 B:CYS70 3.2 35.9 1.0
HB2 B:CYS70 3.2 35.9 1.0
S2 B:SF4301 3.6 33.5 1.0
H2 B:DTT303 3.7 38.0 1.0
HB B:VAL72 3.7 45.0 1.0
HB2 B:CYS67 3.8 43.4 1.0
HS1 B:DTT303 4.2 56.8 1.0
HG21 B:VAL72 4.2 46.5 1.0
HZ2 B:LYS74 4.2 59.2 1.0
O B:HOH468 4.2 35.5 1.0
HG23 B:VAL72 4.3 46.5 1.0
S1 B:DTT303 4.5 47.3 1.0
H B:VAL72 4.5 47.6 1.0
CB B:VAL72 4.5 37.5 1.0
CG2 B:VAL72 4.6 38.7 1.0
HZ1 B:LYS74 4.6 59.2 1.0
CA B:CYS70 4.6 32.3 1.0
C2 B:DTT303 4.6 31.7 1.0
CB B:CYS67 4.7 36.2 1.0
SG B:CYS67 4.7 36.9 1.0
HB3 B:CYS63 4.8 43.3 1.0
HB2 B:CYS63 4.8 43.3 1.0
SG B:CYS63 4.8 33.8 1.0
H12 B:DTT303 4.8 51.6 1.0
NZ B:LYS74 4.9 49.3 1.0
HA B:CYS70 4.9 38.8 1.0
C1 B:DTT303 4.9 43.0 1.0

Iron binding site 3 out of 8 in 4u0o

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Iron binding site 3 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:31.4
occ:1.00
 FE3 B:SF4301 0.0 31.4 1.0
S1 B:SF4301 2.1 32.6 1.0
S2 B:SF4301 2.2 33.5 1.0
S4 B:SF4301 2.2 30.3 1.0
SG B:CYS67 2.3 36.9 1.0
FE2 B:SF4301 2.7 30.3 1.0
FE1 B:SF4301 2.8 34.9 1.0
FE4 B:SF4301 2.8 32.8 1.0
HB2 B:CYS67 2.8 43.4 1.0
CB B:CYS67 3.1 36.2 1.0
H B:CYS67 3.5 41.0 1.0
S3 B:SF4301 3.7 30.9 1.0
HB3 B:CYS67 3.7 43.4 1.0
O B:HOH569 3.8 32.9 1.0
HB2 B:ARG65 3.9 48.5 1.0
O B:HOH480 4.2 35.4 1.0
HB2 B:CYS70 4.2 35.9 1.0
N B:CYS67 4.2 34.2 1.0
HB3 B:CYS70 4.2 35.9 1.0
CA B:CYS67 4.3 34.2 1.0
HB3 B:ARG65 4.3 48.5 1.0
HD2 B:ARG65 4.4 48.2 1.0
HZ B:PHE69 4.5 34.4 1.0
CB B:CYS70 4.5 29.9 1.0
CB B:ARG65 4.6 40.4 1.0
H2 B:DTT303 4.6 38.0 1.0
SG B:CYS70 4.7 32.4 1.0
S4 B:DTT303 4.7 42.2 1.0
HA B:CYS67 4.8 41.1 1.0
SG B:CYS63 4.9 33.8 1.0
O B:HOH483 4.9 40.0 1.0
CZ B:PHE69 4.9 28.6 1.0

Iron binding site 4 out of 8 in 4u0o

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Iron binding site 4 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:32.8
occ:1.00
 FE4 B:SF4301 0.0 32.8 1.0
S2 B:SF4301 2.1 33.5 1.0
S1 B:SF4301 2.2 32.6 1.0
S3 B:SF4301 2.2 30.9 1.0
SG B:CYS63 2.3 33.8 1.0
FE2 B:SF4301 2.7 30.3 1.0
FE3 B:SF4301 2.8 31.4 1.0
FE1 B:SF4301 3.0 34.9 1.0
HB2 B:ARG65 3.3 48.5 1.0
CB B:CYS63 3.3 36.1 1.0
H B:ALA107 3.3 34.9 1.0
HB3 B:CYS63 3.3 43.3 1.0
HB2 B:CYS63 3.3 43.3 1.0
S4 B:SF4301 3.8 30.3 1.0
HA B:VAL106 3.9 35.7 1.0
HB B:VAL106 4.0 36.9 1.0
N B:ALA107 4.2 29.1 1.0
CB B:ARG65 4.3 40.4 1.0
H B:ARG65 4.3 44.2 1.0
HB3 B:ALA107 4.4 35.9 1.0
HG12 B:VAL106 4.5 39.8 1.0
HB2 B:ALA107 4.5 35.9 1.0
CA B:VAL106 4.6 29.7 1.0
HB3 B:ARG65 4.6 48.5 1.0
HD2 B:ARG65 4.6 48.2 1.0
HB B:VAL72 4.7 45.0 1.0
CB B:VAL106 4.7 30.8 1.0
HG3 B:ARG65 4.8 46.5 1.0
CA B:CYS63 4.8 36.0 1.0
SG B:CYS70 4.8 32.4 1.0
CB B:ALA107 4.8 29.9 1.0
HZ2 B:LYS74 4.8 59.2 1.0
SG B:CYS67 4.8 36.9 1.0
H B:CYS67 4.9 41.0 1.0
H2 B:DTT303 4.9 38.0 1.0
C B:VAL106 4.9 28.5 1.0
N B:ARG65 4.9 36.8 1.0
HB2 B:CYS67 4.9 43.4 1.0
CA B:ARG65 5.0 37.7 1.0
HE3 B:LYS74 5.0 64.9 1.0

