Atomistry » Sodium » PDB 2uzz-2vrp » 2vrp
Atomistry »
  Sodium »
    PDB 2uzz-2vrp »
      2vrp »

Sodium in PDB 2vrp: Structure of Rhodocytin

Protein crystallography data

The structure of Structure of Rhodocytin, PDB code: 2vrp was solved by A.A.Watson, C.A.O'callaghan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.76 / 2.41
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 61.933, 89.368, 120.996, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.2

Other elements in 2vrp:

The structure of Structure of Rhodocytin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 2vrp

Go back to Sodium Binding Sites List in 2vrp
Sodium binding site 1 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rhodocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1137

b:73.4
occ:1.00
CA A:SER91 3.7 29.7 1.0
N A:SER92 3.7 31.5 1.0
OG A:SER92 3.8 32.0 1.0
CB A:SER91 4.0 29.4 1.0
C A:SER91 4.2 30.6 1.0
O A:GLY90 4.5 27.7 1.0
CB A:SER92 4.7 32.4 1.0
N A:SER91 4.8 28.4 1.0
CA A:SER92 4.8 32.2 1.0

Sodium binding site 2 out of 4 in 2vrp

Go back to Sodium Binding Sites List in 2vrp
Sodium binding site 2 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rhodocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1138

b:53.2
occ:1.00
OH A:TYR12 3.8 29.4 1.0
CE1 A:TYR12 4.0 25.9 1.0
CZ A:TYR12 4.4 25.6 1.0
CA A:GLY49 5.0 32.6 1.0

Sodium binding site 3 out of 4 in 2vrp

Go back to Sodium Binding Sites List in 2vrp
Sodium binding site 3 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Rhodocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1124

b:48.4
occ:1.00
OD2 B:ASP1 2.2 52.2 1.0
CG B:ASP1 3.3 52.9 1.0
O B:HOH2001 3.4 60.4 1.0
OG B:SER8 3.6 35.5 1.0
N B:SER8 3.7 35.8 1.0
OD1 B:ASP1 3.8 53.9 1.0
O B:TRP6 4.0 35.5 1.0
CA B:SER7 4.0 35.4 1.0
C B:SER7 4.4 35.3 1.0
CB B:SER8 4.5 35.5 1.0
CB B:ASP1 4.6 52.4 1.0
CB B:SER7 4.7 35.7 1.0
CA B:SER8 4.7 35.6 1.0
CB B:CYS2 4.8 48.3 1.0
C B:TRP6 4.9 35.8 1.0
N B:SER7 4.9 35.8 1.0
OG B:SER7 5.0 36.2 1.0

Sodium binding site 4 out of 4 in 2vrp

Go back to Sodium Binding Sites List in 2vrp
Sodium binding site 4 out of 4 in the Structure of Rhodocytin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Rhodocytin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1127

b:51.0
occ:1.00
N B:GLY5 3.5 41.3 1.0
CA B:SER4 4.1 43.8 1.0
C B:SER4 4.3 42.4 1.0
CA B:GLY5 4.3 39.4 1.0
OG B:SER4 4.6 45.7 1.0
CB B:SER4 4.7 44.3 1.0

Reference:

A.A.Watson, J.A.Eble, C.A.O'callaghan. Crystal Structure of Rhodocytin, A Ligand For the Platelet-Activating Receptor Clec-2. Protein Sci. V. 17 1611 2008.
ISSN: ISSN 0961-8368
PubMed: 18583525
DOI: 10.1110/PS.035568.108
Page generated: Tue Dec 15 05:56:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy