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Sodium in PDB 7ov3: Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate

Enzymatic activity of Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate

All present enzymatic activity of Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate:
3.1.3.2;

Protein crystallography data

The structure of Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate, PDB code: 7ov3 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) 34.07 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.085, 71.325, 77.553, 90, 90, 90
R / Rfree (%) 16.5 / 23.2

Other elements in 7ov3:

The structure of Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate (pdb code 7ov3). 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 Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate, PDB code: 7ov3:

Sodium binding site 1 out of 1 in 7ov3

Go back to Sodium Binding Sites List in 7ov3
Sodium binding site 1 out of 1 in the Crystal Structure of Pig Purple Acid Phosphatase in Complex with Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate


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 Maybridge Fragment CC063346, Dimethyl Sulfoxide and Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na431

b:22.0
occ:0.82
 O A:GLY96 2.3 25.7 1.0
O7 A:CIT416 2.3 23.8 0.8
O A:HIS94 2.3 23.8 1.0
O5 A:CIT416 2.4 22.7 0.8
O A:HOH741 2.4 23.3 1.0
O5 A:CIT416 2.6 23.2 0.1
O1 A:CIT416 2.7 21.1 0.8
C2 A:CIT416 2.8 23.3 0.1
C4 A:CIT416 2.8 24.9 0.1
C6 A:CIT416 3.1 23.8 0.8
C3 A:CIT416 3.1 24.3 0.1
C3 A:CIT416 3.1 26.0 0.8
C6 A:CIT416 3.2 23.6 0.1
C A:HIS94 3.3 27.2 1.0
C A:GLY96 3.5 22.0 1.0
C1 A:CIT416 3.6 23.2 0.8
O A:HOH713 3.8 26.8 0.6
CA A:HIS94 3.8 21.5 1.0
C5 A:CIT416 3.8 26.2 0.1
C2 A:CIT416 3.9 21.5 0.8
O A:HOH590 4.0 29.7 0.7
O3 A:CIT416 4.1 26.9 0.1
C A:LEU95 4.2 25.2 1.0
C1 A:CIT416 4.2 22.9 0.1
N A:GLY96 4.2 27.4 1.0
O6 A:CIT416 4.2 22.7 0.8
O3 A:CIT416 4.3 27.1 0.8
N A:ASN97 4.4 24.5 1.0
N A:LEU95 4.4 23.2 1.0
O A:LEU95 4.4 25.7 1.0
CA A:GLY96 4.4 25.2 1.0
ND1 A:HIS94 4.4 21.9 1.0
N A:VAL98 4.4 21.8 1.0
CA A:ASN97 4.4 23.8 1.0
O6 A:CIT416 4.4 23.3 0.1
C4 A:CIT416 4.5 25.8 0.8
O7 A:CIT416 4.5 24.6 0.1
O A:HOH630 4.5 25.7 0.9
CB A:HIS94 4.5 18.7 1.0
O A:ASP93 4.6 22.9 1.0
O A:HOH794 4.6 42.9 0.9
CA A:LEU95 4.6 19.7 1.0
O1 A:CIT416 4.7 23.1 0.1
O2 A:CIT416 4.7 22.0 0.8
C5 A:CIT416 4.7 29.0 0.8
O4 A:CIT416 4.8 26.3 0.1
CG2 A:VAL98 4.8 17.9 1.0
CG A:HIS94 4.9 24.2 1.0
C A:ASN97 5.0 23.9 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: Tue Oct 8 18:23:38 2024

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