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Calcium 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
Sodium (Na) 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 3th2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 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: 3th2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3th2

Go back to Calcium Binding Sites List in 3th2
Calcium binding site 1 out of 6 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:Ca146

b:48.7
occ:1.00
 O L:HOH563 2.0 48.8 1.0
O L:HOH267 2.1 31.0 1.0
O L:HOH428 2.2 36.6 1.0
OE21 L:CGU26 2.5 38.6 1.0
OE11 L:CGU29 2.7 29.3 1.0
OE12 L:CGU29 3.2 28.5 1.0
CD1 L:CGU29 3.3 29.7 1.0
CD2 L:CGU26 3.5 35.8 1.0
CA L:CA147 3.6 70.4 1.0
O L:HOH426 3.6 37.2 1.0
OE22 L:CGU26 3.8 34.1 1.0
CG L:CGU26 4.8 32.0 1.0
CG L:CGU29 4.8 27.1 1.0
OE11 L:CGU25 4.9 35.2 1.0
CA L:CGU26 5.0 27.1 1.0

Calcium binding site 2 out of 6 in 3th2

Go back to Calcium Binding Sites List in 3th2
Calcium binding site 2 out of 6 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
L:Ca147

b:70.4
occ:1.00
 O L:HOH639 2.3 27.9 1.0
O L:HOH267 2.4 31.0 1.0
OE11 L:CGU29 2.5 29.3 1.0
O L:HOH564 2.7 50.8 1.0
O L:HOH490 2.8 38.8 1.0
OE22 L:CGU26 3.0 34.1 1.0
OE21 L:CGU26 3.2 38.6 1.0
CD2 L:CGU26 3.3 35.8 1.0
OE21 L:CGU16 3.4 28.1 1.0
CA L:CA146 3.6 48.7 1.0
O L:HOH397 3.7 30.7 1.0
CD1 L:CGU29 3.8 29.7 1.0
CB L:CGU29 3.9 28.7 1.0
OE22 L:CGU16 4.0 31.5 1.0
CD2 L:CGU16 4.1 26.7 1.0
O L:CGU26 4.3 27.4 1.0
MG L:MG148 4.4 27.7 1.0
CA L:CGU26 4.4 27.1 1.0
CG L:CGU29 4.4 27.1 1.0
O L:HOH511 4.5 39.9 1.0
CG L:CGU26 4.6 32.0 1.0
OE12 L:CGU29 4.7 28.5 1.0
O L:HOH636 4.8 36.4 1.0
C L:CGU26 4.8 27.4 1.0
CB L:CGU26 4.8 28.3 1.0
O L:HOH428 5.0 36.6 1.0

Calcium binding site 3 out of 6 in 3th2

Go back to Calcium Binding Sites List in 3th2
Calcium binding site 3 out of 6 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 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:Ca149

b:73.1
occ:1.00
 OE12 L:CGU16 2.2 22.3 1.0
OE11 L:CGU16 2.4 29.4 1.0
O L:HOH568 2.4 45.0 1.0
CD1 L:CGU16 2.6 27.1 1.0
OE21 L:CGU20 2.8 53.9 1.0
O L:HOH565 2.9 44.9 1.0
O L:ALA1 3.2 60.8 1.0
CB L:ALA1 3.4 60.5 1.0
O L:HOH638 3.5 31.7 1.0
CD2 L:CGU20 3.5 53.8 1.0
OE11 L:CGU7 3.7 38.9 1.0
OE22 L:CGU20 3.8 55.9 1.0
MG L:MG148 3.8 27.7 1.0
CA L:CA150 3.9 57.5 1.0
CG L:CGU16 4.0 28.2 1.0
C L:ALA1 4.1 60.5 1.0
CA L:CGU16 4.1 30.8 1.0
OE12 L:CGU26 4.3 24.6 1.0
CA L:ALA1 4.4 60.9 1.0
CB L:CGU16 4.4 29.7 1.0
CD1 L:CGU7 4.5 36.7 1.0
N L:CGU16 4.6 33.0 1.0
O L:HOH397 4.7 30.7 1.0
O L:ARG15 4.7 34.2 1.0
OE12 L:CGU7 4.7 32.8 1.0
CG L:CGU20 4.8 50.2 1.0
C L:ARG15 4.8 34.0 1.0
CB L:CGU20 4.9 44.2 1.0
CD2 L:CGU16 5.0 26.7 1.0

