Atomistry » Sodium » PDB 5fje-5g3f » 5g0c
Atomistry »
  Sodium »
    PDB 5fje-5g3f »
      5g0c »

Sodium in PDB 5g0c: An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C

Enzymatic activity of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C

All present enzymatic activity of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C:
4.2.1.1;

Protein crystallography data

The structure of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C, PDB code: 5g0c was solved by P.Mujumdar, C.T.Supuran, T.S.Peat, S.A.Poulsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.50 / 1.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.885, 41.263, 71.681, 90.00, 104.19, 90.00
R / Rfree (%) 13 / 16.3

Other elements in 5g0c:

The structure of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C (pdb code 5g0c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C, PDB code: 5g0c:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5g0c

Go back to Sodium Binding Sites List in 5g0c
Sodium binding site 1 out of 3 in the An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1262

b:28.8
occ:0.70
O1 A:SO41266 2.1 30.2 0.5
OG1 A:THR91 2.9 11.2 1.0
O A:HOH2321 2.9 36.3 1.0
S A:SO41266 3.3 29.4 0.5
O A:HOH2320 3.4 39.2 1.0
O2 A:SO41266 3.4 34.9 0.5
CG2 A:THR91 3.6 9.6 1.0
CB A:ALA131 3.7 12.8 1.0
CB A:THR91 3.8 8.8 1.0
O3 A:SO41266 3.9 26.3 0.5
O A:HOH2133 4.1 14.1 1.0
O A:HOH2166 4.2 29.4 1.0
O4 A:SO41266 4.4 27.8 0.5
ND2 A:ASN69 4.6 12.6 1.0
OD2 A:ASP72 4.7 11.4 1.0
O A:HOH2143 5.0 18.6 1.0

Sodium binding site 2 out of 3 in 5g0c

Go back to Sodium Binding Sites List in 5g0c
Sodium binding site 2 out of 3 in the An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1263

b:27.8
occ:0.70
OE2 A:GLU214 2.2 12.1 0.5
O A:HOH2273 2.2 24.4 1.0
O A:HOH2217 2.6 30.3 1.0
O A:HOH2254 2.9 35.0 1.0
OE2 A:GLU214 3.1 14.0 0.5
N A:GLU187 3.1 9.4 1.0
CD A:GLU214 3.4 10.3 0.5
CG A:GLU187 3.5 13.8 1.0
CD A:GLU214 3.6 10.5 0.5
CA A:PRO186 3.7 9.3 1.0
C A:PRO186 3.8 9.3 1.0
CB A:GLU187 3.9 12.2 1.0
OE1 A:GLU214 3.9 10.5 0.5
CB A:PRO186 4.0 9.5 1.0
CA A:GLU187 4.0 10.2 1.0
O A:HOH2253 4.0 40.2 1.0
CD A:GLU187 4.1 16.5 1.0
OE1 A:GLU214 4.2 11.9 0.5
O A:HOH2274 4.3 23.7 1.0
OE2 A:GLU187 4.3 21.0 1.0
CG A:GLU214 4.3 9.2 0.5
CG A:GLU214 4.6 9.1 0.5
OE1 A:GLU187 4.8 18.3 1.0
O A:PRO215 4.9 9.1 1.0

Sodium binding site 3 out of 3 in 5g0c

Go back to Sodium Binding Sites List in 5g0c
Sodium binding site 3 out of 3 in the An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structure of Psammaplin C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1264

b:31.2
occ:0.70
O A:HOH2018 2.2 28.4 1.0
O A:HOH2323 2.6 0.1 1.0
O A:ASP243 2.8 8.8 1.0
O A:HOH2322 2.9 42.9 1.0
O A:HOH2303 3.0 29.8 1.0
O A:TYR7 3.3 14.8 1.0
CB A:ASP243 3.7 7.9 1.0
O A:HOH2301 3.9 18.9 1.0
C A:ASP243 3.9 7.8 1.0
CB A:TYR7 4.0 9.0 1.0
C A:TYR7 4.3 11.6 1.0
O A:HOH2009 4.4 30.8 1.0
CA A:ASP243 4.4 7.6 1.0
O A:TRP245 4.5 8.4 1.0
CD1 A:TYR7 4.6 8.2 1.0
CA A:TYR7 4.6 10.2 1.0
CG A:TYR7 4.7 8.8 1.0
CG A:ASP243 4.9 8.3 1.0

Reference:

P.Mujumdar, K.Teruya, K.F.Tonissen, D.Vullo, C.T.Supuran, T.S.Peat, S.Poulsen. An Unusual Natural Product Primary Sulfonamide: Synthesis, Carbonic Anhydrase Inhibition and Protein X-Ray Structures of Psammaplin C. J.Med.Chem. V. 59 5462 2016.
ISSN: ISSN 0022-2623
PubMed: 27172398
DOI: 10.1021/ACS.JMEDCHEM.6B00443
Page generated: Mon Oct 7 21:07:39 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy