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Iron in PDB 4u0p: The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine

Enzymatic activity of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine

All present enzymatic activity of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine:
2.8.1.8;

Protein crystallography data

The structure of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine, PDB code: 4u0p was solved by J.E.Harmer, M.J.Hiscox, J.Sandy, P.C.Dinis, P.L.Roach, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.89 / 1.62
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 71.090, 161.130, 59.470, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.7

Other elements in 4u0p:

The structure of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine also contains other interesting chemical elements:

Sodium (Na) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine (pdb code 4u0p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine, PDB code: 4u0p:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4u0p

Go back to Iron Binding Sites List in 4u0p
Iron binding site 1 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:36.8
occ:1.00
FE1 B:SF4301 0.0 36.8 1.0
N B:SAH303 1.3 28.7 1.0
S2 B:SF4301 2.1 35.6 1.0
S4 B:SF4301 2.2 34.1 1.0
S3 B:SF4301 2.2 32.7 1.0
OXT B:SAH303 2.3 39.4 1.0
CA B:SAH303 2.4 50.2 1.0
C B:SAH303 2.6 41.5 1.0
FE3 B:SF4301 2.7 32.2 1.0
FE2 B:SF4301 2.7 30.0 1.0
FE4 B:SF4301 2.7 31.5 1.0
HA B:SAH303 2.8 60.2 1.0
O B:SAH303 3.6 52.6 1.0
HB1 B:SAH303 3.6 63.5 1.0
CB B:SAH303 3.7 52.9 1.0
S1 B:SF4301 3.7 31.9 1.0
H B:ALA107 3.8 39.3 1.0
HA B:VAL106 4.1 34.4 1.0
HB2 B:ALA107 4.1 41.8 1.0
HB2 B:SAH303 4.2 63.5 1.0
N B:ALA107 4.4 32.8 1.0
CG B:SAH303 4.7 50.4 1.0
HG2 B:SAH303 4.7 60.4 1.0
SG B:CYS63 4.7 31.3 1.0
SG B:CYS67 4.8 35.2 1.0
SD B:SAH303 4.8 56.3 1.0
CB B:ALA107 4.8 34.9 1.0
HB3 B:ALA107 4.8 41.8 1.0
C5' B:SAH303 4.9 44.9 1.0
SG B:CYS70 4.9 32.0 1.0
CA B:VAL106 4.9 28.7 1.0
O B:HOH479 4.9 35.8 1.0
O B:SER105 4.9 31.0 1.0
HB2 B:ARG65 5.0 45.5 1.0

Iron binding site 2 out of 8 in 4u0p

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Iron binding site 2 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.0
occ:1.00
FE2 B:SF4301 0.0 30.0 1.0
S1 B:SF4301 2.1 31.9 1.0
S3 B:SF4301 2.1 32.7 1.0
S4 B:SF4301 2.2 34.1 1.0
SG B:CYS70 2.3 32.0 1.0
FE3 B:SF4301 2.7 32.2 1.0
FE4 B:SF4301 2.7 31.5 1.0
FE1 B:SF4301 2.7 36.8 1.0
N B:SAH303 2.9 28.7 1.0
HB2 B:CYS70 3.2 37.2 1.0
CB B:CYS70 3.2 31.0 1.0
HB3 B:CYS70 3.4 37.2 1.0
HB B:VAL72 3.6 39.0 1.0
S2 B:SF4301 3.7 35.6 1.0
HG21 B:VAL72 4.0 42.0 1.0
HB2 B:CYS67 4.0 36.0 1.0
HG23 B:VAL72 4.2 42.0 1.0
O B:HOH474 4.4 38.0 1.0
CG2 B:VAL72 4.4 35.0 1.0
CA B:SAH303 4.4 50.2 1.0
CB B:VAL72 4.4 32.5 1.0
HB3 B:CYS63 4.5 39.2 1.0
H B:VAL72 4.5 39.0 1.0
H B:CYS67 4.6 46.2 1.0
SG B:CYS67 4.7 35.2 1.0
CA B:CYS70 4.7 30.9 1.0
H5'1 B:SAH303 4.7 53.9 1.0
HA B:SAH303 4.7 60.2 1.0
HB2 B:CYS63 4.7 39.2 1.0
CB B:CYS67 4.8 30.0 1.0
HB1 B:SAH303 4.8 63.5 1.0
C5' B:SAH303 4.8 44.9 1.0
SG B:CYS63 4.8 31.3 1.0
HG11 B:VAL72 4.9 40.4 1.0
HA B:CYS70 4.9 37.1 1.0
CB B:CYS63 4.9 32.6 1.0
SD B:SAH303 5.0 56.3 1.0

