Atomistry » Magnesium » PDB 4um5-4uuw » 4usx
Atomistry »
  Magnesium »
    PDB 4um5-4uuw »
      4usx »

Magnesium in PDB 4usx: The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei

Protein crystallography data

The structure of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei, PDB code: 4usx was solved by L.Perletti, L.J.Gourlay, C.Peano, A.Pietrelli, G.Debellis, C.Deantonio, C.Santoro, D.Sblattero, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.690 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.115, 58.852, 74.407, 90.00, 104.65, 90.00
R / Rfree (%) 16.85 / 20.42

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei (pdb code 4usx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei, PDB code: 4usx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 1 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1892

b:21.9
occ:1.00
 OD1 C:ASN747 2.6 15.8 1.0
N A:TYR727 3.0 13.7 1.0
O A:GLY750 3.1 15.4 1.0
ND2 C:ASN747 3.2 13.6 1.0
CG C:ASN747 3.2 16.0 1.0
O A:HOH2035 3.5 13.1 1.0
CA A:ILE751 3.6 12.7 1.0
CA A:VAL726 3.7 12.6 1.0
C A:VAL726 3.8 15.7 1.0
CB A:VAL726 3.9 12.8 1.0
CD1 A:TYR727 3.9 16.8 1.0
CB A:TYR727 3.9 14.6 1.0
CA A:TYR727 4.0 13.3 1.0
C A:GLY750 4.0 14.3 1.0
O A:TYR727 4.1 11.1 1.0
N A:ILE751 4.3 11.7 1.0
CG1 A:VAL726 4.3 15.1 1.0
CB A:ILE751 4.3 12.4 1.0
N A:LYS752 4.3 12.3 1.0
CG2 A:ILE751 4.4 13.1 1.0
C A:ILE751 4.4 13.0 1.0
CG A:TYR727 4.4 16.6 1.0
C A:TYR727 4.5 14.9 1.0
CG1 A:ILE746 4.5 16.2 1.0
CB C:ASN747 4.7 15.6 1.0
O A:THR725 4.8 13.0 1.0
CE1 A:TYR727 5.0 16.6 1.0

Magnesium binding site 2 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 2 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1891

b:20.1
occ:1.00
 O A:SER763 2.7 12.1 1.0
O B:ASN728 2.7 15.1 1.0
N B:GLY731 2.9 14.2 1.0
C B:ALA729 3.1 15.2 1.0
OD2 A:ASP762 3.3 11.7 1.0
N B:ASP730 3.3 14.8 1.0
O B:ALA729 3.3 13.2 1.0
CA B:ALA729 3.4 14.5 1.0
MG B:MG1892 3.5 24.4 1.0
CA B:GLY731 3.6 13.9 1.0
C B:ASN728 3.6 12.8 1.0
NE2 B:HIS755 3.7 10.2 1.0
CD2 B:HIS755 3.8 13.0 1.0
C A:SER763 3.8 11.2 1.0
CG A:GLN764 3.8 10.3 1.0
CA A:GLN764 3.8 10.9 1.0
CG A:ASP762 3.9 12.6 1.0
N B:ALA729 3.9 15.7 1.0
C B:ASP730 3.9 14.0 1.0
CA B:ASP730 4.1 15.2 1.0
CB A:GLN764 4.2 9.5 1.0
N A:GLN764 4.3 9.8 1.0
CB A:ASP762 4.4 11.4 1.0
CE1 B:HIS755 4.4 14.2 1.0
C B:GLY731 4.4 18.5 1.0
CG B:HIS755 4.5 11.7 1.0
OD1 A:ASP762 4.5 11.7 1.0
N B:THR732 4.5 13.9 1.0
CB B:ALA729 4.8 13.3 1.0
O B:THR732 4.8 13.9 1.0
ND1 B:HIS755 4.8 11.7 1.0
CD A:GLN764 4.9 16.9 1.0
CA B:ASN728 4.9 10.4 1.0
N A:ALA765 4.9 11.3 1.0
C A:GLN764 5.0 11.4 1.0

