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Sodium in PDB 6sb7: Human Carbonic Anhydrase II in Complex with Fragment.

Enzymatic activity of Human Carbonic Anhydrase II in Complex with Fragment.

All present enzymatic activity of Human Carbonic Anhydrase II in Complex with Fragment.:
4.2.1.1;

Protein crystallography data

The structure of Human Carbonic Anhydrase II in Complex with Fragment., PDB code: 6sb7 was solved by S.Gloeckner, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.83 / 1.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.497, 41.657, 72.496, 90.00, 104.33, 90.00
R / Rfree (%) 11.8 / 13.7

Other elements in 6sb7:

The structure of Human Carbonic Anhydrase II in Complex with Fragment. also contains other interesting chemical elements:

Mercury (Hg) 4 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Carbonic Anhydrase II in Complex with Fragment. (pdb code 6sb7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Carbonic Anhydrase II in Complex with Fragment., PDB code: 6sb7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6sb7

Go back to Sodium Binding Sites List in 6sb7
Sodium binding site 1 out of 2 in the Human Carbonic Anhydrase II in Complex with Fragment.


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 Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:18.1
occ:0.54
O A:HOH542 2.2 29.1 1.0
OG A:SER73 2.3 17.5 1.0
O A:HOH476 2.4 31.6 1.0
O A:HOH527 2.5 15.8 1.0
HB2 A:SER73 3.0 20.0 1.0
CB A:SER73 3.2 16.6 1.0
HG3 A:GLN74 3.5 24.8 1.0
HB3 A:SER73 3.6 20.0 1.0
O A:SER73 4.3 16.6 1.0
OE1 A:GLN74 4.3 23.2 1.0
CA A:SER73 4.4 15.3 1.0
C A:SER73 4.4 15.9 1.0
CG A:GLN74 4.4 20.6 1.0
OD1 A:ASP71 4.5 14.9 1.0
OD2 A:ASP71 4.6 15.4 1.0
CD A:GLN74 4.7 22.2 1.0
HG2 A:GLN74 4.8 24.8 1.0
H A:SER73 4.9 16.6 1.0

Sodium binding site 2 out of 2 in 6sb7

Go back to Sodium Binding Sites List in 6sb7
Sodium binding site 2 out of 2 in the Human Carbonic Anhydrase II in Complex with Fragment.


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 Fragment. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:30.0
occ:0.59
O A:THR37 2.2 13.6 0.4
O A:HOH540 2.5 32.8 1.0
O A:THR37 2.6 12.8 0.6
O A:HOH498 2.8 16.9 1.0
HG22 A:THR37 2.9 19.4 0.6
HA A:ALA38 3.4 12.7 0.4
C A:THR37 3.4 12.8 0.4
HG23 A:THR37 3.7 19.4 0.6
HB2 A:LYS39 3.7 18.9 0.6
HA A:ALA38 3.7 12.6 0.6
C A:THR37 3.7 12.3 0.6
CG2 A:THR37 3.8 16.1 0.6
HB2 A:LYS39 3.8 13.2 0.4
O A:HOH465 3.9 25.7 1.0
H A:LYS39 3.9 15.1 0.6
HA A:GLN255 4.0 17.1 1.0
CA A:ALA38 4.0 10.6 0.4
H A:ILE256 4.0 11.8 1.0
HB A:THR37 4.0 18.4 0.4
N A:ALA38 4.1 11.6 0.4
H A:LYS39 4.1 12.3 0.4
O A:ILE256 4.2 9.8 1.0
C A:ALA38 4.2 10.0 0.4
N A:LYS39 4.2 10.2 0.4
CB A:GLN255 4.3 16.2 1.0
N A:LYS39 4.3 12.5 0.6
HG21 A:THR37 4.3 19.4 0.6
HB3 A:LYS39 4.3 18.9 0.6
CA A:ALA38 4.4 10.5 0.6
CB A:LYS39 4.4 15.8 0.6
CA A:THR37 4.5 13.9 0.4
HA A:THR37 4.5 16.7 0.4
N A:ALA38 4.5 11.0 0.6
CB A:LYS39 4.6 11.0 0.4
CA A:GLN255 4.6 14.3 1.0
N A:ILE256 4.6 9.8 1.0
HB3 A:LYS39 4.6 13.2 0.4
C A:ALA38 4.6 12.1 0.6
CB A:THR37 4.7 15.3 0.4
CA A:THR37 4.7 13.5 0.6
HA A:THR37 4.7 16.1 0.6
CB A:THR37 4.8 15.6 0.6
O A:ALA38 4.8 9.9 0.4
HG1 A:THR37 4.9 19.0 0.4
H A:ALA38 4.9 13.9 0.4
HB A:THR37 5.0 18.6 0.6
CA A:LYS39 5.0 13.3 0.6

Reference:

S.Glockner, A.Heine, G.Klebe. A Proof-of-Concept Fragment Screening of A Hit-Validated 96-Compounds Library Against Human Carbonic Anhydrase II. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 32235320
DOI: 10.3390/BIOM10040518
Page generated: Tue Dec 15 12:58:24 2020

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