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: Tue Dec 15 06:11:23 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