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Sodium in PDB 1y0b: Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.

Protein crystallography data

The structure of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis., PDB code: 1y0b was solved by M.E.Cuff, R.Wu, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.503, 115.902, 73.985, 90.00, 94.30, 90.00
R / Rfree (%) 17.8 / 22.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. (pdb code 1y0b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis., PDB code: 1y0b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1y0b

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Sodium binding site 1 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na886

b:19.0
occ:1.00
 O A:HOH906 2.3 15.4 1.0
OD2 A:ASP125 2.3 14.1 1.0
O2' A:G4P888 2.4 16.6 1.0
O2C A:G4P888 2.5 21.3 1.0
OD1 A:ASP125 2.9 16.6 1.0
CG A:ASP125 2.9 16.4 1.0
O3' A:G4P888 3.1 19.4 1.0
PC A:G4P888 3.2 19.5 1.0
O1D A:G4P888 3.3 19.4 1.0
C2' A:G4P888 3.5 17.8 1.0
NA A:NA887 3.6 17.9 1.0
O3C A:G4P888 3.8 18.1 1.0
C3' A:G4P888 3.9 20.4 1.0
OD1 A:ASN27 3.9 15.9 1.0
C1' A:G4P888 3.9 16.8 1.0
CB A:SER60 4.0 13.5 1.0
PD A:G4P888 4.0 18.0 1.0
CD2 A:PHE126 4.1 16.1 1.0
O A:HOH900 4.2 21.5 1.0
OG A:SER60 4.2 13.5 1.0
O A:HOH901 4.3 15.9 1.0
O2D A:G4P888 4.3 17.8 1.0
CB A:ASP125 4.4 15.0 1.0
CB A:PHE126 4.5 16.0 1.0
N3 A:G4P888 4.5 15.4 1.0
O1C A:G4P888 4.6 19.6 1.0
N A:PHE126 4.7 15.9 1.0
CG A:PHE126 4.7 16.3 1.0
CG A:ASN27 4.7 14.8 1.0
O A:HOH895 4.7 10.1 1.0
N9 A:G4P888 4.7 17.0 1.0
C4 A:G4P888 4.9 15.8 1.0
CE2 A:PHE126 5.0 16.6 1.0
C4' A:G4P888 5.0 21.9 1.0

Sodium binding site 2 out of 8 in 1y0b

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Sodium binding site 2 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na887

b:17.9
occ:1.00
 OD1 A:ASP125 2.3 16.6 1.0
OD1 A:ASP124 2.3 19.3 1.0
O2C A:G4P888 2.4 21.3 1.0
O A:HOH895 2.5 10.1 1.0
O A:HOH892 2.5 14.7 1.0
CG A:ASP124 3.2 18.9 1.0
CG A:ASP125 3.4 16.4 1.0
OD2 A:ASP124 3.5 21.4 1.0
O A:HOH901 3.6 15.9 1.0
NA A:NA886 3.6 19.0 1.0
PC A:G4P888 3.7 19.5 1.0
CG2 A:ILE57 4.0 15.7 1.0
OD2 A:ASP125 4.1 14.1 1.0
O2' A:G4P888 4.1 16.6 1.0
N A:ASP125 4.1 15.3 1.0
O1C A:G4P888 4.2 19.6 1.0
O2D A:G4P888 4.2 17.8 1.0
N A:GLY61 4.4 13.6 1.0
O A:HOH898 4.5 21.8 1.0
CB A:ASP125 4.5 15.0 1.0
CB A:ASP124 4.6 16.1 1.0
N A:PHE126 4.6 15.9 1.0
O3' A:G4P888 4.6 19.4 1.0
O3C A:G4P888 4.7 18.1 1.0
O A:ILE57 4.7 14.4 1.0
CA A:ASP125 4.8 15.5 1.0
CA A:GLY61 4.8 13.9 1.0
CB A:SER60 4.9 13.5 1.0
CA A:ASP124 5.0 16.1 1.0
PD A:G4P888 5.0 18.0 1.0

Sodium binding site 3 out of 8 in 1y0b

Go back to Sodium Binding Sites List in 1y0b
Sodium binding site 3 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na886

b:21.9
occ:1.00
 O B:HOH922 2.3 25.0 1.0
OD2 B:ASP125 2.3 17.4 1.0
O2C B:G4P888 2.4 22.9 1.0
O2' B:G4P888 2.5 22.4 1.0
OD1 B:ASP125 2.8 18.2 1.0
CG B:ASP125 2.9 18.6 1.0
O3' B:G4P888 3.0 23.6 1.0
PC B:G4P888 3.1 23.8 1.0
O1D B:G4P888 3.3 23.0 1.0
NA B:NA887 3.5 19.8 1.0
C2' B:G4P888 3.6 23.4 1.0
O3C B:G4P888 3.7 22.7 1.0
C3' B:G4P888 3.8 25.6 1.0
C1' B:G4P888 3.9 22.2 1.0
OD1 B:ASN27 4.0 20.5 1.0
PD B:G4P888 4.0 22.5 1.0
CB B:SER60 4.0 15.9 1.0
CD2 B:PHE126 4.1 17.8 1.0
O B:HOH937 4.2 31.7 1.0
OG B:SER60 4.2 16.9 1.0
O2D B:G4P888 4.3 21.6 1.0
CB B:ASP125 4.4 17.4 1.0
O1C B:G4P888 4.5 26.3 1.0
O B:HOH936 4.5 26.5 1.0
CB B:PHE126 4.5 16.7 1.0
N3 B:G4P888 4.6 20.4 1.0
CG B:ASN27 4.6 17.8 1.0
N B:PHE126 4.7 17.1 1.0
O B:HOH903 4.7 12.5 1.0
CG B:PHE126 4.8 16.6 1.0
N9 B:G4P888 4.8 21.5 1.0
ND2 B:ASN27 4.9 17.9 1.0
C4' B:G4P888 4.9 27.3 1.0
O B:HOH891 4.9 38.1 1.0
O4' B:G4P888 4.9 25.2 1.0
C4 B:G4P888 5.0 20.6 1.0

