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Sodium in PDB 7agn: Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide

Enzymatic activity of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide

All present enzymatic activity of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide:
4.2.1.1;

Protein crystallography data

The structure of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide, PDB code: 7agn was solved by V.Paketuryte, A.Smirnov, E.Manakova, S.Grazulis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.65 / 1.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.888, 41.141, 84.258, 90, 109.51, 90
R / Rfree (%) 14.7 / 18.6

Other elements in 7agn:

The structure of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide (pdb code 7agn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide, PDB code: 7agn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7agn

Go back to Sodium Binding Sites List in 7agn
Sodium binding site 1 out of 4 in the Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:34.9
occ:1.00
 O A:HOH610 2.4 35.6 1.0
OG A:SER48 2.7 19.9 1.0
CB A:SER48 3.5 18.5 1.0
O A:HOH548 3.7 33.1 1.0
CA A:SER48 3.7 14.9 1.0
OG A:SER50 3.9 27.9 1.0
N A:VAL49 4.2 14.3 1.0
C A:SER48 4.2 13.4 1.0
O A:HOH469 4.5 20.3 1.0
O A:VAL49 4.5 23.1 1.0
C A:VAL49 4.8 17.6 1.0

Sodium binding site 2 out of 4 in 7agn

Go back to Sodium Binding Sites List in 7agn
Sodium binding site 2 out of 4 in the Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:33.0
occ:1.00
 O A:HOH546 2.4 26.7 1.0
OG B:SER48 2.7 19.4 1.0
CG A:PRO21 3.1 22.0 0.5
CB B:SER48 3.5 17.1 1.0
O B:HOH654 3.7 43.1 1.0
CA B:SER48 3.7 15.0 1.0
CG A:PRO21 3.8 17.9 0.5
CD A:PRO21 3.8 16.4 0.5
OG B:SER50 3.8 24.1 1.0
CD A:PRO21 3.9 16.2 0.5
O B:HOH559 4.0 23.5 1.0
O A:LYS18 4.1 22.7 1.0
O A:HOH651 4.2 33.7 1.0
N B:VAL49 4.3 15.7 1.0
C B:SER48 4.3 14.0 1.0
CB A:PRO21 4.5 20.3 0.5
CB A:PRO21 4.5 17.8 0.5
O B:HOH427 4.6 19.0 1.0
O B:VAL49 4.6 23.8 1.0
C B:VAL49 4.9 17.0 1.0

Sodium binding site 3 out of 4 in 7agn

Go back to Sodium Binding Sites List in 7agn
Sodium binding site 3 out of 4 in the Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:37.5
occ:1.00
 O B:HOH704 1.8 33.1 1.0
O B:HIS17 2.7 13.5 1.0
O B:HOH498 2.8 19.0 1.0
C B:HIS17 3.6 12.3 1.0
O B:LYS18 3.7 20.6 1.0
CB B:PRO21 3.7 16.1 1.0
CA B:LYS18 3.8 13.1 1.0
C B:LYS18 4.0 14.9 1.0
CA B:PRO21 4.1 12.7 1.0
CG B:PRO21 4.1 22.1 1.0
ND1 B:HIS17 4.1 17.6 1.0
N B:LYS18 4.1 13.1 1.0
CD B:PRO21 4.2 14.9 1.0
O B:HOH736 4.3 36.3 1.0
O B:HOH586 4.4 27.6 1.0
N B:PRO21 4.4 13.0 1.0
CA B:HIS17 4.8 10.8 1.0
CB B:HIS17 4.9 13.3 1.0
CG B:HIS17 4.9 14.0 1.0
CE1 B:HIS17 4.9 18.9 1.0

Sodium binding site 4 out of 4 in 7agn

Go back to Sodium Binding Sites List in 7agn
Sodium binding site 4 out of 4 in the Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Carbonic Anhydrase II in Complex with 4-(2-Aminoethylsulfanyl)- 2,3,5,6-Tetrafluoro-N-Methyl-Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:42.1
occ:1.00
 O D:HOH409 2.4 32.4 1.0
O D:THR35 3.0 17.1 1.0
O D:HOH705 3.1 44.4 1.0
O D:HOH625 3.5 29.7 1.0
CA D:HIS36 3.9 11.9 0.5
O D:HOH587 3.9 17.7 1.0
O D:HIS36 4.0 13.1 0.5
C D:THR35 4.0 13.5 1.0
C D:HIS36 4.2 11.4 0.5
CA D:HIS36 4.3 15.5 0.5
O D:ALA38 4.3 25.4 1.0
N D:HIS36 4.4 12.8 0.5
ND1 D:HIS36 4.5 15.3 0.5
N D:HIS36 4.6 15.2 0.5
C D:HIS36 4.9 19.6 0.5
CB D:HIS36 5.0 14.6 0.5
O D:HOH672 5.0 32.4 1.0

Reference:

D.Baronas, V.Dudutiene, V.Paketuryte, V.Kairys, A.Smirnov, V.Juozapaitiene, A.Vaskevicius, E.Manakova, S.Grazulis, A.Zubriene, D.Matulis. Structure and Mechanism of Secondary Sulfonamide Binding to Carbonic Anhydrases. Eur.Biophys.J. 2021.
ISSN: ISSN 0175-7571
PubMed: 34328515
DOI: 10.1007/S00249-021-01561-1
Page generated: Tue Oct 8 15:54:45 2024

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