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Magnesium in PDB 3jtc: Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins

Enzymatic activity of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins

All present enzymatic activity of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins:
3.4.21.69;

Protein crystallography data

The structure of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins, PDB code: 3jtc was solved by S.P.Bajaj, K.Vadivel, S.Agah, D.Cascio, S.Krishnaswamy, C.Esmon, K.Padmanabhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.22 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.220, 62.360, 71.030, 90.00, 101.81, 90.00
R / Rfree (%) 19.1 / 22.6

Other elements in 3jtc:

The structure of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins also contains other interesting chemical elements:

Calcium (Ca) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins (pdb code 3jtc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins, PDB code: 3jtc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3jtc

Go back to Magnesium Binding Sites List in 3jtc
Magnesium binding site 1 out of 4 in the Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg34

b:15.8
occ:1.00
 OE22 C:CGU29 2.0 15.1 1.0
OE11 C:CGU29 2.0 17.2 1.0
OE1 A:GLU86 2.1 14.8 1.0
OE22 C:CGU25 2.1 16.5 1.0
OE12 C:CGU25 2.1 14.7 1.0
O A:HOH615 2.1 16.9 1.0
CD1 C:CGU29 2.9 16.5 1.0
CD1 C:CGU25 3.0 13.2 1.0
CD2 C:CGU29 3.1 15.0 1.0
CD2 C:CGU25 3.1 17.3 1.0
CD A:GLU86 3.2 16.1 1.0
CG C:CGU25 3.3 15.9 1.0
CG C:CGU29 3.3 15.4 1.0
OE2 A:GLU86 3.6 17.0 1.0
O C:HOH47 3.8 14.3 1.0
NH1 A:ARG87 4.0 16.7 1.0
CA C:CA35 4.0 14.4 1.0
O A:HOH703 4.1 27.8 1.0
OE21 C:CGU29 4.2 14.0 1.0
OE11 C:CGU25 4.2 18.4 1.0
OE12 C:CGU29 4.2 18.3 1.0
O C:HOH89 4.2 30.4 1.0
OE21 C:CGU25 4.2 19.3 1.0
CG A:GLU86 4.5 14.9 1.0
O A:GLU86 4.5 18.9 1.0
O C:HOH800 4.5 46.2 1.0
CB A:GLU86 4.6 16.6 1.0
O C:CGU25 4.7 14.6 1.0
CA A:GLU86 4.7 16.8 1.0
CB C:CGU25 4.8 15.2 1.0
CB C:CGU29 4.8 15.4 1.0

Magnesium binding site 2 out of 4 in 3jtc

Go back to Magnesium Binding Sites List in 3jtc
Magnesium binding site 2 out of 4 in the Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg40

b:31.8
occ:1.00
 OE22 C:CGU19 2.0 26.8 1.0
OE21 C:CGU14 2.1 29.6 1.0
OE11 C:CGU14 2.1 34.1 1.0
O C:HOH67 2.2 33.0 1.0
OE11 C:CGU19 2.2 30.0 1.0
O C:HOH99 2.3 34.4 1.0
CD2 C:CGU14 2.9 27.0 1.0
CD1 C:CGU19 3.0 27.9 1.0
CD1 C:CGU14 3.0 31.5 1.0
CD2 C:CGU19 3.1 28.1 1.0
CG C:CGU14 3.2 23.7 1.0
CG C:CGU19 3.2 25.6 1.0
OE21 C:CGU19 4.2 34.2 1.0
OE22 C:CGU14 4.2 33.0 1.0
OE12 C:CGU19 4.2 27.6 1.0
OE12 C:CGU14 4.3 34.4 1.0
CB C:CGU14 4.7 21.2 1.0
CB C:CGU19 4.7 24.4 1.0
O C:CGU14 5.0 20.0 1.0

