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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

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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

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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

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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

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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

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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

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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

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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

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