Atomistry » Sodium » PDB 2p0o-2plo » 2p76
Atomistry »
  Sodium »
    PDB 2p0o-2plo »
      2p76 »

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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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

Go back to Sodium Binding Sites List in 2p76
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: Tue Dec 15 05:53:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy