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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

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