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Calcium in PDB 3th4: 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: 3th4 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) 68.36 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.919, 81.230, 126.534, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.5

Other elements in 3th4:

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) 2 atoms
Chlorine (Cl) 3 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 3th4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 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: 3th4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 1 out of 7 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:Ca204

b:28.4
occ:1.00
 OE22 L:CGU7 2.2 29.1 1.0
OE21 L:CGU29 2.3 31.1 1.0
O L:HOH361 2.3 29.9 1.0
OE22 L:CGU29 2.3 24.9 1.0
OE11 L:CGU7 2.4 20.3 1.0
OE11 L:CGU26 2.5 24.6 1.0
CD2 L:CGU29 2.6 24.9 1.0
O L:HOH365 2.7 28.6 1.0
CD1 L:CGU7 3.2 23.1 1.0
CD2 L:CGU7 3.3 28.6 1.0
CD1 L:CGU26 3.4 26.4 1.0
OE12 L:CGU26 3.5 25.3 1.0
CG L:CGU7 3.7 26.6 1.0
CA L:CA205 3.9 22.3 1.0
O L:HOH357 3.9 26.1 1.0
MG L:MG203 4.1 30.5 1.0
OE12 L:CGU7 4.1 25.4 1.0
OE12 L:CGU25 4.1 25.2 1.0
CG L:CGU29 4.1 28.2 1.0
CB L:CGU7 4.4 24.5 1.0
O L:HOH325 4.4 22.1 1.0
OE21 L:CGU7 4.5 33.6 1.0
ND2 L:ASN2 4.5 23.1 1.0
CD1 L:CGU25 4.5 29.4 1.0
CG L:CGU26 4.8 19.1 1.0
CD1 L:CGU29 4.8 34.1 1.0
OD1 L:ASN2 4.8 24.3 1.0
CG L:CGU25 4.9 26.6 1.0
OE12 L:CGU29 5.0 35.0 1.0
CB L:CGU29 5.0 27.9 1.0

Calcium binding site 2 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 2 out of 7 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:Ca205

b:22.3
occ:1.00
 O L:HOH309 2.2 19.7 1.0
O L:HOH325 2.3 22.1 1.0
OE12 L:CGU26 2.4 25.3 1.0
OE11 L:CGU7 2.4 20.3 1.0
OE22 L:CGU29 2.6 24.9 1.0
O L:HOH320 2.6 23.5 1.0
OE21 L:CGU16 2.7 21.1 1.0
OE12 L:CGU7 2.7 25.4 1.0
CD1 L:CGU7 2.9 23.1 1.0
CD1 L:CGU26 3.5 26.4 1.0
CD2 L:CGU16 3.5 23.4 1.0
CA L:CA206 3.6 21.6 1.0
OE22 L:CGU16 3.6 24.4 1.0
CA L:CA204 3.9 28.4 1.0
CD2 L:CGU29 3.9 24.9 1.0
OE11 L:CGU26 4.0 24.6 1.0
CB L:CGU29 4.3 27.9 1.0
CG L:CGU7 4.4 26.6 1.0
CA L:GLY11 4.4 27.0 1.0
OE11 L:CGU6 4.5 22.5 1.0
CA L:CGU26 4.6 21.4 1.0
CG L:CGU26 4.6 19.1 1.0
CB L:CGU26 4.6 21.3 1.0
O L:CGU26 4.7 21.7 1.0
CG L:CGU29 4.7 28.2 1.0
OE21 L:CGU29 4.8 31.1 1.0
O L:HOH361 4.8 29.9 1.0
OD1 L:ASN2 4.9 24.3 1.0
CG L:CGU16 4.9 18.6 1.0
OE22 L:CGU7 5.0 29.1 1.0
OE22 L:CGU26 5.0 18.6 1.0
N L:GLY11 5.0 27.4 1.0
CB L:CGU7 5.0 24.5 1.0
O L:ARG9 5.0 30.0 1.0

Calcium binding site 3 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 3 out of 7 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:Ca206

b:21.6
occ:1.00
 OE12 L:CGU16 2.3 19.2 1.0
OE21 L:CGU16 2.3 21.1 1.0
OE12 L:CGU7 2.4 25.4 1.0
OD1 L:ASN2 2.4 24.3 1.0
OE22 L:CGU26 2.4 18.6 1.0
OE12 L:CGU6 2.5 22.9 1.0
OE12 L:CGU26 2.6 25.3 1.0
CD1 L:CGU16 3.2 22.1 1.0
O L:ALA1 3.2 22.7 1.0
OE11 L:CGU6 3.3 22.5 1.0
CD1 L:CGU6 3.3 23.4 1.0
CD1 L:CGU26 3.3 26.4 1.0
CD2 L:CGU16 3.4 23.4 1.0
CD1 L:CGU7 3.5 23.1 1.0
CD2 L:CGU26 3.5 21.6 1.0
CA L:CA205 3.6 22.3 1.0
CG L:ASN2 3.6 27.4 1.0
CG L:CGU16 3.8 18.6 1.0
CA L:CA207 3.8 24.6 1.0
C L:ALA1 3.9 25.0 1.0
CG L:CGU26 3.9 19.1 1.0
OE11 L:CGU16 4.1 23.6 1.0
OE11 L:CGU26 4.2 24.6 1.0
OE11 L:CGU7 4.2 20.3 1.0
O L:HOH320 4.3 23.5 1.0
N L:ALA1 4.3 23.4 1.0
CG L:CGU7 4.4 26.6 1.0
ND2 L:ASN2 4.4 23.1 1.0
CA L:ASN2 4.4 28.6 1.0
CB L:CGU16 4.5 19.7 1.0
N L:ASN2 4.5 26.7 1.0
OE22 L:CGU16 4.5 24.4 1.0
OE21 L:CGU26 4.6 24.8 1.0
CB L:CGU26 4.6 21.3 1.0
CB L:ASN2 4.6 27.3 1.0
CA L:ALA1 4.7 23.7 1.0
CG L:CGU6 4.7 26.6 1.0
O L:HOH309 4.8 19.7 1.0
CD2 L:CGU7 4.9 28.6 1.0
OE22 L:CGU20 5.0 17.1 1.0

Calcium binding site 4 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 4 out of 7 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:Ca207

b:24.6
occ:1.00
 OE22 L:CGU6 2.3 26.0 1.0
O L:HOH327 2.4 27.1 1.0
O L:ALA1 2.4 22.7 1.0
OE12 L:CGU6 2.5 22.9 1.0
OE22 L:CGU20 2.5 17.1 1.0
OE11 L:CGU16 2.5 23.6 1.0
OE12 L:CGU16 2.5 19.2 1.0
OE21 L:CGU20 2.6 25.9 1.0
CD2 L:CGU20 2.9 24.9 1.0
CD1 L:CGU16 2.9 22.1 1.0
CD1 L:CGU6 3.1 23.4 1.0
CD2 L:CGU6 3.3 28.9 1.0
C L:ALA1 3.6 25.0 1.0
CG L:CGU6 3.7 26.6 1.0
CA L:CA206 3.8 21.6 1.0
OE11 L:CGU6 3.9 22.5 1.0
N L:ALA1 4.0 23.4 1.0
O L:HOH367 4.3 26.2 1.0
CA L:ALA1 4.3 23.7 1.0
CG L:CGU16 4.4 18.6 1.0
CG L:CGU20 4.4 25.0 1.0
CB L:CGU6 4.4 24.1 1.0
OE21 L:CGU6 4.4 30.5 1.0
N L:ASN2 4.6 26.7 1.0
CA L:ASN2 4.8 28.6 1.0
NE L:ARG15 4.8 25.4 1.0
CB L:ALA1 4.8 23.9 1.0
O L:ARG15 4.8 20.9 1.0
OE22 L:CGU26 4.8 18.6 1.0
CA L:CA208 4.9 34.7 1.0
CA L:CGU16 4.9 20.0 1.0
OE21 L:CGU16 4.9 21.1 1.0

Calcium binding site 5 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 5 out of 7 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:Ca208

b:34.7
occ:1.00
 O L:HOH332 2.3 29.5 1.0
O L:HOH367 2.4 26.2 1.0
O L:HOH368 2.4 38.2 1.0
O L:HOH366 2.4 43.6 1.0
OE12 L:CGU20 2.5 31.4 1.0
OE21 L:CGU20 2.6 25.9 1.0
CD1 L:CGU20 3.4 27.4 1.0
CD2 L:CGU20 3.5 24.9 1.0
CG L:CGU20 3.6 25.0 1.0
O L:ARG15 4.4 20.9 1.0
OE22 L:CGU6 4.6 26.0 1.0
OE11 L:CGU20 4.6 27.5 1.0
OE22 L:CGU20 4.7 17.1 1.0
CG L:ARG15 4.7 22.3 1.0
OE22 L:CGU19 4.7 36.0 1.0
CA L:CA207 4.9 24.6 1.0
O L:HOH327 4.9 27.1 1.0