Sodium binding site 4 out of 8 in 1y0b

Go back to Sodium Binding Sites List in 1y0b
Sodium binding site 4 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na887

b:19.8
occ:1.00
 O2C B:G4P888 2.3 22.9 1.0
O B:HOH894 2.4 18.8 1.0
OD1 B:ASP124 2.4 20.7 1.0
OD1 B:ASP125 2.4 18.2 1.0
O B:HOH903 2.4 12.5 1.0
CG B:ASP124 3.3 19.8 1.0
OD2 B:ASP124 3.5 21.1 1.0
CG B:ASP125 3.5 18.6 1.0
NA B:NA886 3.5 21.9 1.0
PC B:G4P888 3.6 23.8 1.0
O B:HOH936 3.7 26.5 1.0
O1C B:G4P888 4.0 26.3 1.0
CG2 B:ILE57 4.0 16.9 1.0
O2' B:G4P888 4.1 22.4 1.0
OD2 B:ASP125 4.2 17.4 1.0
N B:ASP125 4.2 17.5 1.0
O2D B:G4P888 4.2 21.6 1.0
O B:HOH949 4.3 26.9 1.0
N B:GLY61 4.4 15.9 1.0
O3' B:G4P888 4.5 23.6 1.0
CB B:ASP125 4.6 17.4 1.0
CB B:ASP124 4.6 18.4 1.0
O3C B:G4P888 4.6 22.7 1.0
O B:ILE57 4.7 14.7 1.0
N B:PHE126 4.7 17.1 1.0
CB B:SER60 4.8 15.9 1.0
CA B:GLY61 4.8 15.8 1.0
CA B:ASP125 4.9 17.6 1.0
PD B:G4P888 5.0 22.5 1.0
C3' B:G4P888 5.0 25.6 1.0

Sodium binding site 5 out of 8 in 1y0b

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Sodium binding site 5 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na886

b:21.8
occ:1.00
 O C:HOH913 2.2 18.2 1.0
OD2 C:ASP125 2.3 16.6 1.0
O2C C:G4P888 2.4 19.5 1.0
O2' C:G4P888 2.6 22.1 1.0
OD1 C:ASP125 2.9 18.5 1.0
CG C:ASP125 2.9 17.4 1.0
O3' C:G4P888 3.1 20.3 1.0
PC C:G4P888 3.2 19.2 1.0
O1D C:G4P888 3.5 18.1 1.0
NA C:NA887 3.5 17.2 1.0
C2' C:G4P888 3.6 20.8 1.0
OD1 C:ASN27 3.8 17.3 1.0
O3C C:G4P888 3.8 18.7 1.0
C3' C:G4P888 3.9 22.0 1.0
CB C:SER60 3.9 14.8 1.0
C1' C:G4P888 4.0 19.0 1.0
PD C:G4P888 4.1 18.1 1.0
CD2 C:PHE126 4.1 18.4 1.0
OG C:SER60 4.2 14.4 1.0
O2D C:G4P888 4.3 19.7 1.0
O C:HOH900 4.3 21.9 1.0
CB C:ASP125 4.4 16.3 1.0
CB C:PHE126 4.5 17.2 1.0
N3 C:G4P888 4.5 17.0 1.0
O1C C:G4P888 4.6 16.4 1.0
O C:HOH891 4.6 19.0 1.0
O C:HOH890 4.6 11.9 1.0
CG C:ASN27 4.7 15.2 1.0
N C:PHE126 4.7 17.0 1.0
CG C:PHE126 4.7 17.6 1.0
N9 C:G4P888 4.8 18.8 1.0
C4 C:G4P888 5.0 17.8 1.0
O D:HOH898 5.0 24.6 1.0

Sodium binding site 6 out of 8 in 1y0b

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Sodium binding site 6 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na887

b:17.2
occ:1.00
 OD1 C:ASP125 2.3 18.5 1.0
O C:HOH890 2.3 11.9 1.0
OD1 C:ASP124 2.3 21.4 1.0
O2C C:G4P888 2.4 19.5 1.0
O C:HOH895 2.5 16.6 1.0
CG C:ASP124 3.3 20.0 1.0
CG C:ASP125 3.4 17.4 1.0
OD2 C:ASP124 3.5 22.0 1.0
NA C:NA886 3.5 21.8 1.0
PC C:G4P888 3.7 19.2 1.0
O C:HOH891 3.9 19.0 1.0
OD2 C:ASP125 4.1 16.6 1.0
CG2 C:ILE57 4.1 16.5 1.0
O2' C:G4P888 4.1 22.1 1.0
O1C C:G4P888 4.2 16.4 1.0
N C:ASP125 4.2 16.5 1.0
O2D C:G4P888 4.2 19.7 1.0
N C:GLY61 4.3 14.6 1.0
O C:HOH923 4.4 32.0 1.0
CB C:ASP125 4.5 16.3 1.0
CB C:ASP124 4.6 17.7 1.0
N C:PHE126 4.7 17.0 1.0
O3' C:G4P888 4.7 20.3 1.0
CB C:SER60 4.7 14.8 1.0
O C:ILE57 4.7 16.0 1.0
O3C C:G4P888 4.8 18.7 1.0
CA C:GLY61 4.8 14.4 1.0
CA C:ASP125 4.8 16.7 1.0

Sodium binding site 7 out of 8 in 1y0b

Go back to Sodium Binding Sites List in 1y0b
Sodium binding site 7 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na886

b:25.5
occ:1.00
 OD2 D:ASP125 2.3 18.8 1.0
O D:HOH943 2.3 25.0 1.0
O2C D:G4P888 2.4 23.2 1.0
O2' D:G4P888 2.4 23.4 1.0
OD1 D:ASP125 2.9 19.7 1.0
CG D:ASP125 2.9 19.6 1.0
O3' D:G4P888 3.1 23.1 1.0
PC D:G4P888 3.2 22.4 1.0
O1D D:G4P888 3.3 23.7 1.0
C2' D:G4P888 3.5 22.8 1.0
NA D:NA887 3.6 21.4 1.0
O3C D:G4P888 3.7 22.6 1.0
OD1 D:ASN27 3.8 22.7 1.0
C3' D:G4P888 3.9 25.0 1.0
C1' D:G4P888 3.9 22.1 1.0
PD D:G4P888 4.0 21.9 1.0
CB D:SER60 4.0 15.1 1.0
OG D:SER60 4.1 14.5 1.0
O D:HOH997 4.2 38.6 1.0
O2D D:G4P888 4.2 21.4 1.0
CD2 D:PHE126 4.2 18.6 1.0
O D:HOH903 4.4 25.6 1.0
CB D:ASP125 4.4 18.4 1.0
CB D:PHE126 4.5 17.9 1.0
O1C D:G4P888 4.5 23.8 1.0
N3 D:G4P888 4.6 20.8 1.0
CG D:ASN27 4.6 18.8 1.0
O D:HOH896 4.7 13.2 1.0
N9 D:G4P888 4.7 22.2 1.0
N D:PHE126 4.7 18.3 1.0
CG D:PHE126 4.9 18.2 1.0
ND2 D:ASN27 4.9 20.7 1.0
C4 D:G4P888 4.9 20.9 1.0
C4' D:G4P888 5.0 26.2 1.0

Sodium binding site 8 out of 8 in 1y0b

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Sodium binding site 8 out of 8 in the Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na887

b:21.4
occ:1.00
 O2C D:G4P888 2.2 23.2 1.0
O D:HOH896 2.3 13.2 1.0
OD1 D:ASP124 2.3 20.4 1.0
OD1 D:ASP125 2.4 19.7 1.0
O D:HOH902 2.4 15.2 1.0
CG D:ASP124 3.2 19.7 1.0
OD2 D:ASP124 3.5 21.4 1.0
CG D:ASP125 3.5 19.6 1.0
NA D:NA886 3.6 25.5 1.0
PC D:G4P888 3.6 22.4 1.0
O D:HOH903 3.6 25.6 1.0
CG2 D:ILE57 4.0 16.2 1.0
O2' D:G4P888 4.0 23.4 1.0
O1C D:G4P888 4.0 23.8 1.0
O2D D:G4P888 4.1 21.4 1.0
OD2 D:ASP125 4.1 18.8 1.0
N D:ASP125 4.2 18.1 1.0
O D:HOH890 4.3 26.6 1.0
N D:GLY61 4.4 14.8 1.0
CB D:ASP125 4.5 18.4 1.0
O3' D:G4P888 4.6 23.1 1.0
CB D:ASP124 4.6 18.2 1.0
O3C D:G4P888 4.6 22.6 1.0
O D:ILE57 4.7 15.2 1.0
N D:PHE126 4.7 18.3 1.0
CB D:SER60 4.8 15.1 1.0
CA D:ASP125 4.9 18.5 1.0
CA D:GLY61 4.9 14.7 1.0
PD D:G4P888 4.9 21.9 1.0

Reference:

M.E.Cuff, R.Wu, A.Joachimiak, Mcsg. Crystal Structure of Xanthine Phosphoribosyltransferase From Bacillus Subtilis To Be Published.
Page generated: Mon Oct 7 00:35:32 2024

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