	Home \| Site Map \| Copyright \| Contact us \| Privacy \|

Chemical elements
  Sodium
    Isotopes
    Energy
    Preparation
    Applications
    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
      3tfs
      3th2
      3th4
      3tif
      3tij
      3tjl
      3tkw
      3tl9
      3tmu
      3tmv
      3tmw
      3tmx
      3tok
      3tp2
      3tvb
      3twf
      3typ
      3u18
      3u4m
      3u69
      3u8o
      3u8r
      3u8t
      3ua6
      3ua7
      3ucy
      3ues
      3uet
      3ug3
      3unx
      3upq
      3upw
      3uq0
      3uq1
      3uq2
      3uq4
      3uq5
      3ur7
      3uu5
      3uu6
      3uu8
      3uub
      3uvf
      3uwp
      3uy7
      3uz5
      3v31
      3v4m
      3v6k
      3v6o
    PDB 3v72-4ag2
    PDB 4aga-4eae
    PDB 4ecn-4g8t
    PDB 4gdt-8icw
    PDB 8icx-9icy

Sodium in the structure of MG2+ Is Required For Optimal Folding Of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological CA2+ (pdb 3th4)

Follow @Atomistry

The binding sites of Sodium atom in the structure of MG2+ Is Required For Optimal Folding Of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological CA2+ (pdb code 3th4). This binding sites where shown with 5.0 Angstroms radius around Sodium atom.
The 3th4 structure was solved by K.VADIVEL, S.AGAH, D.CASCIO, K.PADMANABHAN, S.P.BAJAJ, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:

*Resolution (A)*	68.4-1.8
*Space group*	P2₁2₁2₁
*a (A)*	69.919
*b (A)*	81.230
*c (A)*	126.534
*alpha (°)*	90.00
*beta (°)*	90.00
*gamma (°)*	90.00
*R_factor (%)*	20.4
*R_free (%)*	23.5

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 3th4

Click to enlarge

stereopicture of Sodium binding site 1 out of 1 in 3th4

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Sodium in the PDB 3th4. 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: Tyr184, H: Ser185, H: Asp186, H: Gly187, H: Ser188A, H: Lys188, H: Ala221A, H: Thr221, H: Val222, H: Gly223, H: His224, H: Hoh313, H: Hoh350,

conact list:

Atom	Atom	Distance (A)
Na	O H:*Tyr*184	2.68
Na	C H:*Tyr*184	3.57
Na	CA H:*Tyr*184	4.89
Na	O H:*Ser*185	3.47
Na	N H:*Ser*185	3.87
Na	CB H:*Ser*185	4.83
Na	C H:*Ser*185	3.23
Na	CA H:*Ser*185	3.47
Na	N H:*Asp*186	3.53
Na	C H:*Asp*186	3.96
Na	OD1 H:*Asp*186	4.86
Na	CA H:*Asp*186	4.30
Na	N H:*Gly*187	2.82
Na	C H:*Gly*187	4.20
Na	CA H:*Gly*187	3.33
Na	N H:*Ser*188A	4.41
Na	O H:*Lys*188	4.97
Na	O H:*Ala*221A	3.90
Na	N H:*Ala*221A	4.78
Na	C H:*Ala*221A	3.49
Na	CB H:*Ala*221A	4.43
Na	CA H:*Ala*221A	3.62
Na	O H:*Thr*221	2.51
Na	N H:*Thr*221	3.64
Na	C H:*Thr*221	3.36
Na	CA H:*Thr*221	4.24
Na	N H:*Val*222	4.06
Na	C H:*Val*222	4.84
Na	CA H:*Val*222	4.21
Na	N H:*Gly*223	4.78
Na	O H:*His*224	3.31
Na	N H:*His*224	4.71
Na	C H:*His*224	4.48
Na	O H:*Hoh*313	4.82
Na	O H:*Hoh*350	3.29

Sodium in the structure of MG2+ Is Required For Optimal Folding Of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors At Physiological CA2+ (pdb 3th4)

Sodium Binding Sites:

Sodium binding site 1 out of 1 in 3th4

conact list:

interactive model: