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Calcium in PDB 3th3: 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: 3th3 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) 55.01 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.079, 68.894, 79.153, 90.00, 91.19, 90.00
R / Rfree (%) 22.8 / 29.8

Other elements in 3th3:

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:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 3th3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where 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: 3th3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3th3

Go back to Calcium Binding Sites List in 3th3
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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
L:Ca202

b:98.2
occ:1.00
 O L:HOH304 1.9 30.0 1.0
OE1 L:GLN49 2.1 90.3 1.0
OD1 L:ASP63 2.3 88.5 1.0
O L:GLN64 2.4 86.8 1.0
O L:GLY47 2.6 92.1 1.0
CG L:ASP63 3.0 88.0 1.0
OD2 L:ASP63 3.0 88.5 1.0
CD L:GLN49 3.1 90.9 1.0
C L:GLN64 3.5 86.5 1.0
NE2 L:GLN49 3.6 90.2 1.0
C L:GLY47 3.6 92.2 1.0
O L:SER67 3.6 81.9 1.0
N L:GLN66 3.6 86.0 1.0
N L:GLN49 4.0 92.3 1.0
N L:SER67 4.1 84.0 1.0
CA L:LEU65 4.1 86.5 1.0
N L:GLN64 4.1 86.4 1.0
CA L:ASP48 4.2 92.8 1.0
N L:ASP48 4.3 92.5 1.0
C L:LEU65 4.3 86.4 1.0
CD2 L:LEU65 4.3 86.6 1.0
N L:LEU65 4.3 86.4 1.0
N L:GLY47 4.3 91.7 1.0
CB L:ASP63 4.4 87.1 1.0
CA L:GLN66 4.4 85.7 1.0
C L:ASP48 4.5 92.6 1.0
CG L:GLN49 4.5 91.4 1.0
CA L:GLN64 4.6 86.5 1.0
CA L:GLY47 4.6 91.9 1.0
C L:SER67 4.6 82.0 1.0
CB L:GLN49 4.7 91.9 1.0
C L:GLN66 4.7 85.0 1.0
C L:ASP63 4.8 86.5 1.0
CA L:SER67 4.9 83.1 1.0
CA L:ASP63 4.9 86.8 1.0
CA L:GLN49 5.0 92.0 1.0

Calcium binding site 2 out of 2 in 3th3

Go back to Calcium Binding Sites List in 3th3
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca302

b:63.5
occ:1.00
 OE1 H:GLU80 2.3 47.7 1.0
OE2 H:GLU70 2.3 25.5 1.0
O H:HOH442 2.4 60.9 1.0
O H:GLU75 2.4 47.8 1.0
O H:HOH419 2.5 31.8 1.0
O H:ASP72 2.6 39.1 1.0
C H:GLU75 3.2 47.0 1.0
CA H:HIS76 3.2 45.4 1.0
CD H:GLU80 3.3 45.4 1.0
CD H:GLU70 3.4 31.4 1.0
N H:HIS76 3.6 46.0 1.0
OE2 H:GLU80 3.7 44.8 1.0
OE1 H:GLU70 3.7 31.0 1.0
C H:ASP72 3.8 38.4 1.0
CB H:HIS76 4.0 45.5 1.0
N H:ASP77 4.1 43.4 1.0
C H:HIS76 4.2 44.1 1.0
CA H:GLU75 4.4 47.1 1.0
N H:GLU75 4.5 46.3 1.0
CG H:GLU80 4.5 41.6 1.0
N H:ASP72 4.5 35.6 1.0
CA H:ASP72 4.6 37.5 1.0
O H:HOH437 4.7 34.0 1.0
CG H:GLU70 4.7 28.0 1.0
O H:LEU73 4.7 41.3 1.0
N H:LEU73 4.7 39.3 1.0
C H:LEU73 4.7 41.6 1.0
CG H:HIS76 4.8 48.0 1.0
ND1 H:HIS76 4.8 50.8 1.0
CA H:LEU73 4.8 40.5 1.0
CB H:ASP72 4.9 37.7 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: Sat Jul 13 19:42:33 2024

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