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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

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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

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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: Mon Dec 14 09:00:06 2020

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