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
|