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Zinc 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:

Iron (Fe) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2a5h

Go back to Zinc Binding Sites List in 2a5h
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn421

b:36.0
occ:1.00
 SG B:CYS375 2.3 35.4 1.0
SG B:CYS377 2.3 37.0 1.0
SG B:CYS380 2.3 36.7 1.0
SG A:CYS268 2.3 29.6 1.0
CB A:CYS268 3.2 27.5 1.0
CB B:CYS377 3.2 36.6 1.0
CB B:CYS375 3.3 34.8 1.0
CB B:CYS380 3.4 37.8 1.0
CG2 A:VAL271 3.9 27.2 1.0
N B:CYS377 4.0 37.7 1.0
N B:CYS380 4.1 39.0 1.0
CA B:CYS377 4.1 38.3 1.0
CA B:CYS380 4.4 39.0 1.0
CA B:CYS375 4.5 35.9 1.0
C B:CYS375 4.6 37.4 1.0
CA A:CYS268 4.6 26.5 1.0
C B:CYS377 4.7 39.2 1.0
O B:CYS377 4.8 39.7 1.0
O B:CYS375 4.8 37.5 1.0
CB A:HIS270 4.9 29.0 1.0
CD2 A:HIS270 4.9 32.0 1.0
O A:HOH704 4.9 39.3 1.0
N A:VAL271 4.9 27.1 1.0
N B:ASN376 5.0 38.6 1.0

Zinc binding site 2 out of 4 in 2a5h

Go back to Zinc Binding Sites List in 2a5h
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn421

b:45.1
occ:1.00
 SG B:CYS268 2.3 35.2 1.0
SG A:CYS380 2.3 42.5 1.0
SG A:CYS375 2.3 42.3 1.0
SG A:CYS377 2.4 43.9 1.0
CB B:CYS268 3.1 33.7 1.0
CB A:CYS375 3.4 42.0 1.0
CB A:CYS377 3.4 44.1 1.0
CB A:CYS380 3.4 44.8 1.0
CG2 B:VAL271 3.9 33.9 1.0
N A:CYS380 4.1 45.7 1.0
N A:CYS377 4.2 45.8 1.0
CA A:CYS377 4.3 46.2 1.0
CA A:CYS380 4.4 45.9 1.0
CA B:CYS268 4.5 31.9 1.0
CA A:CYS375 4.6 43.5 1.0
C A:CYS375 4.6 45.4 1.0
O A:CYS375 4.7 44.9 1.0
CB B:HIS270 4.8 34.5 1.0
C A:CYS377 4.8 47.3 1.0
CD2 B:HIS270 4.9 37.3 1.0
N B:VAL271 5.0 32.8 1.0
O A:CYS377 5.0 47.5 1.0

Zinc binding site 3 out of 4 in 2a5h

Go back to Zinc Binding Sites List in 2a5h
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
C:Zn421

b:36.5
occ:1.00
 SG D:CYS375 2.3 34.2 1.0
SG D:CYS380 2.3 36.0 1.0
SG C:CYS268 2.3 28.0 1.0
SG D:CYS377 2.4 35.0 1.0
CB C:CYS268 3.1 26.5 1.0
CB D:CYS375 3.4 34.0 1.0
CB D:CYS377 3.4 35.1 1.0
CB D:CYS380 3.4 37.1 1.0
CG2 C:VAL271 3.8 25.9 1.0
N D:CYS377 4.1 36.5 1.0
N D:CYS380 4.2 38.3 1.0
CA D:CYS377 4.3 36.9 1.0
CA D:CYS380 4.4 38.4 1.0
CA C:CYS268 4.5 25.5 1.0
O C:HOH765 4.6 40.1 1.0
CA D:CYS375 4.6 34.8 1.0
C D:CYS375 4.6 36.3 1.0
O D:CYS375 4.8 36.6 1.0
CB C:HIS270 4.8 27.4 1.0
C D:CYS377 4.8 37.7 1.0
CD2 C:HIS270 4.9 30.8 1.0
N C:VAL271 4.9 25.2 1.0

Zinc binding site 4 out of 4 in 2a5h

Go back to Zinc Binding Sites List in 2a5h
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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
D:Zn421

b:31.1
occ:1.00
 SG C:CYS375 2.3 30.4 1.0
SG C:CYS380 2.3 31.3 1.0
SG D:CYS268 2.3 24.2 1.0
SG C:CYS377 2.4 30.7 1.0
CB D:CYS268 3.2 23.4 1.0
CB C:CYS377 3.3 30.1 1.0
CB C:CYS375 3.3 30.6 1.0
CB C:CYS380 3.4 32.8 1.0
CG2 D:VAL271 3.9 21.1 1.0
N C:CYS377 4.0 31.6 1.0
N C:CYS380 4.1 33.0 1.0
CA C:CYS377 4.1 31.7 1.0
CA C:CYS380 4.3 33.4 1.0
CA C:CYS375 4.5 31.3 1.0
CA D:CYS268 4.6 22.4 1.0
C C:CYS375 4.6 32.7 1.0
C C:CYS377 4.7 32.2 1.0
O C:CYS375 4.7 32.5 1.0
O C:CYS377 4.8 32.6 1.0
CD2 D:HIS270 4.9 26.4 1.0
CB D:HIS270 4.9 22.7 1.0
O D:HOH657 4.9 33.4 1.0
N D:VAL271 4.9 20.6 1.0
O C:HOH703 5.0 33.9 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: Wed Oct 16 21:30:31 2024

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