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Magnesium 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:

Chlorine (Cl) 2 atoms
Calcium (Ca) 6 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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: 3th2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3th2

Go back to Magnesium Binding Sites List in 3th2
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg145

b:33.1
occ:1.00
 OE21 L:CGU29 1.9 28.3 1.0
O L:HOH424 2.1 32.9 1.0
OE21 L:CGU25 2.1 33.8 1.0
OE12 L:CGU29 2.1 28.5 1.0
O L:HOH635 2.1 33.8 1.0
OE11 L:CGU25 2.1 35.2 1.0
CD2 L:CGU29 2.9 28.8 1.0
CD2 L:CGU25 3.0 33.2 1.0
CD1 L:CGU29 3.0 29.7 1.0
CD1 L:CGU25 3.0 34.5 1.0
CG L:CGU29 3.1 27.1 1.0
CG L:CGU25 3.3 31.1 1.0
NH2 L:ARG28 3.5 45.9 1.0
O L:HOH426 3.9 37.2 1.0
OE22 L:CGU29 4.0 28.1 1.0
OE22 L:CGU25 4.1 38.3 1.0
CZ L:ARG28 4.1 50.8 1.0
O L:HOH563 4.1 48.8 1.0
OE11 L:CGU29 4.1 29.3 1.0
NH1 L:ARG28 4.2 55.3 1.0
OE12 L:CGU25 4.2 37.3 1.0
O L:HOH223 4.3 45.7 1.0
O L:CGU25 4.6 28.5 1.0
CB L:CGU29 4.7 28.7 1.0
CB L:CGU25 4.8 30.0 1.0

Magnesium binding site 2 out of 3 in 3th2

Go back to Magnesium Binding Sites List in 3th2
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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
L:Mg148

b:27.7
occ:1.00
 O L:HOH638 1.8 31.7 1.0
OE12 L:CGU16 1.9 22.3 1.0
OE12 L:CGU26 1.9 24.6 1.0
OE22 L:CGU26 2.0 34.1 1.0
OE21 L:CGU16 2.0 28.1 1.0
O L:HOH397 2.1 30.7 1.0
CD1 L:CGU16 2.7 27.1 1.0
CD2 L:CGU16 2.8 26.7 1.0
CD1 L:CGU26 2.8 30.0 1.0
CD2 L:CGU26 3.0 35.8 1.0
CG L:CGU16 3.1 28.2 1.0
CG L:CGU26 3.3 32.0 1.0
CB L:CGU16 3.7 29.7 1.0
CA L:CA149 3.8 73.1 1.0
OE11 L:CGU26 3.9 31.9 1.0
OE11 L:CGU16 4.0 29.4 1.0
OE22 L:CGU16 4.1 31.5 1.0
OE21 L:CGU26 4.1 38.6 1.0
OE12 L:CGU7 4.2 32.8 1.0
O L:HOH490 4.2 38.8 1.0
O L:HOH267 4.2 31.0 1.0
O L:HOH433 4.3 49.8 1.0
CB L:CGU26 4.3 28.3 1.0
O L:ALA1 4.4 60.8 1.0
OE11 L:CGU7 4.4 38.9 1.0
CA L:CA147 4.4 70.4 1.0
O L:HOH639 4.5 27.9 1.0
CB L:ALA1 4.7 60.5 1.0
CA L:CGU16 4.7 30.8 1.0
CD1 L:CGU7 4.7 36.7 1.0

Magnesium binding site 3 out of 3 in 3th2

Go back to Magnesium Binding Sites List in 3th2
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg151

b:55.8
occ:1.00
 OE11 L:CGU19 1.9 53.0 1.0
OE22 L:CGU19 1.9 51.5 1.0
OE12 L:CGU14 2.0 52.1 1.0
OE22 L:CGU14 2.1 50.9 1.0
O L:HOH648 2.1 30.0 1.0
CD2 L:CGU19 2.8 50.1 1.0
CD1 L:CGU19 2.8 50.6 1.0
CD1 L:CGU14 2.8 48.2 1.0
CD2 L:CGU14 2.9 47.3 1.0
CG L:CGU14 3.0 45.1 1.0
CG L:CGU19 3.1 46.9 1.0
OE21 L:CGU19 3.8 53.5 1.0
OE12 L:CGU19 3.9 50.9 1.0
OE21 L:CGU14 4.0 47.9 1.0
O L:HOH573 4.0 54.7 1.0
OE11 L:CGU14 4.1 51.9 1.0
CB L:CGU14 4.5 38.8 1.0
O L:HOH572 4.5 46.3 1.0
CB L:CGU19 4.6 42.8 1.0
O L:CGU14 4.8 36.7 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: Thu Aug 15 12:06:42 2024

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