Iron binding site 5 out of 8 in 4u0o

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Iron binding site 5 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:29.2
occ:1.00
 FE1 B:SF4302 0.0 29.2 1.0
S4 B:SF4302 2.2 30.9 1.0
S3 B:SF4302 2.2 25.8 1.0
S2 B:SF4302 2.2 24.9 1.0
SG B:CYS48 2.2 35.0 1.0
FE4 B:SF4302 2.7 26.4 1.0
FE2 B:SF4302 2.9 29.1 1.0
FE3 B:SF4302 3.0 32.8 1.0
CB B:CYS48 3.3 31.6 1.0
HB3 B:CYS48 3.3 37.9 1.0
HB2 B:CYS48 3.4 37.9 1.0
HB2 B:ASN44 3.4 54.3 1.0
HD1 B:TYR284 3.7 52.0 1.0
HA B:TYR284 3.7 31.9 1.0
HB3 B:ASN44 3.8 54.3 1.0
S1 B:SF4302 3.8 26.2 1.0
CB B:ASN44 4.1 45.3 1.0
OG B:SER283 4.3 26.6 1.0
HG23 B:THR53 4.4 43.1 1.0
CA B:TYR284 4.5 26.6 1.0
HB2 B:TYR284 4.5 38.2 1.0
HA B:ARG45 4.5 54.5 1.0
HD22 B:ASN44 4.5 44.7 1.0
CD1 B:TYR284 4.6 43.3 1.0
O B:SER283 4.6 31.4 1.0
O B:ASN44 4.6 41.9 1.0
C B:ASN44 4.7 39.9 1.0
HB2 B:SER283 4.7 33.9 1.0
CA B:CYS48 4.7 39.9 1.0
HG1 B:THR55 4.7 30.1 1.0
C B:SER283 4.8 31.3 1.0
N B:TYR284 4.8 28.3 1.0
H B:CYS48 4.8 52.9 1.0
SG B:CYS37 4.8 31.7 1.0
SG B:CYS42 4.8 38.6 1.0
HB3 B:CYS42 4.9 61.5 1.0
HG21 B:THR53 4.9 43.1 1.0
H B:HIS285 4.9 42.7 1.0
N B:ARG45 4.9 37.5 1.0
HA B:CYS48 5.0 47.9 1.0
CB B:TYR284 5.0 31.8 1.0
CA B:ASN44 5.0 43.0 1.0

Iron binding site 6 out of 8 in 4u0o

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Iron binding site 6 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:29.1
occ:1.00
 FE2 B:SF4302 0.0 29.1 1.0
S4 B:SF4302 2.2 30.9 1.0
S1 B:SF4302 2.2 26.2 1.0
S3 B:SF4302 2.2 25.8 1.0
SG B:CYS37 2.2 31.7 1.0
FE3 B:SF4302 2.7 32.8 1.0
FE4 B:SF4302 2.7 26.4 1.0
FE1 B:SF4302 2.9 29.2 1.0
CB B:CYS37 3.4 38.5 1.0
HG1 B:THR55 3.4 30.1 1.0
HA B:CYS37 3.5 45.5 1.0
HB3 B:CYS37 3.6 46.2 1.0
H B:THR55 3.7 34.9 1.0
S2 B:SF4302 3.7 24.9 1.0
HB B:THR55 3.7 32.8 1.0
CA B:CYS37 3.9 37.9 1.0
OG1 B:THR55 4.0 25.1 1.0
HA B:ALA54 4.1 41.2 1.0
HB3 B:CYS42 4.2 61.5 1.0
HB2 B:CYS37 4.2 46.2 1.0
OG B:SER283 4.2 26.6 1.0
N B:THR55 4.3 29.1 1.0
CB B:THR55 4.3 27.3 1.0
H B:CYS37 4.4 48.7 1.0
HH21 B:ARG45 4.4 77.8 1.0
HB2 B:CYS42 4.4 61.5 1.0
N B:CYS37 4.5 40.5 1.0
CB B:CYS42 4.6 51.2 1.0
SG B:CYS42 4.7 38.6 1.0
HG23 B:ILE36 4.7 36.8 1.0
HE1 B:TYR49 4.8 49.0 1.0
HB2 B:SER283 4.9 33.9 1.0
HB2 B:CYS48 4.9 37.9 1.0
SG B:CYS48 4.9 35.0 1.0
CA B:THR55 4.9 24.6 1.0
CA B:ALA54 4.9 34.4 1.0
HB3 B:CYS48 5.0 37.9 1.0
C B:ALA54 5.0 35.1 1.0

