Sodium in PDB 6t3m: Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative

Enzymatic activity of Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative:
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative, PDB code: 6t3m was solved by K.Ngo, C.Collins, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.74 / 1.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.301, 71.476, 72.573, 90.00, 100.62, 90.00
R / Rfree (%) 13.3 / 15.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative (pdb code 6t3m). 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 A D-Phe-Pro-P-Phenol Derivative, PDB code: 6t3m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6t3m

Go back to Sodium Binding Sites List in 6t3m
Sodium binding site 1 out of 2 in the Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative


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 A D-Phe-Pro-P-Phenol Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na305

b:13.3
occ:1.00
O H:THR172 2.3 13.6 1.0
O H:LYS169 2.3 13.5 1.0
O H:HOH579 2.4 29.8 1.0
O H:HOH583 2.4 16.5 1.0
O H:HOH480 2.8 20.7 1.0
HA H:ASP170 3.3 15.6 1.0
HG2 H:LYS169 3.4 22.4 1.0
C H:LYS169 3.5 12.7 1.0
H H:THR172 3.5 15.3 1.0
C H:THR172 3.5 13.5 1.0
HA H:ARG173 3.6 16.2 1.0
CA H:ASP170 4.0 13.0 1.0
N H:ASP170 4.1 12.5 1.0
N H:THR172 4.2 12.7 1.0
CG H:LYS169 4.3 18.6 1.0
HG3 H:LYS169 4.3 22.4 1.0
HG23 H:THR172 4.4 15.9 1.0
C H:ASP170 4.4 12.9 1.0
N H:ARG173 4.4 13.1 1.0
CA H:ARG173 4.4 13.5 1.0
O H:HOH463 4.4 34.0 1.0
HA H:LYS169 4.5 14.5 1.0
CA H:THR172 4.5 13.2 1.0
CA H:LYS169 4.5 12.1 1.0
HG22 H:THR172 4.6 15.9 1.0
O H:ASP170 4.7 13.7 1.0
OD1 H:ASP170 4.7 17.8 1.0
HE2 H:LYS169 4.8 32.4 1.0
N H:SER171 4.8 12.5 1.0
CG2 H:THR172 4.9 13.3 1.0
H H:SER171 4.9 15.0 1.0
HE3 H:LYS169 4.9 32.4 1.0
CB H:LYS169 4.9 14.7 1.0
H H:ASP170 5.0 15.0 1.0

Sodium binding site 2 out of 2 in 6t3m

Go back to Sodium Binding Sites List in 6t3m
Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative


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 A D-Phe-Pro-P-Phenol Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na306

b:16.9
occ:1.00
O H:HOH561 2.3 19.2 1.0
O H:ARG221A 2.3 18.0 1.0
O H:HOH488 2.4 16.4 1.0
O H:LYS224 2.4 13.9 1.0
O H:HOH489 2.5 14.7 1.0
O H:HOH497 2.7 20.1 1.0
H H:LYS224 3.2 20.0 1.0
C H:ARG221A 3.4 18.9 1.0
C H:LYS224 3.4 13.9 1.0
HA H:ASP221 3.6 21.6 1.0
HB2 H:LYS224 3.8 19.6 1.0
HA H:ASP222 3.8 25.0 1.0
O H:HOH522 3.8 17.1 1.0
N H:LYS224 3.9 16.6 1.0
N H:ARG221A 3.9 17.8 1.0
H H:ARG221A 4.0 21.4 1.0
H H:GLY223 4.0 24.1 1.0
HA H:TYR225 4.0 14.4 1.0
O H:HOH471 4.0 21.9 1.0
C H:ASP221 4.1 18.3 1.0
CA H:LYS224 4.1 15.5 1.0
O H:TYR184A 4.2 16.3 1.0
N H:ASP222 4.2 20.3 1.0
O H:HOH470 4.2 15.8 1.0
CA H:ARG221A 4.3 18.7 1.0
N H:GLY223 4.3 20.1 1.0
CA H:ASP221 4.3 18.0 1.0
CA H:ASP222 4.4 20.8 1.0
N H:TYR225 4.4 12.9 1.0
CB H:LYS224 4.5 16.3 1.0
C H:ASP222 4.6 21.2 1.0
O H:ASP221 4.6 20.5 1.0
OD1 H:ASP221 4.6 18.8 1.0
CA H:TYR225 4.7 12.0 1.0
HB2 H:ARG221A 4.8 23.0 1.0
C H:GLY223 4.9 17.5 1.0
H H:ASP221 4.9 20.6 1.0
O H:HOH518 4.9 19.5 1.0
HB3 H:LYS224 4.9 19.6 1.0
HA3 H:GLY184 5.0 14.7 1.0
HB2 H:ASP189 5.0 16.9 1.0
HA H:ARG221A 5.0 22.4 1.0

Reference:

K.Ngo, C.Collins, A.Heine, G.Klebe. Thrombin in Complex with A D-Phe-Pro-P-Phenol Derivative To Be Published.
Page generated: Tue Dec 15 13:01:23 2020

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