Calcium binding site 4 out of 6 in 3th2

Go back to Calcium Binding Sites List in 3th2
Calcium binding site 4 out of 6 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 4 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:Ca150

b:57.5
occ:1.00
 OE21 L:CGU20 2.1 53.9 1.0
O L:HOH570 2.4 40.6 1.0
OE11 L:CGU20 2.6 55.3 1.0
O L:HOH568 2.8 45.0 1.0
CD2 L:CGU20 3.2 53.8 1.0
CD1 L:CGU20 3.4 54.3 1.0
CG L:CGU20 3.7 50.2 1.0
OE21 L:CGU6 3.8 46.0 1.0
O L:ARG15 3.8 34.2 1.0
CA L:CA149 3.9 73.1 1.0
OE22 L:CGU20 4.2 55.9 1.0
OE12 L:CGU20 4.4 56.4 1.0
CB L:CGU20 4.4 44.2 1.0
O L:HOH567 4.4 49.3 1.0
OE11 L:CGU16 4.5 29.4 1.0
C L:ARG15 4.5 34.0 1.0
OE12 L:CGU6 4.5 49.8 1.0
O L:HOH565 4.6 44.9 1.0
CD2 L:CGU6 4.7 44.9 1.0
CG L:ARG15 4.8 38.1 1.0

Calcium binding site 5 out of 6 in 3th2

Go back to Calcium Binding Sites List in 3th2
Calcium binding site 5 out of 6 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 5 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:Ca152

b:22.9
occ:1.00
 O L:GLN64 2.3 22.0 1.0
O L:GLY47 2.4 23.8 1.0
O L:HOH571 2.4 21.2 1.0
OE1 L:GLN49 2.4 26.5 1.0
OD2 L:ASP46 2.5 23.2 1.0
OD2 L:ASP63 2.5 27.7 1.0
O L:HOH375 2.6 26.6 1.0
OD1 L:ASP63 2.6 28.6 1.0
CG L:ASP63 2.9 26.4 1.0
C L:GLN64 3.5 21.4 1.0
CD L:GLN49 3.5 29.5 1.0
C L:GLY47 3.6 27.4 1.0
CG L:ASP46 3.6 24.7 1.0
NE2 L:GLN49 4.0 22.5 1.0
N L:GLN66 4.1 24.9 1.0
N L:GLN49 4.1 27.0 1.0
CB L:ASP46 4.2 23.4 1.0
CA L:LEU65 4.2 25.1 1.0
N L:GLN64 4.2 21.6 1.0
N L:LEU65 4.3 22.1 1.0
CA L:ASP48 4.3 29.0 1.0
N L:ASP48 4.4 27.3 1.0
CB L:ASP63 4.4 20.4 1.0
CA L:GLN64 4.5 21.2 1.0
C L:LEU65 4.6 25.6 1.0
N L:GLY47 4.6 26.1 1.0
C L:ASP46 4.6 24.4 1.0
OD1 L:ASP46 4.7 28.0 1.0
CA L:GLY47 4.7 25.6 1.0
O L:SER67 4.7 20.0 1.0
C L:ASP48 4.7 29.4 1.0
O L:ASP46 4.7 27.0 1.0
CG L:GLN49 4.8 27.8 1.0
C L:ASP63 4.9 23.1 1.0
O L:HOH613 4.9 41.0 1.0

Calcium binding site 6 out of 6 in 3th2

Go back to Calcium Binding Sites List in 3th2
Calcium binding site 6 out of 6 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 6 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:Ca9

b:27.8
occ:1.00
 OE2 H:GLU80 2.2 23.8 1.0
O H:GLU75 2.2 21.9 1.0
OE2 H:GLU70 2.2 15.0 1.0
O H:HOH375 2.3 27.5 1.0
O H:HOH301 2.3 16.4 1.0
O H:ASP72 2.3 15.0 1.0
CD H:GLU80 3.1 31.0 1.0
CD H:GLU70 3.1 16.2 1.0
C H:GLU75 3.4 24.2 1.0
OE1 H:GLU70 3.4 19.5 1.0
C H:ASP72 3.4 14.9 1.0
OE1 H:GLU80 3.7 31.8 1.0
N H:ASP72 3.9 14.4 1.0
CA H:HIS76 3.9 26.6 1.0
N H:HIS76 4.1 22.3 1.0
CG H:GLU80 4.1 21.1 1.0
CA H:ASP72 4.1 15.3 1.0
O H:HOH278 4.2 19.7 1.0
O H:HOH263 4.2 32.9 1.0
N H:GLU75 4.2 19.6 1.0
N H:LEU73 4.3 14.0 1.0
CA H:GLU75 4.4 22.7 1.0
N H:HIS71 4.4 13.0 1.0
CA H:LEU73 4.5 14.8 1.0
CG H:GLU70 4.5 13.5 1.0
N H:ASP77 4.5 25.0 1.0
CB H:ASP72 4.5 14.8 1.0
C H:HIS76 4.6 26.6 1.0
C H:LEU73 4.7 17.6 1.0
C H:HIS71 4.8 14.0 1.0
CB H:GLU75 4.9 23.3 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 19:42:30 2024

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