Atomistry » Magnesium » PDB 3vth-3wca » 3w15
Atomistry »
  Magnesium »
    PDB 3vth-3wca »
      3w15 »

Magnesium in PDB 3w15: Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P

Protein crystallography data

The structure of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P, PDB code: 3w15 was solved by D.Pan, T.Nakatsu, H.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.20 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.890, 52.750, 97.570, 90.00, 106.59, 90.00
R / Rfree (%) 18.9 / 22.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P (pdb code 3w15). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P, PDB code: 3w15:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3w15

Go back to Magnesium Binding Sites List in 3w15
Magnesium binding site 1 out of 6 in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:22.5
occ:1.00
 O A:CYS110 2.3 14.4 1.0
O A:LEU66 2.4 11.3 1.0
O A:HOH506 2.5 25.4 1.0
O A:HOH508 2.5 19.7 1.0
OD1 A:ASN111 2.6 11.7 0.5
OD2 A:ASP65 2.8 12.2 1.0
OD1 A:ASP65 3.3 12.5 1.0
CG A:ASP65 3.4 11.9 1.0
CG A:ASN111 3.5 13.6 0.5
O A:HOH507 3.5 27.3 1.0
C A:CYS110 3.5 13.6 1.0
C A:LEU66 3.5 10.3 1.0
O A:HOH535 3.8 22.3 1.0
CB A:ALA67 4.0 10.5 1.0
O A:HOH592 4.0 32.6 1.0
ND2 A:ASN111 4.1 12.4 0.5
CA A:ASN111 4.2 14.1 0.5
CA A:ALA67 4.2 10.5 1.0
N A:ALA67 4.3 10.4 1.0
CA A:ASN111 4.3 14.1 0.5
N A:ASN111 4.3 13.7 1.0
N A:LEU66 4.3 10.0 1.0
N A:CYS110 4.4 11.8 1.0
CB A:ASN111 4.4 13.9 0.5
O A:HOH586 4.5 30.9 1.0
CA A:CYS110 4.6 13.0 1.0
CA A:LEU66 4.6 10.2 1.0
SG A:CYS110 4.6 14.8 1.0
CB A:ASP65 4.7 10.2 1.0
O A:HOH510 4.7 17.0 1.0
OE1 A:GLN15 4.9 15.5 1.0
ND2 A:ASN111 4.9 13.3 0.5
CB A:ASN111 4.9 13.8 0.5

Magnesium binding site 2 out of 6 in 3w15

Go back to Magnesium Binding Sites List in 3w15
Magnesium binding site 2 out of 6 in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg407

b:19.0
occ:1.00
 O C:HOH608 2.0 17.1 1.0
O C:HOH610 2.0 20.6 1.0
O C:HOH609 2.0 18.8 1.0
O C:HOH607 2.0 18.4 1.0
O C:HOH611 2.1 20.5 1.0
O C:HOH612 2.1 23.0 1.0
O C:HOH606 4.0 16.0 1.0
OE1 C:GLN270 4.2 17.0 1.0
O C:HOH604 4.2 14.3 1.0
NZ C:LYS273 4.3 15.6 1.0
O C:ALA180 4.4 14.1 1.0
O C:HOH613 4.4 22.9 1.0
O C:HOH605 4.6 13.3 1.0
O C:HOH831 4.8 37.8 1.0
CE C:LYS273 5.0 16.1 1.0
O C:HOH794 5.0 22.2 1.0

Magnesium binding site 3 out of 6 in 3w15

Go back to Magnesium Binding Sites List in 3w15
Magnesium binding site 3 out of 6 in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg408

b:31.8
occ:1.00
 O C:HOH506 1.8 27.7 1.0
OD1 C:ASP72 2.0 26.0 1.0
O C:HOH508 2.2 23.0 1.0
O C:HOH505 2.2 27.7 1.0
O C:HOH504 2.2 32.0 1.0
O C:HOH507 2.3 25.8 1.0
CG C:ASP72 3.0 24.9 1.0
OD2 C:ASP72 3.3 26.8 1.0
N C:GLY73 4.1 21.1 1.0
O C:HOH510 4.1 33.3 1.0
O C:HOH509 4.2 21.7 1.0
O C:LYS18 4.2 25.7 1.0
O C:GLY73 4.2 18.6 1.0
CB C:ASP72 4.4 23.5 1.0
C C:LYS18 4.5 26.1 1.0
CA C:ILE19 4.6 25.7 1.0
O C:HOH705 4.6 38.3 1.0
N C:ILE19 4.7 25.8 1.0
CA C:ASP72 4.7 23.1 1.0
CA C:GLY73 4.8 19.5 1.0
C C:GLY73 4.9 18.4 1.0
C C:ASP72 4.9 22.2 1.0

Magnesium binding site 4 out of 6 in 3w15

Go back to Magnesium Binding Sites List in 3w15
Magnesium binding site 4 out of 6 in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg409

b:24.9
occ:1.00
 O C:HOH671 1.9 23.1 1.0
O C:HOH673 2.0 22.9 1.0
O C:HOH674 2.1 24.6 1.0
O C:HOH675 2.1 15.7 1.0
O C:HOH672 2.2 29.6 1.0
O C:HOH744 2.3 27.4 1.0
O C:SER323 4.1 12.4 1.0
OD2 C:ASP304 4.2 14.6 1.0
O C:HOH714 4.3 18.7 1.0
OE1 C:GLU327 4.5 25.9 1.0
CB C:GLU327 4.6 17.2 1.0
C C:SER323 4.9 12.7 1.0

Magnesium binding site 5 out of 6 in 3w15

Go back to Magnesium Binding Sites List in 3w15
Magnesium binding site 5 out of 6 in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg410

b:18.6
occ:1.00
 O C:HOH636 2.0 16.2 1.0
O C:HOH637 2.0 21.9 1.0
OD2 C:ASP226 2.1 14.7 1.0
O C:HOH633 2.1 16.8 1.0
O C:HOH635 2.2 19.2 1.0
O C:HOH634 2.2 18.4 1.0
CG C:ASP226 3.1 13.3 1.0
OD1 C:ASP226 3.6 12.5 1.0
O C:HOH772 3.7 27.9 1.0
O C:HOH638 4.1 13.5 1.0
O C:HOH718 4.3 34.1 1.0
CB C:ASP226 4.4 11.8 1.0
O C:HOH788 4.5 32.9 1.0
CD1 C:ILE229 5.0 11.2 1.0

Magnesium binding site 6 out of 6 in 3w15

Go back to Magnesium Binding Sites List in 3w15
Magnesium binding site 6 out of 6 in the Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Peroxisomal Targeting Signal 2 (PTS2) of Saccharomyces Cerevisiae 3-Ketoacyl-Coa Thiolase in Complex with PEX7P and PEX21P within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg411

b:39.3
occ:1.00
 O C:HOH798 2.0 25.7 1.0
O C:HOH888 2.4 50.2 1.0
O C:HOH865 2.4 37.7 1.0
O C:HOH889 2.5 48.7 1.0
O C:HOH887 2.6 40.4 1.0
OE2 C:GLU61 4.0 23.0 1.0
OE1 C:GLU61 4.1 21.8 1.0
O C:HOH513 4.2 24.5 1.0
N C:LYS59 4.4 19.3 1.0
OD1 C:ASN29 4.4 18.6 1.0
O C:HOH775 4.4 30.8 1.0
CD C:GLU61 4.5 21.6 1.0
CA C:LYS59 4.6 19.3 1.0
CH2 C:TRP79 4.6 15.8 1.0

Reference:

D.Pan, T.Nakatsu, H.Kato. Crystal Structure of Peroxisomal Targeting Signal-2 Bound to Its Receptor Complex PEX7P-PEX21P Nat.Struct.Mol.Biol. V. 20 987 2013.
ISSN: ISSN 1545-9993
PubMed: 23812376
DOI: 10.1038/NSMB.2618
Page generated: Thu Aug 15 13:10:39 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy