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Sodium in PDB 7ov8: Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol

Enzymatic activity of Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol

All present enzymatic activity of Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol, PDB code: 7ov8 was solved by D.Feder, R.P.Mcgeary, L.W.Guddat, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.57 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.382, 69.772, 75.309, 90, 90, 90
R / Rfree (%) 16.2 / 25.6

Other elements in 7ov8:

The structure of Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol (pdb code 7ov8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol, PDB code: 7ov8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7ov8

Go back to Sodium Binding Sites List in 7ov8
Sodium binding site 1 out of 2 in the Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na731

b:22.0
occ:1.00
 O A:TRP111 2.5 19.0 1.0
O A:SER105 2.5 24.1 1.0
O A:SER108 2.8 29.7 1.0
O A:LYS109 2.8 33.1 1.0
O A:HOH1073 2.9 31.9 1.0
O A:HOH1095 3.1 49.4 1.0
O A:HOH1127 3.5 43.1 1.0
C A:TRP111 3.5 27.3 1.0
OD1 A:ASN112 3.5 36.9 1.0
C A:LYS109 3.5 31.2 1.0
C A:SER105 3.6 27.4 1.0
C A:SER108 3.9 28.3 1.0
CA A:LYS109 3.9 36.0 1.0
N A:TRP111 3.9 28.6 1.0
CA A:SER105 4.0 24.7 1.0
CG A:ASN112 4.2 23.3 1.0
CA A:TRP111 4.3 24.9 1.0
N A:ASN112 4.3 17.4 1.0
N A:LYS109 4.4 28.6 1.0
CB A:SER105 4.5 26.6 1.0
N A:ARG110 4.5 26.8 1.0
CA A:ASN112 4.5 19.3 1.0
C A:ARG110 4.6 23.6 1.0
ND2 A:ASN112 4.8 27.9 1.0
N A:LYS106 4.8 31.0 1.0
CB A:TRP111 4.8 20.3 1.0
O A:HOH1052 4.9 27.6 1.0
CB A:ASN112 4.9 23.5 1.0

Sodium binding site 2 out of 2 in 7ov8

Go back to Sodium Binding Sites List in 7ov8
Sodium binding site 2 out of 2 in the Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Pig Purple Acid Phosphatase in Complex with 4-(2- Hydroxyethyl)-1-Piperazineethanesulfonic Acid (Hepes) and Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na732

b:32.7
occ:0.86
 O1S A:EPE702 2.1 62.3 0.7
S A:EPE702 3.4 77.5 0.7
C3 A:GOL722 3.5 49.8 0.8
O3S A:EPE702 3.6 62.1 0.7
C1 A:GOL722 4.1 58.6 0.8
C2 A:GOL722 4.3 48.3 0.8
O2S A:EPE702 4.4 68.5 0.7
C10 A:EPE702 4.5 61.6 0.7
O3 A:GOL722 4.5 42.1 0.8
O1S A:EPE702 4.7 50.9 0.3
O A:HOH831 4.8 40.2 1.0

Reference:

D.Feder, S.H.Mohd-Pahmi, W.M.Hussein, L.W.Guddat, R.P.Mcgeary, G.Schenk. Rational Design of Potent Inhibitors of A Metallohydrolase Using A Fragment-Based Approach. Chemmedchem V. 16 3342 2021.
ISSN: ESSN 1860-7187
PubMed: 34331400
DOI: 10.1002/CMDC.202100486
Page generated: Fri Apr 7 15:28:24 2023

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