Atomistry » Zinc » PDB 2a25-2aer » 2a5h
Atomistry »
  Zinc »
    PDB 2a25-2aer »
      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 Dec 16 03:16:35 2020

Last articles

Zn in 7RRP
Zn in 7OKY
Zn in 7OL0
Zn in 7OKX
Zn in 7ONB
Zn in 7RSF
Zn in 7OUF
Zn in 7OUG
Zn in 7OUH
Zn in 7RGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy