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Sodium in PDB 3th2: MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+

Enzymatic activity of MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+

All present enzymatic activity of MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+:
3.4.21.21;

Protein crystallography data

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: 3th2 was solved by K.Vadivel, S.Agah, D.Cascio, K.Padmanabhan, S.P.Bajaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.20 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.940, 80.874, 126.430, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.3

Other elements in 3th2:

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+ also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Chlorine (Cl) 2 atoms
Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+ (pdb code 3th2). 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 MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+, PDB code: 3th2:

Sodium binding site 1 out of 1 in 3th2

Go back to Sodium Binding Sites List in 3th2
Sodium binding site 1 out of 1 in the MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na10

b:25.4
occ:1.00
 O H:THR221 2.5 18.3 1.0
O H:TYR184 2.6 16.0 1.0
N H:GLY187 2.9 16.0 1.0
O H:HOH385 3.1 31.1 1.0
C H:THR221 3.3 17.6 1.0
O H:HIS224 3.3 16.5 1.0
CA H:GLY187 3.4 16.0 1.0
C H:SER185 3.4 17.8 1.0
C H:ALA221A 3.4 16.6 1.0
N H:THR221 3.4 15.9 1.0
C H:TYR184 3.6 15.7 1.0
O H:SER185 3.6 18.7 1.0
CA H:ALA221A 3.6 16.5 1.0
CA H:SER185 3.6 16.6 1.0
N H:ASP186 3.7 18.4 1.0
O H:ALA221A 3.9 16.3 1.0
N H:SER185 4.0 16.6 1.0
N H:VAL222 4.0 15.4 1.0
C H:ASP186 4.0 18.3 1.0
CA H:THR221 4.1 16.8 1.0
CA H:VAL222 4.2 16.0 1.0
C H:GLY187 4.2 16.9 1.0
O H:HOH339 4.3 26.4 1.0
N H:SER188A 4.4 15.7 1.0
CB H:ALA221A 4.4 17.3 1.0
C H:HIS224 4.5 16.1 1.0
CA H:ASP186 4.5 18.8 1.0
O H:HOH317 4.6 15.6 1.0
N H:HIS224 4.7 13.8 1.0
N H:ALA221A 4.7 15.1 1.0
O H:LYS188 4.8 15.9 1.0
N H:GLY223 4.8 15.8 1.0
OD1 H:ASP186 4.9 20.6 1.0
C H:VAL222 4.9 15.2 1.0
CB H:SER185 4.9 17.4 1.0
CA H:TYR184 4.9 14.8 1.0

Reference:

K.Vadivel, S.Agah, A.Messer, D.Cascio, M.S Bajaj, S.Krishnaswamy, C.T Esmon, K.Padmanabhan, S.P.Bajaj. MG2+ Is Required For Optimal Folding of the Gamma-Carboxyglutamic Acid (Gla) Domains of Vitamin K-Dependent Clotting Factors at Physiological CA2+ To Be Published.
Page generated: Sun Aug 17 17:38:32 2025

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