Iron binding site 3 out of 8 in 4u0p

Go back to Iron Binding Sites List in 4u0p
Iron binding site 3 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:32.2
occ:1.00
FE3 B:SF4301 0.0 32.2 1.0
S4 B:SF4301 2.1 34.1 1.0
S2 B:SF4301 2.2 35.6 1.0
S1 B:SF4301 2.2 31.9 1.0
SG B:CYS67 2.3 35.2 1.0
FE4 B:SF4301 2.7 31.5 1.0
FE2 B:SF4301 2.7 30.0 1.0
FE1 B:SF4301 2.7 36.8 1.0
HB2 B:CYS67 3.0 36.0 1.0
CB B:CYS67 3.3 30.0 1.0
H B:CYS67 3.3 46.2 1.0
HB2 B:ARG65 3.4 45.5 1.0
N B:SAH303 3.6 28.7 1.0
S3 B:SF4301 3.7 32.7 1.0
HB3 B:CYS67 4.0 36.0 1.0
HB3 B:ARG65 4.0 45.5 1.0
HB2 B:CYS70 4.1 37.2 1.0
N B:CYS67 4.1 38.5 1.0
CB B:ARG65 4.1 37.9 1.0
CA B:CYS67 4.3 33.7 1.0
HB3 B:CYS70 4.4 37.2 1.0
HG3 B:ARG65 4.4 53.4 1.0
OXT B:SAH303 4.5 39.4 1.0
CB B:CYS70 4.5 31.0 1.0
SG B:CYS70 4.6 32.0 1.0
O B:HOH479 4.7 35.8 1.0
SG B:CYS63 4.7 31.3 1.0
HA B:CYS67 4.8 40.5 1.0
H B:ARG182 4.8 49.1 1.0
CG B:ARG65 4.8 44.5 1.0
HD2 B:ARG65 4.8 52.9 1.0
HZ B:PHE69 4.9 40.1 1.0
HH11 B:ARG65 4.9 52.9 1.0
C B:SAH303 4.9 41.5 1.0
H B:ALA66 4.9 41.5 1.0
CA B:SAH303 4.9 50.2 1.0
HE1 B:PHE69 5.0 44.1 1.0

Iron binding site 4 out of 8 in 4u0p

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Iron binding site 4 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:31.5
occ:1.00
FE4 B:SF4301 0.0 31.5 1.0
S1 B:SF4301 2.2 31.9 1.0
S3 B:SF4301 2.2 32.7 1.0
S2 B:SF4301 2.2 35.6 1.0
SG B:CYS63 2.3 31.3 1.0
FE3 B:SF4301 2.7 32.2 1.0
FE2 B:SF4301 2.7 30.0 1.0
FE1 B:SF4301 2.7 36.8 1.0
HB2 B:ARG65 3.0 45.5 1.0
HB3 B:CYS63 3.0 39.2 1.0
CB B:CYS63 3.1 32.6 1.0
HB2 B:CYS63 3.2 39.2 1.0
H B:ALA107 3.3 39.3 1.0
S4 B:SF4301 3.7 34.1 1.0
HG3 B:ARG65 3.8 53.4 1.0
N B:SAH303 3.8 28.7 1.0
HB B:VAL106 3.9 36.5 1.0
H B:ARG65 4.0 44.4 1.0
CB B:ARG65 4.0 37.9 1.0
HA B:VAL106 4.1 34.4 1.0
HB3 B:ALA107 4.1 41.8 1.0
N B:ALA107 4.2 32.8 1.0
H B:ALA66 4.3 41.5 1.0
CG B:ARG65 4.4 44.5 1.0
HB2 B:ALA107 4.4 41.8 1.0
HB3 B:ARG65 4.4 45.5 1.0
OXT B:SAH303 4.4 39.4 1.0
H B:CYS67 4.5 46.2 1.0
CA B:CYS63 4.6 34.1 1.0
HB B:VAL72 4.6 39.0 1.0
CB B:ALA107 4.7 34.9 1.0
N B:ARG65 4.7 37.0 1.0
CB B:VAL106 4.7 30.4 1.0
CA B:VAL106 4.8 28.7 1.0
SG B:CYS67 4.8 35.2 1.0
HG11 B:VAL72 4.8 40.4 1.0
HG12 B:VAL106 4.8 38.0 1.0
SG B:CYS70 4.8 32.0 1.0
CA B:ARG65 4.8 35.7 1.0
HG2 B:ARG65 4.9 53.4 1.0
O B:HOH468 4.9 40.1 1.0
N B:ALA66 4.9 34.6 1.0
HA B:CYS63 4.9 40.9 1.0
O B:HOH474 4.9 38.0 1.0
CA B:SAH303 4.9 50.2 1.0

