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Sodium in PDB 2p76: Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus

Enzymatic activity of Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus

All present enzymatic activity of Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus:
3.1.4.46;

Protein crystallography data

The structure of Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus, PDB code: 2p76 was solved by A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.97 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.164, 115.164, 451.335, 90.00, 90.00, 120.00
R / Rfree (%) 24.9 / 26.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus (pdb code 2p76). 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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus, PDB code: 2p76:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2p76

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Sodium binding site 1 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:41.5
occ:1.00
 OE1 A:GLU169 2.5 55.0 1.0
OD1 A:ASP89 2.6 46.7 1.0
O1 A:GOL501 2.6 42.8 1.0
OE2 A:GLU87 2.7 53.0 1.0
O2 A:GOL501 2.9 48.3 1.0
OD2 A:ASP89 3.2 45.7 1.0
CG A:ASP89 3.2 45.0 1.0
CD A:GLU169 3.4 51.1 1.0
C2 A:GOL501 3.5 48.9 1.0
C3 A:GOL501 3.6 47.8 1.0
C1 A:GOL501 3.6 44.2 1.0
CD A:GLU87 3.6 49.0 1.0
OE1 A:GLU87 3.9 50.4 1.0
O3 A:GOL501 3.9 53.3 1.0
OE2 A:GLU169 3.9 54.1 1.0
NE2 A:HIS59 4.2 47.6 1.0
CB A:GLU169 4.4 42.8 1.0
ND1 A:HIS102 4.5 41.3 1.0
CD2 A:HIS59 4.5 45.3 1.0
CG A:GLU169 4.5 46.7 1.0
NE2 A:GLN206 4.6 45.9 1.0
CE1 A:HIS102 4.6 41.0 1.0
OE1 A:GLN206 4.7 46.6 1.0
CB A:ASP89 4.7 43.5 1.0
CD A:GLN206 4.8 46.7 1.0
CG A:GLU87 5.0 46.1 1.0

Sodium binding site 2 out of 8 in 2p76

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Sodium binding site 2 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:55.1
occ:1.00
 OD1 B:ASP89 2.6 51.1 1.0
OE2 B:GLU87 2.8 59.4 1.0
OE1 B:GLU169 2.8 63.2 1.0
O2 B:GOL501 2.9 62.8 1.0
O1 B:GOL501 2.9 58.4 1.0
OD2 B:ASP89 3.0 50.4 1.0
O3 B:GOL501 3.1 68.5 1.0
CG B:ASP89 3.2 49.8 1.0
C3 B:GOL501 3.4 64.0 1.0
C2 B:GOL501 3.5 65.0 1.0
CD B:GLU87 3.7 55.1 1.0
C1 B:GOL501 3.7 61.1 1.0
CD B:GLU169 3.7 62.2 1.0
OE1 B:GLU87 3.8 54.5 1.0
NE2 B:HIS59 3.9 63.3 1.0
OE2 B:GLU169 4.1 62.5 1.0
ND1 B:HIS102 4.2 46.0 1.0
CD2 B:HIS59 4.3 60.7 1.0
CE1 B:HIS102 4.3 45.5 1.0
CB B:ASP89 4.6 49.4 1.0
CB B:GLU169 4.7 59.0 1.0
NE2 B:GLN206 4.8 47.6 1.0
CG B:GLU169 4.8 59.7 1.0
NE B:ARG60 4.9 54.0 1.0
OE1 B:GLN206 5.0 45.8 1.0

Sodium binding site 3 out of 8 in 2p76

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Sodium binding site 3 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:32.0
occ:1.00
 OE2 C:GLU87 2.6 51.5 1.0
OD1 C:ASP89 2.6 47.7 1.0
OE1 C:GLU169 2.6 55.9 1.0
O1 C:GOL501 2.8 50.1 1.0
O2 C:GOL501 2.8 52.5 1.0
OD2 C:ASP89 3.2 46.8 1.0
CG C:ASP89 3.3 44.0 1.0
CD C:GLU87 3.5 49.0 1.0
C1 C:GOL501 3.5 49.5 1.0
CD C:GLU169 3.6 53.2 1.0
C2 C:GOL501 3.6 54.7 1.0
O3 C:GOL501 3.6 60.0 1.0
OE1 C:GLU87 3.7 47.1 1.0
NE2 C:HIS59 4.0 46.4 1.0
C3 C:GOL501 4.0 53.5 1.0
OE2 C:GLU169 4.0 53.3 1.0
CD2 C:HIS59 4.3 44.4 1.0
ND1 C:HIS102 4.5 43.0 1.0
CB C:GLU169 4.5 47.5 1.0
NE2 C:GLN206 4.6 48.2 1.0
CE1 C:HIS102 4.6 42.7 1.0
CG C:GLU169 4.6 51.5 1.0
OE1 C:GLN206 4.7 50.0 1.0
CB C:ASP89 4.7 40.9 1.0
CD C:GLN206 4.8 48.2 1.0
CG C:GLU87 4.9 45.7 1.0

Sodium binding site 4 out of 8 in 2p76

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Sodium binding site 4 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:46.7
occ:1.00
 OE2 D:GLU87 2.5 48.5 1.0
OD1 D:ASP89 2.6 45.7 1.0
O1 D:GOL501 2.6 52.9 1.0
OE1 D:GLU169 2.8 54.2 1.0
O2 D:GOL501 2.9 54.7 1.0
OD2 D:ASP89 3.0 47.0 1.0
CG D:ASP89 3.2 45.1 1.0
CD D:GLU87 3.4 45.4 1.0
OE1 D:GLU87 3.6 45.2 1.0
C1 D:GOL501 3.6 53.8 1.0
C2 D:GOL501 3.6 56.9 1.0
O3 D:GOL501 3.7 61.0 1.0
CD D:GLU169 3.8 51.4 1.0
C3 D:GOL501 3.9 55.8 1.0
NE2 D:HIS59 3.9 46.5 1.0
CD2 D:HIS59 4.2 44.5 1.0
OE2 D:GLU169 4.2 51.2 1.0
ND1 D:HIS102 4.4 38.4 1.0
CE1 D:HIS102 4.6 38.3 1.0
NE2 D:GLN206 4.6 36.0 1.0
CB D:GLU169 4.6 46.5 1.0
CB D:ASP89 4.7 42.3 1.0
OE1 D:GLN206 4.8 35.6 1.0
CG D:GLU169 4.8 48.8 1.0
CG D:GLU87 4.8 43.5 1.0
CD D:GLN206 4.9 38.9 1.0
NE D:ARG60 5.0 42.4 1.0

Sodium binding site 5 out of 8 in 2p76

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Sodium binding site 5 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na401

b:36.7
occ:1.00
 OD1 E:ASP89 2.5 49.4 1.0
OE2 E:GLU87 2.6 52.8 1.0
OE1 E:GLU169 2.7 59.0 1.0
O1 E:GOL501 2.9 53.5 1.0
O2 E:GOL501 2.9 60.1 1.0
OD2 E:ASP89 3.0 49.6 1.0
CG E:ASP89 3.1 49.8 1.0
CD E:GLU87 3.5 49.2 1.0
C1 E:GOL501 3.6 55.3 1.0
CD E:GLU169 3.6 58.4 1.0
O3 E:GOL501 3.6 64.3 1.0
C2 E:GOL501 3.7 60.6 1.0
OE1 E:GLU87 3.7 47.3 1.0
OE2 E:GLU169 4.1 60.0 1.0
NE2 E:HIS59 4.1 61.0 1.0
C3 E:GOL501 4.2 59.1 1.0
ND1 E:HIS102 4.4 46.3 1.0
CD2 E:HIS59 4.4 58.9 1.0
CB E:GLU169 4.5 55.5 1.0
CE1 E:HIS102 4.5 47.4 1.0
CB E:ASP89 4.6 49.0 1.0
NE2 E:GLN206 4.6 48.9 1.0
CG E:GLU169 4.7 56.8 1.0
OE1 E:GLN206 4.8 50.4 1.0
CD E:GLN206 4.9 50.2 1.0
CG E:GLU87 4.9 47.0 1.0

Sodium binding site 6 out of 8 in 2p76

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Sodium binding site 6 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na401

b:34.2
occ:1.00
 OE2 F:GLU87 2.6 51.5 1.0
OD1 F:ASP89 2.6 53.4 1.0
OE1 F:GLU169 2.6 54.5 1.0
O2 F:GOL501 2.8 63.0 1.0
O1 F:GOL501 2.8 58.5 1.0
OD2 F:ASP89 3.1 54.6 1.0
CG F:ASP89 3.2 52.6 1.0
C2 F:GOL501 3.5 63.9 1.0
CD F:GLU87 3.5 51.4 1.0
CD F:GLU169 3.5 53.2 1.0
C3 F:GOL501 3.6 63.5 1.0
C1 F:GOL501 3.7 59.1 1.0
OE1 F:GLU87 3.7 51.2 1.0
O3 F:GOL501 3.9 68.4 1.0
OE2 F:GLU169 4.0 53.4 1.0
NE2 F:HIS59 4.1 59.2 1.0
CD2 F:HIS59 4.4 57.6 1.0
CB F:GLU169 4.5 51.6 1.0
ND1 F:HIS102 4.5 47.0 1.0
NE2 F:GLN206 4.6 50.4 1.0
CG F:GLU169 4.6 52.4 1.0
CE1 F:HIS102 4.6 46.8 1.0
OE1 F:GLN206 4.6 47.7 1.0
CB F:ASP89 4.7 50.2 1.0
CD F:GLN206 4.8 50.0 1.0
CG F:GLU87 4.9 48.6 1.0

Sodium binding site 7 out of 8 in 2p76

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Sodium binding site 7 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na401

b:35.6
occ:1.00
 OD1 G:ASP89 2.4 60.3 1.0
OE2 G:GLU87 2.6 55.0 1.0
OE1 G:GLU169 2.6 68.0 1.0
O1 G:GOL501 2.7 52.7 1.0
O2 G:GOL501 2.8 57.6 1.0
OD2 G:ASP89 3.0 61.6 1.0
CG G:ASP89 3.1 59.6 1.0
CD G:GLU169 3.5 66.4 1.0
CD G:GLU87 3.6 53.5 1.0
C2 G:GOL501 3.7 58.0 1.0
C1 G:GOL501 3.7 54.3 1.0
OE1 G:GLU87 3.8 54.3 1.0
OE2 G:GLU169 4.0 66.8 1.0
C3 G:GOL501 4.1 56.8 1.0
NE2 G:HIS59 4.1 63.8 1.0
ND1 G:HIS102 4.4 52.6 1.0
CB G:GLU169 4.4 60.4 1.0
CD2 G:HIS59 4.5 63.0 1.0
CE1 G:HIS102 4.5 53.6 1.0
CB G:ASP89 4.5 57.0 1.0
CG G:GLU169 4.6 63.9 1.0
O3 G:GOL501 4.6 61.9 1.0
NE2 G:GLN206 4.6 59.5 1.0
OE1 G:GLN206 4.8 56.7 1.0
CD G:GLN206 4.9 58.0 1.0
CG G:GLU87 5.0 51.2 1.0

Sodium binding site 8 out of 8 in 2p76

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Sodium binding site 8 out of 8 in the Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus


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 A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na401

b:43.8
occ:1.00
 OE2 H:GLU87 2.5 57.9 1.0
OD1 H:ASP89 2.7 52.0 1.0
OE1 H:GLU169 2.8 62.4 1.0
O1 H:GOL501 2.9 59.2 1.0
O2 H:GOL501 2.9 62.7 1.0
OD2 H:ASP89 3.1 55.1 1.0
CG H:ASP89 3.3 52.6 1.0
C3 H:GOL501 3.5 62.2 1.0
CD H:GLU87 3.5 54.9 1.0
C2 H:GOL501 3.5 63.3 1.0
CD H:GLU169 3.7 59.5 1.0
OE1 H:GLU87 3.7 56.0 1.0
C1 H:GOL501 3.7 58.7 1.0
NE2 H:HIS59 3.9 63.9 1.0
OE2 H:GLU169 4.2 60.6 1.0
CD2 H:HIS59 4.2 62.8 1.0
ND1 H:HIS102 4.5 51.5 1.0
O3 H:GOL501 4.5 67.4 1.0
CE1 H:HIS102 4.6 49.3 1.0
NE2 H:GLN206 4.6 43.9 1.0
CB H:GLU169 4.6 53.0 1.0
OE1 H:GLN206 4.7 45.1 1.0
CB H:ASP89 4.8 51.2 1.0
CG H:GLU169 4.8 57.7 1.0
CD H:GLN206 4.9 45.2 1.0
CG H:GLU87 4.9 52.7 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of A Glycerophosphodiester Phosphodiesterase From Staphylococcus Aureus To Be Published.
Page generated: Mon Oct 7 03:38:41 2024

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