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Iron in PDB 2a5h: 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).

Enzymatic activity of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).

All present enzymatic activity of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).:
5.4.3.2;

Protein crystallography data

The structure of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate)., PDB code: 2a5h was solved by B.W.Lepore, F.J.Ruzicka, P.A.Frey, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.890, 92.926, 177.735, 90.00, 96.74, 90.00
R / Rfree (%) 18.4 / 22.5

Other elements in 2a5h:

The structure of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). (pdb code 2a5h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate)., PDB code: 2a5h:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 1 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe418

b:26.3
occ:1.00
 FE1 A:SF4418 0.0 26.3 1.0
N A:SAM417 2.0 26.7 1.0
OXT A:SAM417 2.0 27.2 1.0
S3 A:SF4418 2.2 26.1 1.0
S4 A:SF4418 2.2 29.6 1.0
S2 A:SF4418 2.3 28.6 1.0
FE3 A:SF4418 2.5 28.0 1.0
FE2 A:SF4418 2.6 24.7 1.0
FE4 A:SF4418 2.6 27.7 1.0
C A:SAM417 3.0 28.6 1.0
CA A:SAM417 3.0 31.1 1.0
SD A:SAM417 3.1 30.9 0.8
CG A:SAM417 3.6 31.7 1.0
S1 A:SF4418 3.6 29.8 1.0
CB A:SAM417 3.9 30.6 1.0
O A:SAM417 4.1 28.1 1.0
ND1 A:HIS230 4.5 30.2 1.0
CE A:SAM417 4.5 36.3 1.0
O A:GLY171 4.5 36.0 1.0
SG A:CYS125 4.6 36.5 1.0
SG A:CYS129 4.7 31.5 1.0
SG A:CYS132 4.7 31.9 1.0
C5' A:SAM417 4.9 28.7 1.0
CE1 A:HIS230 4.9 27.5 1.0
C3' A:SAM417 4.9 27.9 1.0
C A:GLY171 4.9 37.5 1.0

Iron binding site 2 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 2 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe418

b:24.7
occ:1.00
 FE2 A:SF4418 0.0 24.7 1.0
S1 A:SF4418 2.1 29.8 1.0
S4 A:SF4418 2.1 29.6 1.0
S3 A:SF4418 2.2 26.1 1.0
SG A:CYS132 2.3 31.9 1.0
FE4 A:SF4418 2.5 27.7 1.0
FE1 A:SF4418 2.6 26.3 1.0
FE3 A:SF4418 2.6 28.0 1.0
CB A:CYS132 3.2 32.3 1.0
S2 A:SF4418 3.7 28.6 1.0
CA A:CYS132 4.0 31.4 1.0
OXT A:SAM417 4.3 27.2 1.0
N A:SAM417 4.3 26.7 1.0
SD A:SAM417 4.5 30.9 0.8
SG A:CYS125 4.5 36.5 1.0
CB A:ALA138 4.6 38.6 1.0
SG A:CYS129 4.6 31.5 1.0
CB A:CYS129 4.7 30.1 1.0
CE A:SAM417 4.8 36.3 1.0
C A:CYS132 4.9 31.6 1.0

Iron binding site 3 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 3 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe418

b:28.0
occ:1.00
 FE3 A:SF4418 0.0 28.0 1.0
S4 A:SF4418 2.1 29.6 1.0
S1 A:SF4418 2.1 29.8 1.0
S2 A:SF4418 2.2 28.6 1.0
SG A:CYS125 2.3 36.5 1.0
FE1 A:SF4418 2.5 26.3 1.0
FE4 A:SF4418 2.6 27.7 1.0
FE2 A:SF4418 2.6 24.7 1.0
N A:SAM417 3.3 26.7 1.0
CB A:CYS125 3.4 38.0 1.0
S3 A:SF4418 3.6 26.1 1.0
CA A:GLY171 4.3 38.8 1.0
OXT A:SAM417 4.3 27.2 1.0
C A:GLY171 4.4 37.5 1.0
SG A:CYS132 4.6 31.9 1.0
O A:HOH664 4.6 34.3 1.0
O A:MSE127 4.6 35.9 1.0
SG A:CYS129 4.7 31.5 1.0
CB A:ALA138 4.7 38.6 1.0
O A:GLY171 4.7 36.0 1.0
CA A:CYS125 4.7 38.4 1.0
CA A:SAM417 4.8 31.1 1.0
CD2 A:TYR128 4.8 40.4 1.0
N A:ASP172 4.9 37.0 1.0