Iron binding site 5 out of 8 in 4u0p

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Iron binding site 5 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:28.1
occ:1.00
FE1 B:SF4302 0.0 28.1 1.0
S3 B:SF4302 2.2 30.4 1.0
S4 B:SF4302 2.2 27.0 1.0
S2 B:SF4302 2.3 29.1 1.0
SG B:CYS48 2.3 31.1 1.0
FE4 B:SF4302 2.7 29.2 1.0
FE3 B:SF4302 2.7 27.2 1.0
FE2 B:SF4302 2.8 27.1 1.0
HB2 B:CYS48 3.0 36.5 1.0
CB B:CYS48 3.1 30.4 1.0
HB3 B:CYS48 3.2 36.5 1.0
HB2 B:ASN44 3.4 35.8 1.0
S1 B:SF4302 3.8 29.6 1.0
HA B:TYR284 3.9 36.9 1.0
HD1 B:TYR284 4.0 41.0 1.0
HB3 B:ASN44 4.0 35.8 1.0
CB B:ASN44 4.1 29.8 1.0
OG B:SER283 4.4 29.2 1.0
HD22 B:ASN44 4.4 33.7 1.0
HB2 B:SER283 4.4 36.0 1.0
O B:ASN44 4.6 29.3 1.0
CA B:CYS48 4.6 32.5 1.0
HA B:ARG45 4.7 35.2 1.0
H B:CYS48 4.7 41.1 1.0
O B:SER283 4.7 30.4 1.0
SG B:CYS42 4.7 29.7 1.0
O B:HOH540 4.7 40.6 1.0
C B:ASN44 4.7 29.2 1.0
CA B:TYR284 4.8 30.7 1.0
SG B:CYS37 4.8 27.8 1.0
HG1 B:THR55 4.9 31.8 1.0
HB2 B:TYR284 4.9 34.8 1.0
HA B:CYS48 4.9 39.0 1.0
CD1 B:TYR284 4.9 34.2 1.0
C B:SER283 4.9 28.2 1.0
CB B:SER283 4.9 30.0 1.0
N B:TYR284 5.0 27.9 1.0

Iron binding site 6 out of 8 in 4u0p

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Iron binding site 6 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:27.1
occ:1.00
FE2 B:SF4302 0.0 27.1 1.0
S4 B:SF4302 2.2 27.0 1.0
S3 B:SF4302 2.2 30.4 1.0
S1 B:SF4302 2.2 29.6 1.0
SG B:CYS37 2.3 27.8 1.0
FE3 B:SF4302 2.7 27.2 1.0
FE1 B:SF4302 2.8 28.1 1.0
FE4 B:SF4302 2.8 29.2 1.0
HB3 B:CYS37 3.2 34.1 1.0
CB B:CYS37 3.2 28.5 1.0
HA B:CYS37 3.3 33.8 1.0
CA B:CYS37 3.7 28.2 1.0
HG1 B:THR55 3.8 31.8 1.0
HB B:THR55 3.8 32.6 1.0
S2 B:SF4302 3.8 29.1 1.0
H B:THR55 3.9 30.1 1.0
H B:CYS37 3.9 36.6 1.0
HA B:ALA54 4.0 32.5 1.0
HB2 B:CYS37 4.1 34.1 1.0
N B:CYS37 4.1 30.5 1.0
HB3 B:CYS42 4.2 37.5 1.0
OG1 B:THR55 4.3 26.5 1.0
HB2 B:CYS48 4.4 36.5 1.0
N B:THR55 4.4 25.0 1.0
HE1 B:TYR49 4.4 36.3 1.0
OG B:SER283 4.4 29.2 1.0
CB B:THR55 4.5 27.2 1.0
HB2 B:CYS42 4.5 37.5 1.0
HG2 B:ARG45 4.6 33.5 1.0
HB3 B:CYS48 4.6 36.5 1.0
CB B:CYS42 4.7 31.2 1.0
SG B:CYS42 4.7 29.7 1.0
HB B:ILE36 4.8 35.8 1.0
CB B:CYS48 4.8 30.4 1.0
SG B:CYS48 4.8 31.1 1.0
HG22 B:ILE36 4.9 42.6 1.0
CA B:ALA54 4.9 27.1 1.0
HB2 B:SER283 4.9 36.0 1.0
HG3 B:ARG45 4.9 33.5 1.0
HA B:ARG45 4.9 35.2 1.0
C B:ALA54 5.0 28.3 1.0