Magnesium binding site 3 out of 4 in 3jtc

Go back to Magnesium Binding Sites List in 3jtc
Magnesium binding site 3 out of 4 in the Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg34

b:21.9
occ:1.00
 OE11 D:CGU29 2.1 20.1 1.0
OE22 D:CGU25 2.1 21.2 1.0
OE12 D:CGU25 2.1 19.6 1.0
O B:HOH658 2.1 22.4 1.0
OE22 D:CGU29 2.1 17.3 1.0
OE1 B:GLU86 2.1 20.3 1.0
CD1 D:CGU29 2.9 20.7 1.0
CD1 D:CGU25 3.0 23.5 1.0
CD2 D:CGU25 3.1 19.6 1.0
CD2 D:CGU29 3.2 14.1 1.0
CD B:GLU86 3.2 20.6 1.0
CG D:CGU25 3.3 19.5 1.0
CG D:CGU29 3.3 19.9 1.0
O D:HOH54 3.7 22.5 1.0
OE2 B:GLU86 3.7 22.0 1.0
NH1 B:ARG87 4.0 21.3 1.0
O B:HOH715 4.1 32.7 1.0
CA D:CA35 4.1 19.5 1.0
OE11 D:CGU25 4.1 23.6 1.0
OE12 D:CGU29 4.2 23.2 1.0
OE21 D:CGU25 4.2 23.6 1.0
OE21 D:CGU29 4.3 21.9 1.0
O D:HOH96 4.3 39.0 1.0
CG B:GLU86 4.4 21.4 1.0
O B:GLU86 4.5 22.4 1.0
CB B:GLU86 4.5 20.5 1.0
O D:CGU25 4.6 19.5 1.0
CA B:GLU86 4.6 22.4 1.0
CB D:CGU25 4.8 19.4 1.0
CB D:CGU29 4.8 19.3 1.0

Magnesium binding site 4 out of 4 in 3jtc

Go back to Magnesium Binding Sites List in 3jtc
Magnesium binding site 4 out of 4 in the Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Importance of MG2+ in the CA2+-Dependent Folding of the Gamma- Carboxyglutamic Acid Domains of Vitamin K-Dependent Clotting and Anticlotting Proteins within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg40

b:33.8
occ:1.00
 OE22 D:CGU14 1.9 25.6 1.0
OE12 D:CGU14 2.1 29.8 1.0
OE21 D:CGU19 2.1 36.4 1.0
O D:HOH87 2.1 36.2 1.0
O D:HOH68 2.2 24.4 0.5
OE12 D:CGU19 2.3 38.4 1.0
CD2 D:CGU14 2.8 24.0 1.0
CD1 D:CGU14 2.9 28.4 1.0
CD2 D:CGU19 2.9 34.4 1.0
CG D:CGU14 3.0 26.3 1.0
CG D:CGU19 3.3 32.0 1.0
CD1 D:CGU19 3.3 34.0 1.0
OE21 D:CGU14 4.0 28.7 1.0
OE11 D:CGU14 4.0 27.0 1.0
O D:HOH84 4.1 32.4 1.0
OE22 D:CGU19 4.2 27.3 1.0
OE11 D:CGU19 4.5 34.2 1.0
CB D:CGU14 4.5 23.2 1.0
CB D:CGU19 4.8 31.4 1.0
O D:CGU14 4.9 24.6 1.0

Reference:

K.Vadivel, S.Agah, A.S.Messer, D.Cascio, M.S.Bajaj, S.Krishnaswamy, C.T.Esmon, K.Padmanabhan, S.P.Bajaj. Structural and Functional Studies of Gamma-Carboxyglutamic Acid Domains of Factor Viia and Activated Protein C: Role of Magnesium at Physiological Calcium. J.Mol.Biol. V. 425 1961 2013.
ISSN: ISSN 0022-2836
PubMed: 23454357
DOI: 10.1016/J.JMB.2013.02.017
Page generated: Wed Aug 14 17:12:54 2024

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