Iron binding site 4 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 4 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe418

b:27.7
occ:1.00
 FE4 A:SF4418 0.0 27.7 1.0
S1 A:SF4418 2.1 29.8 1.0
S3 A:SF4418 2.1 26.1 1.0
S2 A:SF4418 2.1 28.6 1.0
SG A:CYS129 2.3 31.5 1.0
FE2 A:SF4418 2.5 24.7 1.0
FE3 A:SF4418 2.6 28.0 1.0
FE1 A:SF4418 2.6 26.3 1.0
CB A:CYS129 3.2 30.1 1.0
OXT A:SAM417 3.6 27.2 1.0
S4 A:SF4418 3.7 29.6 1.0
N A:CYS129 3.8 34.0 1.0
N A:SAM417 4.2 26.7 1.0
CA A:CYS129 4.2 32.5 1.0
O A:MSE127 4.2 35.9 1.0
CD A:ARG202 4.3 30.1 1.0
O A:HOH664 4.3 34.3 1.0
CE1 A:HIS230 4.4 27.5 1.0
ND1 A:HIS230 4.5 30.2 1.0
SG A:CYS132 4.5 31.9 1.0
CB A:CYS132 4.6 32.3 1.0
SG A:CYS125 4.7 36.5 1.0
C A:SAM417 4.9 28.6 1.0
C A:TYR128 5.0 36.3 1.0

Iron binding site 5 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 5 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe418

b:36.4
occ:1.00
 FE1 B:SF4418 0.0 36.4 1.0
N B:SAM417 2.0 36.5 1.0
OXT B:SAM417 2.0 36.1 1.0
S3 B:SF4418 2.1 36.2 1.0
S4 B:SF4418 2.2 38.7 1.0
S2 B:SF4418 2.3 40.1 1.0
FE2 B:SF4418 2.5 35.8 1.0
FE3 B:SF4418 2.6 39.6 1.0
FE4 B:SF4418 2.6 38.8 1.0
C B:SAM417 3.0 36.8 1.0
CA B:SAM417 3.0 39.7 1.0
SD B:SAM417 3.4 40.2 0.8
S1 B:SF4418 3.6 40.6 1.0
CG B:SAM417 3.7 39.9 1.0
CB B:SAM417 3.9 38.7 1.0
O B:SAM417 4.2 35.3 1.0
O B:GLY171 4.4 46.0 1.0
ND1 B:HIS230 4.4 38.8 1.0
SG B:CYS125 4.5 47.3 1.0
CE B:SAM417 4.7 44.0 1.0
SG B:CYS129 4.7 43.8 1.0
SG B:CYS132 4.7 42.2 1.0
CE1 B:HIS230 4.9 35.3 1.0
C B:GLY171 4.9 47.6 1.0
CB B:ARG202 4.9 40.3 1.0
C3' B:SAM417 5.0 35.0 1.0

Iron binding site 6 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 6 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe418

b:35.8
occ:1.00
 FE2 B:SF4418 0.0 35.8 1.0
S1 B:SF4418 2.1 40.6 1.0
S4 B:SF4418 2.2 38.7 1.0
S3 B:SF4418 2.2 36.2 1.0
SG B:CYS132 2.3 42.2 1.0
FE3 B:SF4418 2.5 39.6 1.0
FE1 B:SF4418 2.5 36.4 1.0
FE4 B:SF4418 2.5 38.8 1.0
CB B:CYS132 3.4 42.4 1.0
S2 B:SF4418 3.7 40.1 1.0
CA B:CYS132 4.1 41.1 1.0
OXT B:SAM417 4.2 36.1 1.0
N B:SAM417 4.3 36.5 1.0
SG B:CYS125 4.5 47.3 1.0
SG B:CYS129 4.5 43.8 1.0
CB B:ALA138 4.5 49.8 1.0
SD B:SAM417 4.6 40.2 0.8
CB B:CYS129 4.7 41.2 1.0
CE B:SAM417 5.0 44.0 1.0

Iron binding site 7 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 7 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe418

b:39.6
occ:1.00
 FE3 B:SF4418 0.0 39.6 1.0
S1 B:SF4418 2.1 40.6 1.0
S4 B:SF4418 2.2 38.7 1.0
S2 B:SF4418 2.3 40.1 1.0
SG B:CYS125 2.3 47.3 1.0
FE2 B:SF4418 2.5 35.8 1.0
FE1 B:SF4418 2.6 36.4 1.0
FE4 B:SF4418 2.6 38.8 1.0
CB B:CYS125 3.3 50.4 1.0
N B:SAM417 3.4 36.5 1.0
S3 B:SF4418 3.7 36.2 1.0
CA B:GLY171 4.3 49.5 1.0
OXT B:SAM417 4.3 36.1 1.0
C B:GLY171 4.4 47.6 1.0
O B:MSE127 4.5 48.8 1.0
SG B:CYS132 4.5 42.2 1.0
SG B:CYS129 4.6 43.8 1.0
O B:GLY171 4.7 46.0 1.0
CB B:ALA138 4.7 49.8 1.0
CA B:CYS125 4.7 51.5 1.0
CD2 B:TYR128 4.8 53.9 1.0
CA B:SAM417 4.8 39.7 1.0
N B:ASP172 4.9 47.7 1.0

