Chemical elements
    Physical Properties
    Chemical Properties
    PDB 131d-1bli
    PDB 1bph-1d10
    PDB 1d11-1ej2
    PDB 1eja-1gb5
    PDB 1gb6-1goh
    PDB 1gq2-1ikp
    PDB 1ikq-1jz1
    PDB 1jz2-1kvs
    PDB 1kvt-1me8
    PDB 1mg2-1nsz
    PDB 1nta-1oyt
    PDB 1p0s-1qjs
    PDB 1qnj-1s5d
    PDB 1s5e-1tjp
    PDB 1tk6-1uxt
    PDB 1uxu-1vzq
    PDB 1w15-1xc6
    PDB 1xcu-1yf1
    PDB 1ygg-1zko
    PDB 1zkp-2afh
    PDB 2agv-2bhc
    PDB 2bhp-2cc6
    PDB 2cc7-2dec
    PDB 2deg-2ein
    PDB 2eit-2fjb
    PDB 2fld-2gg8
    PDB 2gg9-2h9j
    PDB 2h9k-2ien
    PDB 2ieo-2jih
    PDB 2jin-2omd
    PDB 2omg-2p77
    PDB 2p78-2q68
    PDB 2q69-2qz7
    PDB 2qzi-2v35
    PDB 2v3h-2vwo
    PDB 2vx4-2wig
    PDB 2wij-2x1z
    PDB 2x20-2xmk
    PDB 2xmm-2zfq
    PDB 2zfr-3a6s
    PDB 3a6t-3b1e
    PDB 3b2n-3bos
    PDB 3bov-3ccr
    PDB 3ccs-3d7r
    PDB 3d97-3e3y
    PDB 3e40-3erp
    PDB 3euw-3fgw
    PDB 3fh4-3g3r
    PDB 3g3s-3gxw
    PDB 3gyz-3hwt
    PDB 3hww-3ijp
    PDB 3imm-3k0g
    PDB 3k13-3l7x
    PDB 3l88-3max
    PDB 3mbb-3mr1
    PDB 3mty-3nu3
    PDB 3nu4-3ot1
    PDB 3ow2-3qwc
    PDB 3qx5-3tfr
    PDB 3tfs-3v6o
    PDB 3v72-4ag2
    PDB 4aga-4eae
    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of Thrombin With 3-Cycle With F (pdb 2v3o)

The binding sites of Sodium atom in the structure of Thrombin With 3-Cycle With F (pdb code 2v3o). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 2v3o structure was solved by D.W.BANNER, H.P.WESSEL, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:
Resolution (A)71.1-1.8
Space groupC121
a (A)70.610
b (A)71.820
c (A)72.280
alpha (°)90.00
beta (°)100.60
gamma (°)90.00
Rfactor (%)17.6
Rfree (%)21.2

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 2v3o

Sodium binding site 1 out of 1 in 2v3o
Click to enlarge
stereopicture of Sodium binding site 1 out of 1 in 2v3o
Click to enlarge
Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 2v3o. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Sodium atom, shown by VdW sphere
Residues shown as a stick model or VDW spheres: H: Tyr184A, H: Asp221, H: Arg221A, H: Asp222, H: Gly223, H: Lys224, H: Tyr225, H: Hoh2259, H: Hoh2271, H: Hoh2272, H: Hoh2273, H: Hoh2274, H: Hoh2300, H: Hoh2304, H: Hoh2308,

conact list:

AtomAtomDistance (A)
NaO H:Tyr184A4.06
NaO H:Asp2214.56
NaC H:Asp2214.12
NaOD1 H:Asp2214.70
NaCA H:Asp2214.47
NaO H:Arg221A2.27
NaN H:Arg221A3.99
NaC H:Arg221A3.32
NaCA H:Arg221A4.27
NaN H:Asp2224.15
NaC H:Asp2224.43
NaCA H:Asp2224.24
NaN H:Gly2234.14
NaC H:Gly2234.77
NaCA H:Gly2235.00
NaO H:Lys2242.26
NaN H:Lys2243.76
NaCB H:Lys2244.42
NaC H:Lys2243.36
NaCA H:Lys2244.02
NaN H:Tyr2254.42
NaCA H:Tyr2254.79
NaO H:Hoh22592.69
NaO H:Hoh22714.37
NaO H:Hoh22723.97
NaO H:Hoh22732.46
NaO H:Hoh22744.67
NaO H:Hoh23002.65
NaO H:Hoh23043.90
NaO H:Hoh23082.64

interactive model:

© Copyright 2008-2012 by