Sodium in PDB 6y02: Thrombin in Complex with 13K

Enzymatic activity of Thrombin in Complex with 13K

All present enzymatic activity of Thrombin in Complex with 13K:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with 13K, PDB code: 6y02 was solved by A.Sandner, A.Heine, G.Klebe, N.Abazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.131, 71.404, 72.892, 90, 100.51, 90
R / Rfree (%) 13.9 / 16.4

Other elements in 6y02:

The structure of Thrombin in Complex with 13K also contains other interesting chemical elements:

Bromine (Br) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with 13K (pdb code 6y02). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with 13K, PDB code: 6y02:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6y02

Go back to Sodium Binding Sites List in 6y02
Sodium binding site 1 out of 2 in the Thrombin in Complex with 13K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with 13K within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:16.9
occ:1.00
O H:THR172 2.3 16.0 1.0
O H:LYS169 2.4 16.7 0.4
O H:LYS169 2.4 17.6 0.6
O H:HOH469 2.9 25.8 1.0
HA H:ASP170 3.3 19.6 1.0
HG2 H:LYS169 3.5 27.9 0.6
C H:LYS169 3.5 16.3 0.4
C H:LYS169 3.5 16.9 0.6
HG2 H:LYS169 3.5 25.0 0.4
H H:THR172 3.5 18.5 1.0
C H:THR172 3.6 15.8 1.0
HA H:ARG173 3.6 19.7 1.0
HZ3 H:LYS169 3.8 31.2 0.4
CA H:ASP170 4.0 16.4 1.0
N H:ASP170 4.2 15.6 1.0
HG3 H:LYS169 4.2 27.9 0.6
N H:THR172 4.3 15.4 1.0
CG H:LYS169 4.3 23.2 0.6
CG H:LYS169 4.3 20.8 0.4
C H:ASP170 4.4 16.7 1.0
HG23 H:THR172 4.4 21.2 1.0
HG3 H:LYS169 4.4 25.0 0.4
CA H:ARG173 4.4 16.4 1.0
N H:ARG173 4.4 16.5 1.0
HA H:LYS169 4.5 20.5 0.6
HA H:LYS169 4.5 19.7 0.4
CA H:THR172 4.5 15.9 1.0
CA H:LYS169 4.6 17.1 0.6
CA H:LYS169 4.6 16.4 0.4
NZ H:LYS169 4.6 26.0 0.4
HZ2 H:LYS169 4.7 31.2 0.4
HG22 H:THR172 4.7 21.2 1.0
O H:ASP170 4.7 17.9 1.0
OD1 H:ASP170 4.8 24.6 1.0
N H:SER171 4.8 16.8 1.0
HE2 H:LYS169 4.9 34.1 0.6
H H:SER171 4.9 20.2 1.0
CG2 H:THR172 5.0 17.7 1.0
CB H:LYS169 5.0 19.4 0.6
CB H:LYS169 5.0 18.0 0.4

Sodium binding site 2 out of 2 in 6y02

Go back to Sodium Binding Sites List in 6y02
Sodium binding site 2 out of 2 in the Thrombin in Complex with 13K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with 13K within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:22.4
occ:1.00
O H:ARG221A 2.3 23.7 1.0
O H:HOH474 2.3 23.3 1.0
O H:HOH547 2.3 26.6 1.0
O H:LYS224 2.4 19.4 1.0
O H:HOH484 2.4 20.6 1.0
O H:HOH490 2.8 26.4 1.0
H H:LYS224 3.3 23.1 1.0
C H:ARG221A 3.4 23.7 1.0
C H:LYS224 3.5 18.7 1.0
HA H:ASP221 3.6 29.7 1.0
HA H:ASP222 3.8 30.4 1.0
O H:HOH495 3.8 24.1 1.0
H H:ARG221A 3.8 28.7 1.0
N H:ARG221A 3.8 23.9 1.0
HB2 H:LYS224 3.9 24.1 1.0
N H:LYS224 3.9 19.3 1.0
H H:GLY223 4.0 28.0 1.0
HA H:TYR225 4.0 18.6 1.0
O H:HOH437 4.1 26.1 1.0
C H:ASP221 4.1 25.0 1.0
CA H:LYS224 4.2 18.4 1.0
O H:TYR184A 4.2 19.8 1.0
O H:HOH476 4.2 19.7 1.0
CA H:ARG221A 4.2 24.6 1.0
N H:ASP222 4.3 24.9 1.0
N H:GLY223 4.3 23.3 1.0
CA H:ASP221 4.3 24.7 1.0
CA H:ASP222 4.3 25.4 1.0
N H:TYR225 4.5 16.8 1.0
CB H:LYS224 4.5 20.1 1.0
C H:ASP222 4.6 23.9 1.0
OD1 H:ASP221 4.6 24.1 1.0
O H:ASP221 4.7 27.4 1.0
CA H:TYR225 4.8 15.5 1.0
HB2 H:ARG221A 4.8 31.8 1.0
H H:ASP221 4.8 28.2 1.0
C H:GLY223 4.9 19.9 1.0
O H:HOH499 4.9 26.1 1.0
HA3 H:GLY184 5.0 18.4 1.0
HA H:ARG221A 5.0 29.5 1.0
HB3 H:LYS224 5.0 24.1 1.0
HB2 H:ASP189 5.0 23.9 1.0

Reference:

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with 13K To Be Published.
Page generated: Wed Mar 3 15:29:23 2021

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