Iron binding site 8 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 8 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe418

b:38.8
occ:1.00
 FE4 B:SF4418 0.0 38.8 1.0
S1 B:SF4418 2.1 40.6 1.0
S3 B:SF4418 2.2 36.2 1.0
S2 B:SF4418 2.2 40.1 1.0
SG B:CYS129 2.3 43.8 1.0
FE2 B:SF4418 2.5 35.8 1.0
FE3 B:SF4418 2.6 39.6 1.0
FE1 B:SF4418 2.6 36.4 1.0
CB B:CYS129 3.3 41.2 1.0
OXT B:SAM417 3.5 36.1 1.0
S4 B:SF4418 3.7 38.7 1.0
N B:CYS129 3.9 45.9 1.0
CD B:ARG202 4.1 39.5 1.0
N B:SAM417 4.1 36.5 1.0
CA B:CYS129 4.2 44.1 1.0
O B:MSE127 4.2 48.8 1.0
CE1 B:HIS230 4.4 35.3 1.0
ND1 B:HIS230 4.4 38.8 1.0
SG B:CYS132 4.5 42.2 1.0
SG B:CYS125 4.7 47.3 1.0
CB B:CYS132 4.8 42.4 1.0
C B:SAM417 4.9 36.8 1.0
CB B:ARG202 4.9 40.3 1.0

Iron binding site 9 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 9 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe418

b:22.5
occ:1.00
 FE1 C:SF4418 0.0 22.5 1.0
OXT C:SAM417 2.0 23.0 1.0
N C:SAM417 2.0 21.8 1.0
S4 C:SF4418 2.1 24.3 1.0
S3 C:SF4418 2.2 22.4 1.0
S2 C:SF4418 2.4 25.1 1.0
FE3 C:SF4418 2.6 25.5 1.0
FE2 C:SF4418 2.6 22.0 1.0
FE4 C:SF4418 2.6 24.6 1.0
C C:SAM417 3.0 23.6 1.0
CA C:SAM417 3.0 25.9 1.0
SD C:SAM417 3.2 27.3 0.8
CG C:SAM417 3.6 25.8 1.0
S1 C:SF4418 3.7 26.4 1.0
CB C:SAM417 3.9 25.1 1.0
O C:SAM417 4.1 22.9 1.0
ND1 C:HIS230 4.4 27.1 1.0
O C:GLY171 4.4 29.9 1.0
CE C:SAM417 4.6 31.8 1.0
SG C:CYS125 4.6 31.2 1.0
SG C:CYS129 4.7 28.1 1.0
SG C:CYS132 4.8 27.9 1.0
C C:GLY171 4.8 31.6 1.0
CE1 C:HIS230 4.9 23.7 1.0
C5' C:SAM417 4.9 23.7 1.0
C3' C:SAM417 5.0 23.4 1.0

Iron binding site 10 out of 16 in 2a5h

Go back to Iron Binding Sites List in 2a5h
Iron binding site 10 out of 16 in the 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate).


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of 2.1 Angstrom X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale SB4, with Michaelis Analog (L-Alpha-Lysine External Aldimine Form of Pyridoxal-5'-Phosphate). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe418

b:22.0
occ:1.00
 FE2 C:SF4418 0.0 22.0 1.0
S4 C:SF4418 2.1 24.3 1.0
S1 C:SF4418 2.2 26.4 1.0
S3 C:SF4418 2.2 22.4 1.0
SG C:CYS132 2.3 27.9 1.0
FE4 C:SF4418 2.5 24.6 1.0
FE1 C:SF4418 2.6 22.5 1.0
FE3 C:SF4418 2.6 25.5 1.0
CB C:CYS132 3.3 28.6 1.0
S2 C:SF4418 3.8 25.1 1.0
CA C:CYS132 4.1 28.3 1.0
OXT C:SAM417 4.3 23.0 1.0
N C:SAM417 4.3 21.8 1.0
SD C:SAM417 4.5 27.3 0.8
SG C:CYS129 4.5 28.1 1.0
CB C:ALA138 4.6 33.9 1.0
SG C:CYS125 4.6 31.2 1.0
CB C:CYS129 4.8 27.1 1.0
CE C:SAM417 4.8 31.8 1.0
C C:CYS132 4.9 27.9 1.0
CB C:ARG134 4.9 29.6 1.0

Reference:

B.W.Lepore, F.J.Ruzicka, P.A.Frey, D.Ringe. The X-Ray Crystal Structure of Lysine-2,3-Aminomutase From Clostridium Subterminale. Proc.Natl.Acad.Sci.Usa V. 102 13819 2005.
ISSN: ISSN 0027-8424
PubMed: 16166264
DOI: 10.1073/PNAS.0505726102
Page generated: Sat Aug 3 18:51:45 2024

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