Atomistry » Zinc » PDB 2a2q-2afm » 2a5h
Atomistry »
  Zinc »
    PDB 2a2q-2afm »
      2a5h »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy