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Sodium in PDB 1xmn: Crystal Structure of Thrombin Bound to Heparin

Enzymatic activity of Crystal Structure of Thrombin Bound to Heparin

All present enzymatic activity of Crystal Structure of Thrombin Bound to Heparin:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Thrombin Bound to Heparin, PDB code: 1xmn was solved by W.J.Carter, E.Cama, J.A.Huntington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.60 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.907, 80.841, 114.144, 90.00, 101.05, 90.00
R / Rfree (%) 20.9 / 23.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Thrombin Bound to Heparin (pdb code 1xmn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Thrombin Bound to Heparin, PDB code: 1xmn:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1xmn

Go back to Sodium Binding Sites List in 1xmn
Sodium binding site 1 out of 4 in the Crystal Structure of Thrombin Bound to Heparin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Thrombin Bound to Heparin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3004

b:28.3
occ:1.00
 O B:ARG221A 2.5 20.3 1.0
O B:HOH3046 2.5 20.6 1.0
O B:LYS224 2.5 20.1 1.0
O B:HOH3043 2.6 18.7 1.0
O B:HOH3075 2.6 40.9 1.0
O B:HOH3047 2.8 27.0 1.0
C B:ARG221A 3.5 22.5 1.0
C B:LYS224 3.7 20.9 1.0
O B:HOH3020 3.9 20.8 1.0
N B:ARG221A 3.9 21.7 1.0
N B:LYS224 3.9 21.3 1.0
C B:ASP221 4.0 20.7 1.0
O B:TYR184A 4.0 22.4 1.0
O B:HOH3045 4.1 30.3 1.0
O B:HOH3009 4.1 17.4 1.0
CA B:LYS224 4.3 22.0 1.0
N B:ASP222 4.3 23.5 1.0
CA B:ASP221 4.3 19.9 1.0
CA B:ASP222 4.3 22.6 1.0
CA B:ARG221A 4.3 23.2 1.0
N B:GLY223 4.4 19.9 1.0
O B:HOH3076 4.4 31.5 1.0
O B:ASP221 4.5 19.9 1.0
OD1 B:ASP221 4.6 22.2 1.0
CB B:LYS224 4.6 23.0 1.0
C B:ASP222 4.6 21.8 1.0
N B:TYR225 4.7 20.6 1.0
CA B:TYR225 4.9 19.0 1.0

Sodium binding site 2 out of 4 in 1xmn

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Sodium binding site 2 out of 4 in the Crystal Structure of Thrombin Bound to Heparin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Thrombin Bound to Heparin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na3001

b:26.3
occ:1.00
 O D:ARG221A 2.5 21.2 1.0
O D:HOH3042 2.5 20.0 1.0
O D:LYS224 2.6 20.2 1.0
O D:HOH3043 2.6 23.1 1.0
O D:HOH3047 2.7 36.4 1.0
O D:HOH3041 2.8 23.4 1.0
C D:ARG221A 3.5 23.0 1.0
C D:LYS224 3.6 21.7 1.0
O D:HOH3044 3.8 26.6 1.0
N D:ARG221A 3.9 20.9 1.0
N D:LYS224 3.9 21.3 1.0
O D:HOH3045 4.0 27.6 1.0
O D:TYR184A 4.0 22.4 1.0
C D:ASP221 4.0 21.0 1.0
O D:HOH3005 4.2 17.1 1.0
CA D:LYS224 4.2 23.2 1.0
N D:ASP222 4.3 22.6 1.0
CA D:ASP221 4.3 20.2 1.0
CA D:ASP222 4.3 23.1 1.0
N D:GLY223 4.3 20.8 1.0
CA D:ARG221A 4.3 23.4 1.0
O D:ASP221 4.5 19.9 1.0
O D:HOH3046 4.5 30.9 1.0
CB D:LYS224 4.5 24.9 1.0
OD1 D:ASP221 4.6 22.6 1.0
C D:ASP222 4.6 21.6 1.0
N D:TYR225 4.7 21.4 1.0
CA D:TYR225 4.9 20.3 1.0
CD2 D:TYR225 5.0 21.5 1.0
C D:GLY223 5.0 21.2 1.0

Sodium binding site 3 out of 4 in 1xmn

Go back to Sodium Binding Sites List in 1xmn
Sodium binding site 3 out of 4 in the Crystal Structure of Thrombin Bound to Heparin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Thrombin Bound to Heparin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na3002

b:37.5
occ:1.00
 O F:HOH3040 2.6 35.4 1.0
O F:ARG221A 2.6 34.9 1.0
O F:LYS224 2.7 28.5 1.0
O F:HOH3046 2.7 40.3 1.0
O F:HOH3027 2.8 29.1 1.0
O F:HOH3018 2.8 32.1 1.0
C F:ARG221A 3.4 34.7 1.0
O F:HOH3041 3.7 41.7 1.0
C F:LYS224 3.8 29.7 1.0
N F:ARG221A 3.9 33.0 1.0
O F:HOH3039 4.0 31.4 1.0
O F:TYR184A 4.0 32.5 1.0
C F:ASP221 4.0 32.6 1.0
N F:LYS224 4.1 31.5 1.0
N F:ASP222 4.1 35.6 1.0
CA F:ASP222 4.1 36.6 1.0
O F:HOH3014 4.2 26.2 1.0
N F:GLY223 4.3 34.6 1.0
CA F:ASP221 4.3 31.2 1.0
CA F:ARG221A 4.3 35.0 1.0
CA F:LYS224 4.4 31.4 1.0
OD1 F:ASP221 4.5 31.5 1.0
C F:ASP222 4.5 36.3 1.0
O F:ASP221 4.5 31.7 1.0
CB F:LYS224 4.8 31.5 1.0
N F:TYR225 4.8 29.2 1.0
O F:HOH3071 4.9 30.3 1.0

Sodium binding site 4 out of 4 in 1xmn

Go back to Sodium Binding Sites List in 1xmn
Sodium binding site 4 out of 4 in the Crystal Structure of Thrombin Bound to Heparin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Thrombin Bound to Heparin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na3003

b:30.9
occ:1.00
 O H:ARG221A 2.6 31.9 1.0
O H:LYS224 2.6 28.7 1.0
O H:HOH3060 2.7 33.2 1.0
O H:HOH3027 2.7 35.2 1.0
O H:HOH3055 2.7 37.3 1.0
O H:HOH3028 2.8 26.5 1.0
C H:ARG221A 3.4 32.4 1.0
C H:LYS224 3.7 27.5 1.0
O H:HOH3029 3.8 31.5 1.0
N H:ARG221A 3.9 28.9 1.0
O H:HOH3054 4.0 26.1 1.0
N H:LYS224 4.0 28.9 1.0
O H:TYR184A 4.0 28.1 1.0
C H:ASP221 4.1 29.0 1.0
N H:ASP222 4.1 33.6 1.0
CA H:ASP222 4.1 34.4 1.0
O H:HOH3013 4.1 21.9 1.0
N H:GLY223 4.2 32.7 1.0
CA H:ARG221A 4.3 31.9 1.0
CA H:LYS224 4.3 29.1 1.0
CA H:ASP221 4.4 28.0 1.0
C H:ASP222 4.4 33.5 1.0
O H:ASP221 4.5 28.4 1.0
OD1 H:ASP221 4.6 29.9 1.0
N H:TYR225 4.7 27.0 1.0
CB H:LYS224 4.7 28.7 1.0
O H:HOH3056 4.9 29.5 1.0
C H:GLY223 4.9 30.8 1.0
CA H:TYR225 4.9 26.0 1.0

Reference:

W.J.Carter, E.Cama, J.A.Huntington. Crystal Structure of Thrombin Bound to Heparin J.Biol.Chem. V. 280 2745 2005.
ISSN: ISSN 0021-9258
PubMed: 15548541
DOI: 10.1074/JBC.M411606200
Page generated: Mon Oct 7 00:33:01 2024

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