Magnesium binding site 3 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 3 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1892

b:24.4
occ:1.00
 O B:HOH2026 2.6 23.6 1.0
OD2 A:ASP762 2.8 11.7 1.0
O B:THR732 2.9 13.9 1.0
N B:THR732 3.4 13.9 1.0
C B:GLY731 3.4 18.5 1.0
C B:THR732 3.5 14.3 1.0
MG B:MG1891 3.5 20.1 1.0
CB A:ASP762 3.5 11.4 1.0
CG A:ASP762 3.6 12.6 1.0
CD2 B:TYR727 3.7 16.2 1.0
O B:ASN728 3.7 15.1 1.0
CA B:GLY731 3.8 13.9 1.0
O B:GLY731 3.8 19.0 1.0
CA B:THR732 3.9 14.6 1.0
N B:GLY731 4.2 14.2 1.0
CG2 B:THR733 4.3 17.9 1.0
CB B:TYR727 4.4 15.2 1.0
N B:THR733 4.4 13.4 1.0
N B:ASN728 4.4 12.7 1.0
CG B:TYR727 4.5 16.5 1.0
CE2 B:TYR727 4.6 18.1 1.0
CA B:TYR727 4.6 11.3 1.0
O A:HOH2083 4.7 18.2 1.0
C B:ASN728 4.7 12.8 1.0
O B:HOH2025 4.8 25.7 1.0
OD1 A:ASP762 4.8 11.7 1.0
C B:TYR727 4.8 11.4 1.0
NE2 B:HIS755 4.9 10.2 1.0
CA B:THR733 5.0 13.4 1.0

Magnesium binding site 4 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 4 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1893

b:28.1
occ:1.00
 OD1 A:ASP744 2.8 17.7 1.0
N B:THR725 2.9 12.7 1.0
OG1 B:THR725 3.6 17.3 1.0
CB B:THR725 3.6 14.0 1.0
CA B:TYR724 3.7 12.9 1.0
CG A:ASP744 3.7 18.9 1.0
C B:TYR724 3.7 12.2 1.0
CA B:THR725 3.8 14.6 1.0
OD2 A:ASP744 3.8 18.4 1.0
O A:HOH2058 3.9 15.8 1.0
O B:SER723 3.9 17.1 1.0
O B:THR725 4.4 14.0 1.0
CB B:TYR724 4.5 13.1 1.0
C B:THR725 4.6 15.6 1.0
N B:TYR724 4.7 12.5 1.0
C B:SER723 4.7 17.3 1.0
CD1 B:TYR724 4.8 13.1 1.0
O B:HOH2010 4.9 32.7 1.0
O B:HOH2021 4.9 18.9 1.0
O A:GLY740 4.9 14.9 1.0
O B:TYR724 4.9 16.7 1.0

Magnesium binding site 5 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 5 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1894

b:31.1
occ:1.00
 O B:HOH2132 2.9 18.7 1.0
NH2 B:ARG838 3.3 16.3 1.0
O B:HOH2131 3.7 15.8 1.0
O C:HOH2068 3.7 20.1 1.0
CZ B:ARG838 3.9 16.2 1.0
NH1 B:ARG838 3.9 15.1 1.0
O A:HOH2149 4.0 12.2 1.0
OG1 B:THR844 4.6 15.2 1.0
O B:HOH2137 4.6 22.0 1.0
NE B:ARG838 4.8 12.4 1.0
OD1 B:ASP845 4.9 14.1 1.0

Magnesium binding site 6 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 6 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1893

b:21.6
occ:1.00
 O C:ALA846 2.9 13.9 1.0
O C:ALA835 2.9 13.8 1.0
N B:ILE831 3.0 13.2 1.0
CA B:THR830 3.4 13.3 1.0
CB B:THR830 3.6 12.5 1.0
O B:ILE831 3.7 13.6 1.0
CA C:GLY837 3.7 14.6 1.0
C B:THR830 3.7 15.6 1.0
C C:ALA846 3.7 14.5 1.0
N C:GLY837 3.8 11.9 1.0
N C:ALA846 3.8 11.9 1.0
CG1 C:VAL834 3.9 14.7 1.0
CG2 B:THR830 4.0 13.5 1.0
CA C:ALA846 4.1 11.2 1.0
CB C:ALA846 4.1 13.8 1.0
CA B:ILE831 4.1 12.1 1.0
C C:ALA835 4.1 13.4 1.0
C C:ALA836 4.1 14.8 1.0
C B:ILE831 4.3 12.0 1.0
O C:ALA836 4.3 13.6 1.0
CB C:ASP845 4.3 13.1 1.0
C C:ASP845 4.5 12.7 1.0
CB B:ILE831 4.5 11.5 1.0
N B:THR830 4.7 12.5 1.0
CA C:ASP845 4.8 14.3 1.0
O B:ARG829 4.8 14.2 1.0
N C:ALA835 4.8 13.7 1.0
OG1 B:THR830 4.8 14.1 1.0
N C:ILE847 4.9 13.9 1.0
CA C:ALA836 4.9 12.0 1.0
O B:THR830 4.9 15.7 1.0
N C:ALA836 5.0 12.5 1.0
CA C:ALA835 5.0 13.5 1.0

Magnesium binding site 7 out of 7 in 4usx

Go back to Magnesium Binding Sites List in 4usx
Magnesium binding site 7 out of 7 in the The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of the C-Terminal Yada-Like Domain of BPSL2063 From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1894

b:23.7
occ:1.00
 O C:HOH2114 2.7 22.8 1.0
OD2 B:ASP762 2.9 16.1 1.0
O C:THR732 3.0 17.5 1.0
C C:GLY731 3.2 21.1 1.0
N C:THR732 3.3 16.6 1.0
O B:HOH2067 3.5 18.5 1.0
CB B:ASP762 3.5 13.6 1.0
CA C:GLY731 3.5 18.1 1.0
C C:THR732 3.5 22.0 1.0
O C:GLY731 3.5 21.0 1.0
CG B:ASP762 3.6 14.9 1.0
CD2 C:TYR727 3.8 12.2 1.0
CA C:THR732 3.9 20.4 1.0
O C:ASN728 3.9 16.6 1.0
N C:GLY731 4.0 16.4 1.0
CG2 C:THR733 4.1 19.1 1.0
CB C:TYR727 4.4 13.6 1.0
N C:ASN728 4.4 14.8 1.0
O B:HOH2064 4.4 20.5 1.0
N C:THR733 4.4 20.0 1.0
O C:HOH2018 4.5 27.4 1.0
CG C:TYR727 4.5 13.4 1.0
CE2 C:TYR727 4.6 15.2 1.0
CA C:TYR727 4.7 13.4 1.0
C C:ASN728 4.8 16.6 1.0
C C:TYR727 4.9 14.7 1.0
OD1 B:ASP762 4.9 14.6 1.0
NE2 C:HIS755 4.9 11.8 1.0
CA B:ASP762 5.0 14.2 1.0
CA C:THR733 5.0 19.9 1.0

Reference:

L.J.Gourlay, C.Peano, C.Deantonio, L.Perletti, A.Pietrelli, R.Villa, E.Matterazzo, P.Lassaux, C.Santoro, S.Puccio, D.Sblattero, M.Bolognesi. Selecting Soluble/Foldable Protein Domains Through Single- Gene or Genomic Orf Filtering: Structure of the Head Domain of Burkholderia Pseudomallei Antigen BPSL2063. Acta Crystallogr.,Sect.D V. 71 2227 2015.
ISSN: ISSN 0907-4449
PubMed: 26527140
DOI: 10.1107/S1399004715015680
Page generated: Tue Aug 20 04:59:23 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy