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Sodium in PDB 9fdn: Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal

Enzymatic activity of Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal

All present enzymatic activity of Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal:
2.7.2.3;

Protein crystallography data

The structure of Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal, PDB code: 9fdn was solved by M.J.Cliff, J.P.Waltho, M.W.Bowler, N.J.Baxter, C.Bisson, G.M.Blackburn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.10 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.04, 91.1, 108.2, 90, 90, 90
R / Rfree (%) 17.9 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal (pdb code 9fdn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal, PDB code: 9fdn:

Sodium binding site 1 out of 1 in 9fdn

Go back to Sodium Binding Sites List in 9fdn
Sodium binding site 1 out of 1 in the Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Phosphoglycerate Kinase in Complex with Atp and 3PG Formed By Cross-Soaking A Tsa Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:24.2
occ:1.00
 O1B A:ATP502 2.2 21.5 1.0
O A:HOH827 2.3 26.2 1.0
O1A A:ATP502 2.3 20.7 1.0
O A:HOH909 2.3 31.2 1.0
OD2 A:ASP374 2.4 24.5 1.0
O2G A:ATP502 3.1 21.9 1.0
H5'2 A:ATP502 3.3 24.3 1.0
HE3 A:LYS215 3.3 21.9 1.0
PB A:ATP502 3.4 18.8 1.0
CG A:ASP374 3.4 23.1 1.0
HZ2 A:LYS215 3.5 22.9 1.0
PA A:ATP502 3.5 18.3 1.0
H A:ASP374 3.5 21.9 1.0
O3A A:ATP502 3.7 17.2 1.0
HZ1 A:LYS215 3.8 22.9 1.0
HB2 A:ASP374 3.8 23.5 1.0
O A:HOH785 3.8 22.1 1.0
O A:HOH677 3.9 28.2 1.0
O A:HOH851 3.9 29.0 1.0
NZ A:LYS215 3.9 19.1 1.0
O3B A:ATP502 4.0 21.0 1.0
O A:HOH749 4.0 28.9 1.0
CE A:LYS215 4.0 18.2 1.0
CB A:ASP374 4.1 19.6 1.0
PG A:ATP502 4.2 23.4 1.0
N A:ASP374 4.2 18.3 1.0
C5' A:ATP502 4.2 20.2 1.0
OD1 A:ASP374 4.3 23.1 1.0
HA3 A:GLY373 4.3 20.9 1.0
O5' A:ATP502 4.4 18.7 1.0
HD2 A:LYS215 4.4 21.8 1.0
H A:GLY373 4.6 20.1 1.0
O1 A:3PG503 4.6 18.5 1.0
O2B A:ATP502 4.7 19.8 1.0
O2A A:ATP502 4.7 21.4 1.0
H4' A:ATP502 4.7 22.7 1.0
HE2 A:LYS215 4.8 21.9 1.0
HZ3 A:LYS215 4.8 22.9 1.0
O A:HOH825 4.8 21.1 1.0
CA A:ASP374 4.8 20.1 1.0
CD A:LYS215 4.8 18.2 1.0
O3G A:ATP502 4.8 20.2 1.0
H5'1 A:ATP502 4.9 24.3 1.0
CA A:GLY373 4.9 17.5 1.0
HG3 A:LYS215 4.9 20.0 1.0
HB3 A:ASP374 4.9 23.5 1.0
C A:GLY373 4.9 20.4 1.0
O A:HOH967 5.0 29.4 1.0
N A:GLY373 5.0 16.8 1.0

Reference:

M.J.Cliff, Z.Serimbetov, C.Bisson, N.J.Baxter, G.M.Blackburn, S.Hay, M.W.Bowler, J.P.Waltho. The Role of Magnesium in Catalysis By Phosphoglycerate Kinase To Be Published.
Page generated: Mon Aug 18 16:57:29 2025

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