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Zinc in PDB 2oog: Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus

Enzymatic activity of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus

All present enzymatic activity of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus:
3.1.4.46;

Protein crystallography data

The structure of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus, PDB code: 2oog was solved by Y.Patskovsky, E.Fedorov, R.Toro, J.M.Sauder, D.Smith, J.Freeman, M.Maletic, A.Powell, T.Gheyi, S.R.Wasserman, 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) 20.00 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 156.312, 183.546, 176.790, 90.00, 90.00, 90.00
R / Rfree (%) 23.5 / 28

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus (pdb code 2oog). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus, PDB code: 2oog:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2oog

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Zinc binding site 1 out of 6 in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:53.2
occ:1.00
 OE1 A:GLU169 2.3 36.7 1.0
OE2 A:GLU87 2.4 34.6 1.0
OD1 A:ASP89 2.5 46.0 1.0
O A:HOH593 2.5 41.0 1.0
O A:HOH639 2.6 42.8 1.0
O2 A:GOL455 2.7 30.6 1.0
O1 A:GOL455 2.8 36.5 1.0
C1 A:GOL455 3.3 45.1 1.0
C2 A:GOL455 3.3 45.1 1.0
CG A:ASP89 3.4 44.9 1.0
CD A:GLU169 3.5 47.6 1.0
CD A:GLU87 3.5 28.9 1.0
OD2 A:ASP89 3.6 26.3 1.0
C3 A:GOL455 3.8 33.4 1.0
OE1 A:GLU87 3.9 39.7 1.0
NE2 A:GLN206 4.0 34.8 1.0
OE2 A:GLU169 4.1 47.0 1.0
OE1 A:GLN206 4.3 29.8 1.0
O3 A:GOL455 4.3 50.3 1.0
NE2 A:HIS59 4.4 24.3 1.0
CD A:GLN206 4.5 31.8 1.0
CB A:GLU169 4.5 33.6 1.0
CG A:GLU169 4.6 32.6 1.0
CD2 A:HIS59 4.7 34.6 1.0
CG A:GLU87 4.8 31.1 1.0
O A:HOH650 4.8 54.2 1.0
O A:HOH503 4.8 38.4 1.0
CB A:ASP89 4.8 28.8 1.0
ND1 A:HIS102 4.9 33.8 1.0

Zinc binding site 2 out of 6 in 2oog

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Zinc binding site 2 out of 6 in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:46.5
occ:1.00
 O B:HOH652 2.3 27.9 1.0
OE1 B:GLU169 2.3 35.7 1.0
OD1 B:ASP89 2.4 40.5 1.0
O1 B:GOL452 2.4 25.9 1.0
OE2 B:GLU87 2.5 28.3 1.0
O B:HOH642 2.6 31.5 1.0
O2 B:GOL452 2.6 34.5 1.0
C1 B:GOL452 3.3 19.4 1.0
CG B:ASP89 3.4 32.0 1.0
C2 B:GOL452 3.4 31.4 1.0
CD B:GLU87 3.5 31.4 1.0
CD B:GLU169 3.5 42.7 1.0
OD2 B:ASP89 3.7 25.1 1.0
OE1 B:GLU87 3.9 25.3 1.0
NE2 B:GLN206 4.0 23.7 1.0
C3 B:GOL452 4.0 25.1 1.0
OE2 B:GLU169 4.2 39.2 1.0
OE1 B:GLN206 4.3 25.7 1.0
NE2 B:HIS59 4.4 28.8 1.0
CB B:GLU169 4.4 23.2 1.0
CD B:GLN206 4.5 26.2 1.0
O3 B:GOL452 4.5 36.7 1.0
CG B:GLU169 4.5 28.8 1.0
CB B:ASP89 4.7 29.2 1.0
CD2 B:HIS59 4.7 20.7 1.0
CG B:GLU87 4.8 27.2 1.0
O B:HOH598 4.8 41.4 1.0
ND1 B:HIS102 4.9 32.6 1.0
O B:HOH509 5.0 36.2 1.0

Zinc binding site 3 out of 6 in 2oog

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Zinc binding site 3 out of 6 in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn406

b:76.1
occ:1.00
 OD1 C:ASP89 2.2 42.2 1.0
OE1 C:GLU169 2.3 84.4 1.0
OE2 C:GLU87 2.5 54.9 1.0
O C:HOH484 2.5 47.3 1.0
O2 C:GOL451 2.6 58.7 1.0
O C:HOH485 3.2 54.4 1.0
O1 C:GOL451 3.3 61.5 1.0
CG C:ASP89 3.3 48.4 1.0
CD C:GLU169 3.4 71.6 1.0
CD C:GLU87 3.5 64.1 1.0
C2 C:GOL451 3.6 67.8 1.0
OD2 C:ASP89 3.7 55.8 1.0
OE1 C:GLU87 3.8 37.0 1.0
NE2 C:GLN206 3.8 37.1 1.0
C3 C:GOL451 3.9 91.0 1.0
O3 C:GOL451 3.9 89.9 1.0
C1 C:GOL451 4.0 70.8 1.0
OE2 C:GLU169 4.1 70.8 1.0
CB C:GLU169 4.3 53.9 1.0
OE1 C:GLN206 4.4 52.7 1.0
CG C:GLU169 4.4 60.0 1.0
CD C:GLN206 4.4 34.4 1.0
NE2 C:HIS59 4.6 60.9 1.0
CB C:ASP89 4.6 45.7 1.0
ND1 C:HIS102 4.9 50.9 1.0
CG C:GLU87 4.9 49.7 1.0
CD2 C:HIS59 5.0 58.9 1.0

Zinc binding site 4 out of 6 in 2oog

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Zinc binding site 4 out of 6 in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn405

b:60.4
occ:1.00
 OD1 D:ASP89 2.4 44.3 1.0
O2 D:GOL453 2.4 34.4 1.0
OE1 D:GLU169 2.4 50.0 1.0
OE2 D:GLU87 2.5 34.6 1.0
O D:HOH549 2.5 46.1 1.0
O1 D:GOL453 2.6 34.5 1.0
O D:HOH656 2.6 31.9 1.0
CG D:ASP89 3.4 42.5 1.0
C2 D:GOL453 3.4 37.5 1.0
C1 D:GOL453 3.5 41.0 1.0
CD D:GLU87 3.5 42.4 1.0
CD D:GLU169 3.6 45.9 1.0
OD2 D:ASP89 3.6 42.2 1.0
OE1 D:GLU87 3.8 34.4 1.0
NE2 D:GLN206 3.9 30.8 1.0
C3 D:GOL453 3.9 43.8 1.0
O D:HOH602 4.1 36.7 1.0
OE2 D:GLU169 4.2 55.3 1.0
NE2 D:HIS59 4.4 41.0 1.0
OE1 D:GLN206 4.4 46.6 1.0
CD D:GLN206 4.4 27.3 1.0
O3 D:GOL453 4.4 49.6 1.0
CB D:GLU169 4.5 39.1 1.0
CG D:GLU169 4.6 34.0 1.0
O D:HOH664 4.6 39.8 1.0
CD2 D:HIS59 4.7 33.7 1.0
CB D:ASP89 4.7 34.7 1.0
CG D:GLU87 4.8 33.3 1.0
O D:HOH514 4.9 41.4 1.0
ND1 D:HIS102 4.9 34.3 1.0

Zinc binding site 5 out of 6 in 2oog

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Zinc binding site 5 out of 6 in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn404

b:73.0
occ:1.00
 OE2 E:GLU87 2.2 54.6 1.0
O E:HOH534 2.4 35.3 1.0
O E:HOH512 2.4 49.5 1.0
OD1 E:ASP89 2.4 51.8 1.0
OE1 E:GLU169 2.7 60.5 1.0
O2 E:GOL454 2.7 65.2 1.0
C1 E:GOL454 3.2 87.8 1.0
CD E:GLU87 3.3 51.3 1.0
CG E:ASP89 3.4 55.8 1.0
C2 E:GOL454 3.5 73.5 1.0
OD2 E:ASP89 3.7 60.2 1.0
CD E:GLU169 3.7 56.7 1.0
OE1 E:GLU87 3.7 58.1 1.0
NE2 E:GLN206 4.0 55.5 1.0
NE2 E:HIS59 4.3 48.0 1.0
O1 E:GOL454 4.3 77.5 1.0
C3 E:GOL454 4.3 54.9 1.0
OE1 E:GLN206 4.3 67.1 1.0
OE2 E:GLU169 4.4 50.1 1.0
CB E:GLU169 4.5 52.2 1.0
CD2 E:HIS59 4.5 55.3 1.0
CD E:GLN206 4.5 67.2 1.0
O3 E:GOL454 4.6 64.0 1.0
CG E:GLU87 4.6 45.2 1.0
CG E:GLU169 4.7 30.3 1.0
O E:HOH513 4.8 59.0 1.0
CB E:ASP89 4.8 50.8 1.0

Zinc binding site 6 out of 6 in 2oog

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Zinc binding site 6 out of 6 in the Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:76.6
occ:1.00
 OE2 F:GLU87 2.2 58.2 1.0
O F:HOH512 2.3 35.5 1.0
OD1 F:ASP89 2.5 49.8 1.0
O F:HOH554 2.5 44.2 1.0
OE1 F:GLU169 2.7 61.6 1.0
O2 F:GOL456 2.7 50.7 1.0
C2 F:GOL456 3.0 53.3 1.0
O1 F:GOL456 3.1 53.2 1.0
CD F:GLU87 3.2 55.8 1.0
CG F:ASP89 3.4 42.7 1.0
C1 F:GOL456 3.5 43.6 1.0
CD F:GLU169 3.5 45.9 1.0
OE1 F:GLU87 3.5 37.8 1.0
OD2 F:ASP89 3.7 47.2 1.0
NE2 F:GLN206 3.9 40.3 1.0
OE2 F:GLU169 4.0 63.1 1.0
NE2 F:HIS59 4.3 41.9 1.0
C3 F:GOL456 4.4 53.9 1.0
CB F:GLU169 4.4 47.9 1.0
OE1 F:GLN206 4.4 52.6 1.0
CD2 F:HIS59 4.4 34.8 1.0
CD F:GLN206 4.5 52.5 1.0
CG F:GLU87 4.5 50.6 1.0
CG F:GLU169 4.6 51.2 1.0
CB F:ASP89 4.8 33.8 1.0
O3 F:GOL456 4.8 54.0 1.0

Reference:

Y.Patskovsky, J.M.Sauder, D.Smith, J.Freeman, M.Maletic, A.Powell, T.Gheyi, S.R.Wasserman, S.K.Burley, S.C.Almo. Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus To Be Published.
Page generated: Thu Oct 17 02:42:14 2024

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