Iron binding site 7 out of 8 in 4u0p

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Iron binding site 7 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:27.2
occ:1.00
FE3 B:SF4302 0.0 27.2 1.0
S1 B:SF4302 2.2 29.6 1.0
S2 B:SF4302 2.2 29.1 1.0
S4 B:SF4302 2.3 27.0 1.0
SG B:CYS42 2.3 29.7 1.0
FE2 B:SF4302 2.7 27.1 1.0
FE1 B:SF4302 2.7 28.1 1.0
FE4 B:SF4302 2.7 29.2 1.0
HB3 B:CYS42 3.0 37.5 1.0
HB2 B:ASN44 3.1 35.8 1.0
CB B:CYS42 3.1 31.2 1.0
HB2 B:CYS42 3.2 37.5 1.0
HD22 B:ASN44 3.6 33.7 1.0
S3 B:SF4302 3.8 30.4 1.0
HG3 B:ARG281 3.9 39.9 1.0
HA B:CYS37 3.9 33.8 1.0
H B:ASN44 4.0 35.5 1.0
O B:HOH553 4.0 37.5 1.0
CB B:ASN44 4.0 29.8 1.0
ND2 B:ASN44 4.3 28.1 1.0
HB2 B:ARG281 4.3 39.2 1.0
HB3 B:ASN44 4.5 35.8 1.0
HB3 B:CYS37 4.6 34.1 1.0
CA B:CYS42 4.6 34.1 1.0
HG3 B:ARG45 4.6 33.5 1.0
OG B:SER283 4.6 29.2 1.0
N B:ASN44 4.7 29.6 1.0
SG B:CYS48 4.7 31.1 1.0
CG B:ASN44 4.7 28.2 1.0
CA B:ASN44 4.8 28.6 1.0
CG B:ARG281 4.8 33.2 1.0
SG B:CYS37 4.8 27.8 1.0
HH21 B:ARG281 4.8 43.0 1.0
CA B:CYS37 4.8 28.2 1.0
HA B:CYS42 4.9 40.9 1.0
C B:ASN44 4.9 29.2 1.0
CB B:CYS37 4.9 28.5 1.0
CB B:ARG281 5.0 32.7 1.0
N B:ARG45 5.0 29.3 1.0
HD2 B:PRO43 5.0 40.0 1.0
C B:CYS42 5.0 30.2 1.0
H B:ARG45 5.0 35.1 1.0

Iron binding site 8 out of 8 in 4u0p

Go back to Iron Binding Sites List in 4u0p
Iron binding site 8 out of 8 in the The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Crystal Structure of Lipoyl Synthase in Complex with S-Adenosyl Homocysteine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:29.2
occ:1.00
FE4 B:SF4302 0.0 29.2 1.0
OG B:SER283 2.0 29.2 1.0
S1 B:SF4302 2.2 29.6 1.0
S2 B:SF4302 2.2 29.1 1.0
S3 B:SF4302 2.3 30.4 1.0
FE1 B:SF4302 2.7 28.1 1.0
FE3 B:SF4302 2.7 27.2 1.0
FE2 B:SF4302 2.8 27.1 1.0
HB2 B:SER283 3.0 36.0 1.0
CB B:SER283 3.1 30.0 1.0
NA B:NA304 3.5 45.7 1.0
HG1 B:THR55 3.5 31.8 1.0
H B:SER283 3.7 34.6 1.0
HB3 B:SER283 3.7 36.0 1.0
OG1 B:THR55 3.8 26.5 1.0
S4 B:SF4302 3.8 27.0 1.0
HB2 B:ARG281 3.8 39.2 1.0
CA B:SER283 4.0 27.1 1.0
C B:SER283 4.0 28.2 1.0
N B:TYR284 4.2 27.9 1.0
N B:SER283 4.3 28.9 1.0
HB B:THR55 4.3 32.6 1.0
O B:SER283 4.3 30.4 1.0
HA B:TYR284 4.4 36.9 1.0
H B:TYR284 4.4 33.5 1.0
HB3 B:ARG281 4.5 39.2 1.0
CB B:ARG281 4.6 32.7 1.0
CB B:THR55 4.6 27.2 1.0
HG3 B:ARG281 4.7 39.9 1.0
HB2 B:TYR284 4.7 34.8 1.0
SG B:CYS48 4.7 31.1 1.0
SG B:CYS37 4.8 27.8 1.0
CA B:TYR284 4.8 30.7 1.0
SG B:CYS42 4.8 29.7 1.0
HA B:SER283 4.8 32.6 1.0
O B:HOH570 4.9 42.3 1.0
HD22 B:ASN44 4.9 33.7 1.0
O B:HOH553 4.9 37.5 1.0
HB2 B:ASN44 5.0 35.8 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 15:47:47 2020

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