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Sodium in PDB 2pw8: Crystal Structure of Sulfo-Hirudin Complexed to Thrombin

Protein crystallography data

The structure of Crystal Structure of Sulfo-Hirudin Complexed to Thrombin, PDB code: 2pw8 was solved by C.C.Liu, E.Brustad, W.Liu, P.G.Schultz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.95 / 1.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 54.074, 103.567, 139.184, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.3

Other elements in 2pw8:

The structure of Crystal Structure of Sulfo-Hirudin Complexed to Thrombin also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Sulfo-Hirudin Complexed to Thrombin (pdb code 2pw8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Sulfo-Hirudin Complexed to Thrombin, PDB code: 2pw8:

Sodium binding site 1 out of 1 in 2pw8

Go back to Sodium Binding Sites List in 2pw8
Sodium binding site 1 out of 1 in the Crystal Structure of Sulfo-Hirudin Complexed to Thrombin


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 Sulfo-Hirudin Complexed to Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:42.8
occ:1.00
O H:LYS224 2.4 34.1 1.0
O H:HOH412 2.4 43.2 1.0
O H:ARG221A 2.4 38.5 1.0
O H:HOH377 2.4 39.5 1.0
O H:HOH337 2.6 38.5 1.0
O H:HOH317 2.8 37.8 1.0
C H:ARG221A 3.4 37.7 1.0
O H:HOH410 3.4 46.6 1.0
C H:LYS224 3.5 33.9 1.0
N H:ARG221A 3.8 35.9 1.0
C H:ASP221 3.9 35.8 1.0
O H:HOH363 4.0 37.9 1.0
N H:LYS224 4.0 35.6 1.0
O H:HOH430 4.0 91.7 1.0
O H:HOH325 4.1 35.0 1.0
CA H:ASP221 4.2 34.5 1.0
CA H:LYS224 4.2 34.2 1.0
N H:ASP222 4.2 39.2 1.0
CA H:ARG221A 4.3 36.7 1.0
O H:TYR184A 4.3 38.0 1.0
CA H:ASP222 4.4 40.1 1.0
O H:ASP221 4.5 36.8 1.0
N H:GLY223 4.5 39.1 1.0
CB H:LYS224 4.5 34.1 1.0
N H:TYR225 4.5 32.2 1.0
OD1 H:ASP221 4.5 37.0 1.0
C H:ASP222 4.7 40.0 1.0
CA H:TYR225 4.8 32.3 1.0
N H:ASP221 4.9 34.1 1.0

Reference:

C.C.Liu, E.Brustad, W.Liu, P.G.Schultz. Crystal Structure of A Biosynthetic Sulfo-Hirudin Complexed to Thrombin. J.Am.Chem.Soc. V. 129 10648 2007.
ISSN: ISSN 0002-7863
PubMed: 17685615
DOI: 10.1021/JA0735002
Page generated: Tue Dec 15 05:54:15 2020

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