Iron binding site 7 out of 8 in 4u0o

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Iron binding site 7 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:32.8
occ:1.00
 FE3 B:SF4302 0.0 32.8 1.0
S1 B:SF4302 2.1 26.2 1.0
S4 B:SF4302 2.1 30.9 1.0
S2 B:SF4302 2.1 24.9 1.0
SG B:CYS42 2.2 38.6 1.0
FE2 B:SF4302 2.7 29.1 1.0
FE4 B:SF4302 2.7 26.4 1.0
HB3 B:CYS42 2.8 61.5 1.0
CB B:CYS42 2.9 51.2 1.0
HB2 B:CYS42 3.0 61.5 1.0
FE1 B:SF4302 3.0 29.2 1.0
HB2 B:ASN44 3.3 54.3 1.0
HD22 B:ASN44 3.7 44.7 1.0
HG3 B:ARG281 3.7 51.2 1.0
S3 B:SF4302 3.8 25.8 1.0
HD2 B:ARG281 4.0 59.6 1.0
HA B:CYS37 4.1 45.5 1.0
H B:ASN44 4.2 57.0 1.0
CB B:ASN44 4.3 45.3 1.0
OG B:SER283 4.3 26.6 1.0
CA B:CYS42 4.3 48.2 1.0
HB2 B:ARG281 4.3 41.5 1.0
ND2 B:ASN44 4.5 37.2 1.0
CG B:ARG281 4.5 42.7 1.0
HA B:CYS42 4.6 57.9 1.0
SG B:CYS37 4.7 31.7 1.0
CD B:ARG281 4.7 49.7 1.0
HH21 B:ARG45 4.7 77.8 1.0
HB3 B:ASN44 4.7 54.3 1.0
HCS1 B:MTA304 4.8 28.9 1.0
C B:CYS42 4.8 52.7 1.0
CB B:ARG281 4.9 34.5 1.0
N B:ASN44 4.9 47.5 1.0
CG B:ASN44 5.0 44.9 1.0

Iron binding site 8 out of 8 in 4u0o

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Iron binding site 8 out of 8 in the Crystal Structure of Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt


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 Thermosynechococcus Elongatus Lipoyl Synthase 2 Complexed with Mta and Dtt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:26.4
occ:1.00
 FE4 B:SF4302 0.0 26.4 1.0
OG B:SER283 1.8 26.6 1.0
S1 B:SF4302 2.0 26.2 1.0
S2 B:SF4302 2.2 24.9 1.0
S3 B:SF4302 2.2 25.8 1.0
FE2 B:SF4302 2.7 29.1 1.0
FE1 B:SF4302 2.7 29.2 1.0
FE3 B:SF4302 2.7 32.8 1.0
CB B:SER283 2.9 28.3 1.0
HB2 B:SER283 3.0 33.9 1.0
HCS1 B:MTA304 3.3 28.9 1.0
HG1 B:THR55 3.5 30.1 1.0
S4 B:SF4302 3.5 30.9 1.0
HB3 B:SER283 3.6 33.9 1.0
OG1 B:THR55 3.8 25.1 1.0
HB2 B:ARG281 3.8 41.5 1.0
C B:SER283 3.9 31.3 1.0
CA B:SER283 3.9 26.8 1.0
H B:SER283 4.0 31.4 1.0
N B:TYR284 4.1 28.3 1.0
O B:SER283 4.2 31.4 1.0
HA B:TYR284 4.2 31.9 1.0
H B:TYR284 4.3 34.0 1.0
CS B:MTA304 4.3 24.1 1.0
HB B:THR55 4.4 32.8 1.0
N B:SER283 4.4 26.1 1.0
HB2 B:TYR284 4.6 38.2 1.0
HG3 B:ARG281 4.6 51.2 1.0
CB B:THR55 4.7 27.3 1.0
CA B:TYR284 4.7 26.6 1.0
CB B:ARG281 4.7 34.5 1.0
SG B:CYS42 4.7 38.6 1.0
HA B:SER283 4.7 32.2 1.0
HCS2 B:MTA304 4.7 28.9 1.0
SG B:CYS37 4.8 31.7 1.0
HCS3 B:MTA304 4.8 28.9 1.0
SG B:CYS48 4.8 35.0 1.0
HB3 B:ARG281 4.9 41.5 1.0
HB2 B:ASN44 5.0 54.3 1.0

Reference:

J.E.Harmer, M.J.Hiscox, P.C.Dinis, S.J.Fox, A.Iliopoulos, J.E.Hussey, J.Sandy, F.T.Van Beek, J.W.Essex, P.L.Roach. Structures of Lipoyl Synthase Reveal A Compact Active Site For Controlling Sequential Sulfur Insertion Reactions. Biochem.J. V. 464 123 2014.
ISSN: ESSN 1470-8728
PubMed: 25100160
DOI: 10.1042/BJ20140895
Page generated: Sun Dec 13 15:47:45 2020

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