Calcium binding site 6 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 6 out of 7 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
L:Ca210

b:23.8
occ:1.00
 OD2 L:ASP46 2.2 24.1 1.0
O L:HOH326 2.4 20.8 1.0
O L:GLN64 2.4 20.6 1.0
OE1 L:GLN49 2.4 21.9 1.0
O L:GLY47 2.4 24.4 1.0
OD2 L:ASP63 2.4 29.0 1.0
O L:HOH371 2.7 35.7 1.0
OD1 L:ASP63 2.7 24.9 1.0
CG L:ASP63 2.9 26.3 1.0
CG L:ASP46 3.4 24.5 1.0
CD L:GLN49 3.5 27.7 1.0
C L:GLN64 3.5 18.7 1.0
C L:GLY47 3.7 25.7 1.0
NE2 L:GLN49 3.9 27.1 1.0
CB L:ASP46 3.9 23.9 1.0
N L:GLN66 4.1 20.6 1.0
N L:GLN49 4.2 27.2 1.0
CA L:LEU65 4.2 21.4 1.0
N L:GLN64 4.2 17.5 1.0
CA L:ASP48 4.3 28.4 1.0
N L:LEU65 4.3 19.6 1.0
CB L:ASP63 4.3 21.0 1.0
N L:ASP48 4.4 26.8 1.0
OD1 L:ASP46 4.5 25.8 1.0
CA L:GLN64 4.5 18.4 1.0
C L:ASP46 4.5 23.8 1.0
N L:GLY47 4.6 24.3 1.0
C L:LEU65 4.6 22.0 1.0
O L:SER67 4.7 15.5 1.0
O L:ASP46 4.7 23.8 1.0
O L:HOH340 4.8 27.5 1.0
CA L:GLY47 4.8 25.2 1.0
CG L:GLN49 4.8 23.6 1.0
C L:ASP48 4.8 28.5 1.0
C L:ASP63 4.8 20.1 1.0
CA L:ASP46 4.9 23.0 1.0
CB L:GLN49 4.9 26.5 1.0

Calcium binding site 7 out of 7 in 3th4

Go back to Calcium Binding Sites List in 3th4
Calcium binding site 7 out of 7 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 7 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:Ca301

b:14.4
occ:1.00
 OE2 H:GLU80 2.3 18.9 1.0
O H:GLU75 2.3 17.3 1.0
OE2 H:GLU70 2.3 11.8 1.0
O H:ASP72 2.3 11.7 1.0
O H:HOH571 2.4 26.1 1.0
O H:HOH443 2.4 12.7 1.0
OE1 H:GLU70 3.0 17.1 1.0
CD H:GLU70 3.0 17.5 1.0
CD H:GLU80 3.2 21.2 1.0
C H:ASP72 3.5 11.0 1.0
C H:GLU75 3.5 18.6 1.0
OE1 H:GLU80 4.0 20.8 1.0
N H:ASP72 4.0 8.4 1.0
CA H:HIS76 4.1 19.1 1.0
CG H:GLU80 4.1 16.7 1.0
N H:HIS76 4.2 17.1 1.0
N H:LEU73 4.3 8.3 1.0
CA H:LEU73 4.3 11.6 1.0
CA H:ASP72 4.3 10.3 1.0
N H:GLU75 4.3 16.3 1.0
O H:HOH462 4.3 15.4 1.0
O H:HOH475 4.4 28.2 1.0
CA H:GLU75 4.5 19.0 1.0
CG H:GLU70 4.5 17.3 1.0
N H:HIS71 4.6 8.1 1.0
ND1 H:HIS76 4.6 28.1 1.0
N H:ASP77 4.7 18.4 1.0
C H:LEU73 4.7 14.1 1.0
C H:HIS76 4.8 18.7 1.0
CB H:ASP72 4.9 11.5 1.0
O H:HOH417 5.0 29.5 1.0
C H:HIS71 5.0 9.9 1.0

Reference:

K.Vadivel, S.Agah, A.Messer, D.Cascio, S.M.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: Tue Jul 8 16:57:07 2025

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