Atomistry » Sodium » PDB 3fvs-3gdg » 3g25
Atomistry »
  Sodium »
    PDB 3fvs-3gdg »
      3g25 »

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

Go back to Sodium Binding Sites List in 3g25
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

Go back to Sodium Binding Sites List in 3g25
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

Go back to Sodium Binding Sites List in 3g25
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

Go back to Sodium Binding Sites List in 3g25
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

Go back to Sodium Binding Sites List in 3g25
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

Go back to Sodium Binding Sites List in 3g25
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

Go back to Sodium Binding Sites List in 3g25
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

Last articles

Ba in 7ZG5
Ba in 7RJT
Ba in 7RK6
Ba in 7T6Y
Ba in 7ECM
Ba in 7KI3
Ba in 7ECF
Ba in 7OTB
Ba in 7MJT
Ba in 7MHX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy