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Sodium in PDB 3g25: 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.

Enzymatic activity of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.

All present enzymatic activity of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.:
2.7.1.30;

Protein crystallography data

The structure of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol., PDB code: 3g25 was solved by G.Minasov, T.Skarina, O.Onopriyenko, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.81 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.750, 193.742, 91.669, 90.00, 103.60, 90.00
R / Rfree (%) 19.3 / 24.6

Sodium Binding Sites:

The binding sites of Sodium atom in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. (pdb code 3g25). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol., PDB code: 3g25:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 3g25

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Sodium binding site 1 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na500

b:25.1
occ:0.50
 O3 A:PO4502 2.3 36.6 0.8
O1 A:GOL499 2.9 20.7 1.0
N A:GLY267 3.1 6.0 1.0
O2 A:PO4502 3.1 31.2 0.8
N A:THR266 3.2 10.0 1.0
P A:PO4502 3.2 32.2 0.8
O A:HOH599 3.4 27.0 1.0
O A:GLY267 3.5 6.6 1.0
CE1 A:PHE269 3.5 9.7 1.0
C1 A:GOL499 3.6 18.8 1.0
NE2 A:GLN245 3.8 14.5 1.0
C A:GLY265 3.8 11.2 1.0
CB A:THR266 3.8 11.1 1.0
CA A:THR266 3.8 9.4 1.0
CA A:GLY267 3.8 4.9 1.0
CA A:GLY265 3.9 11.2 1.0
C A:THR266 3.9 9.7 1.0
C A:GLY267 3.9 7.8 1.0
O4 A:PO4502 4.0 46.4 0.8
CD1 A:PHE269 4.1 8.5 1.0
O1 A:PO4502 4.4 38.8 0.8
N A:GLY265 4.4 12.0 1.0
OG1 A:THR266 4.5 12.4 1.0
C2 A:GOL499 4.6 18.6 1.0
CZ2 A:TRP102 4.6 17.4 1.0
CZ A:PHE269 4.6 14.9 1.0
OG1 A:THR12 4.7 14.5 1.0
O A:GLY265 4.8 9.7 1.0
CD A:GLN245 4.9 15.8 1.0
CG2 A:THR266 5.0 8.7 1.0

Sodium binding site 2 out of 7 in 3g25

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Sodium binding site 2 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:55.6
occ:1.00
 O2 A:PO4505 2.4 47.5 0.8
O A:PHE452 2.8 10.5 1.0
O4 A:PO4505 3.0 49.9 0.8
P A:PO4505 3.3 50.5 0.8
OE1 A:GLN22 3.4 25.8 1.0
CG A:GLN22 3.6 24.9 1.0
CA A:TRP453 3.8 8.1 1.0
C A:PHE452 3.8 10.0 1.0
CD A:GLN22 3.9 26.7 1.0
CD1 A:TRP453 3.9 2.1 1.0
N A:TRP453 4.3 9.7 1.0
O1 A:PO4505 4.3 52.0 0.8
O3 A:PO4505 4.5 41.1 0.8
N A:GLU454 4.5 9.2 1.0
CG A:TRP453 4.5 4.0 1.0
C A:TRP453 4.6 8.3 1.0
CB A:TRP453 4.6 8.9 1.0
NE1 A:TRP453 4.7 8.0 1.0
CB A:GLN22 5.0 22.5 1.0

Sodium binding site 3 out of 7 in 3g25

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Sodium binding site 3 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na500

b:41.2
occ:1.00
 O1 B:PO4503 2.0 42.8 0.8
P B:PO4503 3.1 31.9 0.8
O4 B:PO4503 3.1 33.9 0.8
OG1 B:THR13 3.2 13.2 1.0
N B:THR13 3.4 12.9 1.0
N B:THR12 3.5 11.3 1.0
O B:HOH555 3.6 34.5 1.0
OG1 B:THR266 3.8 10.4 1.0
N B:SER14 3.8 14.4 1.0
CA B:GLY11 3.9 7.1 1.0
O3 B:PO4503 3.9 23.1 0.8
C B:GLY11 4.0 8.5 1.0
OG B:SER14 4.0 15.3 1.0
CA B:THR13 4.1 13.8 1.0
O2 B:PO4503 4.1 37.5 0.8
CB B:THR13 4.2 14.0 1.0
O B:SER14 4.2 12.3 1.0
CA B:THR12 4.3 9.0 1.0
C B:THR12 4.3 11.3 1.0
C B:THR13 4.4 12.1 1.0
O B:HOH822 4.5 28.5 1.0
O B:HOH784 4.5 37.8 1.0
CA B:SER14 4.7 13.7 1.0
CB B:THR12 4.7 10.1 1.0
CG2 B:THR13 4.7 18.0 1.0
CB B:SER14 4.8 14.8 1.0
C B:SER14 4.9 13.4 1.0
O B:GLY11 4.9 9.1 1.0
N B:GLY11 5.0 8.3 1.0

Sodium binding site 4 out of 7 in 3g25

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Sodium binding site 4 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:60.1
occ:1.00
 O2 A:PO4503 2.4 33.0 0.8
O A:HOH669 3.6 17.9 1.0
O4 A:PO4503 3.6 39.0 0.8
P A:PO4503 3.6 32.7 0.8
NE B:ARG320 3.9 14.9 1.0
CD B:ARG320 3.9 12.6 1.0
CB B:ARG320 4.1 11.8 1.0
ND2 D:ASN323 4.4 39.5 1.0
O B:HOH954 4.4 25.8 1.0
O3 A:PO4503 4.5 33.6 0.8
CG B:ARG320 4.6 15.8 1.0
O1 A:PO4503 4.7 33.1 0.8
OD1 D:ASN323 4.7 40.6 1.0
CG D:ASN323 4.9 35.1 1.0
O B:ARG320 5.0 12.7 1.0

Sodium binding site 5 out of 7 in 3g25

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Sodium binding site 5 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:22.4
occ:0.40
 O1 B:PO4504 1.5 41.1 0.6
NZ B:LYS171 2.6 23.1 1.0
P B:PO4504 2.9 35.3 0.6
NZ B:LYS175 3.3 13.8 0.5
O4 B:PO4504 3.4 37.6 0.6
CE B:LYS175 3.6 13.9 0.5
CE B:LYS171 3.6 16.2 1.0
O3 B:PO4504 3.8 39.5 0.6
CD B:LYS171 3.8 12.2 1.0
CE B:LYS175 3.8 14.5 0.5
O2 B:PO4504 3.9 34.2 0.6
CA B:GLY93 4.0 14.0 1.0
CZ3 B:TRP170 4.1 12.8 1.0
O B:THR92 4.4 13.1 1.0
O B:GLY93 4.6 12.7 1.0
CH2 B:TRP170 4.7 11.8 1.0
CG B:LYS175 4.7 13.4 0.5
C B:GLY93 4.7 14.5 1.0
CD B:LYS175 4.7 12.5 0.5
CG B:LYS175 4.8 13.5 0.5
NZ B:LYS175 4.8 13.5 0.5
N B:GLY93 4.9 14.2 1.0
CE3 B:TRP170 4.9 11.6 1.0
CD B:LYS175 4.9 12.5 0.5
C B:THR92 5.0 16.0 1.0

Sodium binding site 6 out of 7 in 3g25

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Sodium binding site 6 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na500

b:26.4
occ:0.50
 O2 D:PO4502 2.3 38.8 0.8
OG1 D:THR13 3.1 19.4 1.0
NH1 D:ARG16 3.2 58.1 1.0
NH2 D:ARG16 3.2 57.1 1.0
N D:THR13 3.4 17.1 1.0
P D:PO4502 3.4 40.0 0.8
N D:SER14 3.6 25.0 1.0
N D:THR12 3.6 21.1 1.0
CZ D:ARG16 3.6 54.8 1.0
O3 D:PO4502 3.6 36.5 0.8
CA D:GLY11 3.8 21.9 1.0
OG1 D:THR266 3.8 18.4 1.0
C D:GLY11 4.0 23.1 1.0
OG D:SER14 4.0 27.4 1.0
CA D:THR13 4.0 20.9 1.0
O D:SER14 4.0 22.7 1.0
CB D:THR13 4.0 21.5 1.0
O4 D:PO4502 4.0 27.0 0.8
C D:THR13 4.2 22.1 1.0
C D:THR12 4.4 18.5 1.0
CA D:THR12 4.4 19.3 1.0
CA D:SER14 4.5 25.9 1.0
CG2 D:THR13 4.5 24.2 1.0
O1 D:PO4502 4.6 42.5 0.8
C D:SER14 4.7 25.4 1.0
CB D:SER14 4.7 26.9 1.0
CB D:THR12 4.8 18.5 1.0
NE D:ARG16 4.9 48.6 1.0
O D:GLY11 4.9 22.8 1.0
N D:GLY11 4.9 24.3 1.0

Sodium binding site 7 out of 7 in 3g25

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Sodium binding site 7 out of 7 in the 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:35.1
occ:0.50
 O3 D:PO4504 2.6 37.1 0.8
O D:ARG320 2.7 19.7 0.5
O D:ARG320 2.9 20.1 0.5
NZ C:LYS372 3.1 19.2 1.0
O4 D:PO4504 3.4 45.5 0.8
CB D:ARG320 3.4 19.0 0.5
CB D:ARG320 3.6 17.9 0.5
P D:PO4504 3.6 40.8 0.8
O C:HOH619 3.8 23.8 1.0
C D:ARG320 3.8 20.4 0.5
C D:ARG320 3.9 20.8 0.5
O1 D:PO4504 4.2 40.8 0.8
CA D:ARG320 4.3 18.9 0.5
CA D:ARG320 4.3 18.1 0.5
CE C:LYS372 4.3 21.4 1.0
NE D:ARG320 4.4 7.2 0.5
CD C:LYS372 4.4 21.5 1.0
CD D:ARG320 4.5 18.1 0.5
CG D:ARG320 4.5 18.4 0.5
CG D:ARG320 4.8 15.3 0.5
O D:LEU319 4.8 17.9 1.0
O2 D:PO4504 4.9 35.4 0.8
CD D:ARG320 4.9 11.8 0.5
N D:MSE321 5.0 21.7 0.5

Reference:

G.Minasov, T.Skarina, O.Onopriyenko, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.9 Angstrom Crystal Structure of Glycerol Kinase (Glpk) From Staphylococcus Aureus in Complex with Glycerol. To Be Published.
Page generated: Mon Oct 7 09:53:19 2024

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