Calcium in PDB 1lqv: Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.

The structure of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C., PDB code: 1lqv was solved by V.Oganesyan, N.Oganesyan, S.Terzyan, Q.Dongfeng, Z.Dauter, N.L.Esmon, C.T.Esmon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.00 / 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 (%)	18.9 / 22.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. (pdb code 1lqv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C., PDB code: 1lqv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca34 b:15.5 occ:1.00 OE11 C:CGU7 2.3 14.4 1.0 O C:HOH47 2.3 14.3 1.0 OE22 C:CGU7 2.4 17.5 1.0 OE12 C:CGU26 2.4 16.2 1.0 OE22 C:CGU29 2.4 15.6 1.0 OE2 A:GLU86 2.5 16.0 1.0 OE21 C:CGU29 2.5 14.3 1.0 CD2 C:CGU29 2.8 17.9 1.0 CD1 C:CGU7 3.2 16.1 1.0 CD A:GLU86 3.2 19.4 1.0 CD1 C:CGU26 3.3 18.6 1.0 CD2 C:CGU7 3.4 14.8 1.0 OE11 C:CGU26 3.5 14.4 1.0 OE1 A:GLU86 3.5 18.0 1.0 CG C:CGU7 3.7 15.4 1.0 CA C:CA36 3.9 16.7 1.0 CA C:CA35 4.0 25.5 1.0 O C:HOH70 4.0 23.6 1.0 O A:HOH608 4.0 24.7 1.0 OE12 C:CGU7 4.2 16.0 1.0 OE22 C:CGU25 4.2 17.4 1.0 O C:HOH75 4.2 22.2 1.0 CG C:CGU29 4.3 18.1 1.0 CB C:CGU7 4.4 15.6 1.0 CG A:GLU86 4.4 17.8 1.0 OE21 C:CGU7 4.6 17.6 1.0 O C:HOH56 4.6 19.5 1.0 CD2 C:CGU25 4.7 18.5 1.0 CG C:CGU26 4.8 17.7 1.0 OE12 C:CGU29 4.8 17.8 1.0 ND2 C:ASN2 4.8 19.8 1.0 OD1 C:ASN2 4.8 16.9 1.0 CD1 C:CGU29 4.9 19.9 1.0 CG C:CGU25 4.9 17.9 1.0

Calcium binding site 2 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca35 b:25.5 occ:1.00 OE22 C:CGU29 2.1 15.6 1.0 OE12 C:CGU29 2.1 17.8 1.0 OE11 C:CGU25 2.1 15.3 1.0 OE1 A:GLU86 2.1 18.0 1.0 O A:HOH615 2.1 17.1 1.0 OE22 C:CGU25 2.2 17.4 1.0 CD2 C:CGU29 3.0 17.9 1.0 CD1 C:CGU29 3.0 19.9 1.0 CD1 C:CGU25 3.0 16.1 1.0 CD2 C:CGU25 3.0 18.5 1.0 CD A:GLU86 3.2 19.4 1.0 CG C:CGU25 3.2 17.9 1.0 CG C:CGU29 3.3 18.1 1.0 OE2 A:GLU86 3.5 16.0 1.0 O C:HOH47 3.8 14.3 1.0 CA C:CA34 4.0 15.5 1.0 NH1 A:ARG87 4.0 18.8 1.0 OE21 C:CGU29 4.1 14.3 1.0 O A:HOH703 4.2 31.4 1.0 OE11 C:CGU29 4.2 19.4 1.0 OE12 C:CGU25 4.2 18.5 1.0 O C:HOH89 4.2 31.1 1.0 OE21 C:CGU25 4.2 20.2 1.0 CG A:GLU86 4.4 17.8 1.0 O A:GLU86 4.5 20.7 1.0 O C:HOH104 4.5 46.2 1.0 CB A:GLU86 4.6 17.0 1.0 O C:CGU25 4.6 16.3 1.0 CB C:CGU25 4.7 15.5 1.0 CA A:GLU86 4.8 17.2 1.0 CB C:CGU29 4.8 16.8 1.0

Calcium binding site 3 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca36 b:16.7 occ:1.00 O C:HOH74 2.3 15.6 1.0 O C:HOH56 2.4 19.5 1.0 OE11 C:CGU7 2.4 14.4 1.0 OE11 C:CGU26 2.4 14.4 1.0 O C:HOH57 2.5 19.5 1.0 OE12 C:CGU16 2.5 16.8 1.0 OE21 C:CGU29 2.5 14.3 1.0 OE12 C:CGU7 2.7 16.0 1.0 CD1 C:CGU7 2.9 16.1 1.0 CD1 C:CGU16 3.4 17.4 1.0 OE11 C:CGU16 3.5 17.2 1.0 CD1 C:CGU26 3.5 18.6 1.0 CA C:CA42 3.7 16.5 1.0 CD2 C:CGU29 3.8 17.9 1.0 CA C:CA34 3.9 15.5 1.0 OE12 C:CGU26 4.0 16.2 1.0 CB C:CGU29 4.2 16.8 1.0 CG C:CGU7 4.4 15.4 1.0 CB C:SER11 4.4 19.5 1.0 O A:HOH608 4.4 24.7 1.0 CG C:CGU29 4.5 18.1 1.0 OE12 C:CGU6 4.5 20.7 1.0 CA C:SER11 4.5 15.6 1.0 CG C:CGU26 4.7 17.7 1.0 OE22 C:CGU29 4.7 15.6 1.0 CA C:CGU26 4.7 16.0 1.0 O C:CGU26 4.7 16.4 1.0 CB C:CGU26 4.8 14.3 1.0 CG C:CGU16 4.8 21.3 1.0 OD1 C:ASN2 4.9 16.9 1.0 OE22 C:CGU26 4.9 19.3 1.0

Calcium binding site 4 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca42 b:16.5 occ:1.00 OD1 C:ASN2 2.3 16.9 1.0 OE21 C:CGU16 2.3 17.7 1.0 OE22 C:CGU26 2.4 19.3 1.0 OE12 C:CGU7 2.4 16.0 1.0 OE12 C:CGU16 2.4 16.8 1.0 OE11 C:CGU6 2.6 17.2 1.0 OE11 C:CGU26 2.6 14.4 1.0 O C:ALA1 3.0 19.6 1.0 CD2 C:CGU16 3.2 15.9 1.0 OE12 C:CGU6 3.3 20.7 1.0 CD1 C:CGU6 3.3 18.7 1.0 CD1 C:CGU7 3.4 16.1 1.0 CD1 C:CGU26 3.4 18.6 1.0 CD1 C:CGU16 3.4 17.4 1.0 CD2 C:CGU26 3.5 20.1 1.0 CG C:ASN2 3.5 19.0 1.0 CA C:CA36 3.7 16.7 1.0 C C:ALA1 3.7 17.1 1.0 CG C:CGU16 3.7 21.3 1.0 CA C:CA45 3.8 19.3 1.0 CG C:CGU26 3.9 17.7 1.0 OE22 C:CGU16 4.0 17.2 1.0 OE11 C:CGU7 4.1 14.4 1.0 CG C:CGU7 4.2 15.4 1.0 OE12 C:CGU26 4.2 16.2 1.0 CA C:ASN2 4.2 17.7 1.0 O C:HOH57 4.3 19.5 1.0 N C:ASN2 4.3 18.9 1.0 N C:ALA1 4.3 18.1 1.0 CB C:ASN2 4.4 16.9 1.0 ND2 C:ASN2 4.4 19.8 1.0 CB C:CGU16 4.5 14.5 1.0 OE21 C:CGU26 4.5 19.2 1.0 OE11 C:CGU16 4.6 17.2 1.0 CA C:ALA1 4.6 19.2 1.0 CB C:CGU26 4.7 14.3 1.0 CG C:CGU6 4.8 18.6 1.0 OE21 C:CGU20 4.8 19.6 1.0 CD2 C:CGU7 4.8 14.8 1.0 O C:HOH74 5.0 15.6 1.0

Calcium binding site 5 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca43 b:24.3 occ:0.60 O C:HOH66 1.9 39.1 1.0 O C:HOH80 2.1 28.5 1.0 O C:HOH79 2.1 26.9 1.0 OE22 C:CGU20 2.2 21.3 1.0 O C:HOH63 2.3 39.1 1.0 OE12 C:CGU20 2.4 32.0 1.0 CD2 C:CGU20 3.2 22.3 1.0 CD1 C:CGU20 3.3 24.3 1.0 CG C:CGU20 3.5 20.1 1.0 OE22 C:CGU6 4.2 19.9 1.0 O C:ARG15 4.3 21.3 1.0 OE21 C:CGU20 4.3 19.6 1.0 O C:HOH59 4.4 20.7 1.0 OE11 C:CGU20 4.5 26.3 1.0 CG C:ARG15 4.5 30.8 1.0 CA C:CA45 4.5 19.3 1.0 OE11 C:CGU19 4.6 30.2 1.0

Calcium binding site 6 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca45 b:19.3 occ:1.00 O C:ALA1 2.3 19.6 1.0 OE21 C:CGU20 2.3 19.6 1.0 OE22 C:CGU6 2.3 19.9 1.0 OE21 C:CGU16 2.4 17.7 1.0 O C:HOH59 2.4 20.7 1.0 OE11 C:CGU6 2.4 17.2 1.0 OE22 C:CGU16 2.5 17.2 1.0 OE22 C:CGU20 2.6 21.3 1.0 CD2 C:CGU20 2.8 22.3 1.0 CD2 C:CGU16 2.8 15.9 1.0 CD1 C:CGU6 3.1 18.7 1.0 CD2 C:CGU6 3.4 18.9 1.0 C C:ALA1 3.5 17.1 1.0 CG C:CGU6 3.7 18.6 1.0 CA C:CA42 3.8 16.5 1.0 OE12 C:CGU6 3.8 20.7 1.0 O C:HOH80 4.0 28.5 1.0 N C:ALA1 4.2 18.1 1.0 CG C:CGU20 4.3 20.1 1.0 CA C:ALA1 4.3 19.2 1.0 CG C:CGU16 4.3 21.3 1.0 N C:ASN2 4.4 18.9 1.0 CA C:ASN2 4.4 17.7 1.0 CA C:CA43 4.5 24.3 0.6 OE21 C:CGU6 4.5 18.2 1.0 O C:HOH63 4.6 39.1 1.0 O C:ARG15 4.7 21.3 1.0 CB C:CGU6 4.7 17.8 1.0 NE C:ARG15 4.7 23.2 1.0 CB C:ALA1 4.7 20.7 1.0 CA C:CGU16 4.8 19.4 1.0 OE22 C:CGU26 4.8 19.3 1.0 OG C:SER3 4.9 24.3 1.0 N C:SER3 4.9 18.2 1.0 OE12 C:CGU16 4.9 16.8 1.0 CG C:ARG15 5.0 30.8 1.0 OD1 C:ASN2 5.0 16.9 1.0

Calcium binding site 7 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca46 b:29.1 occ:0.50 OE21 C:CGU14 2.1 30.7 1.0 OE22 C:CGU19 2.1 26.9 1.0 O C:HOH67 2.1 34.3 1.0 OE12 C:CGU14 2.1 35.2 1.0 OE12 C:CGU19 2.2 32.3 1.0 O C:HOH99 2.3 39.0 1.0 CD2 C:CGU14 3.0 25.2 1.0 CD1 C:CGU14 3.0 34.9 1.0 CD1 C:CGU19 3.0 27.3 1.0 CD2 C:CGU19 3.0 29.3 1.0 CG C:CGU14 3.2 29.8 1.0 CG C:CGU19 3.3 27.3 1.0 OE22 C:CGU14 4.1 33.8 1.0 OE11 C:CGU19 4.2 30.2 1.0 OE11 C:CGU14 4.2 39.2 1.0 OE21 C:CGU19 4.2 35.1 1.0 CB C:CGU14 4.7 23.7 1.0 CB C:CGU19 4.8 25.2 1.0 O C:CGU14 4.9 22.4 1.0

Calcium binding site 8 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca37 b:20.3 occ:1.00 O D:HOH54 2.3 23.1 1.0 OE11 D:CGU7 2.3 21.0 1.0 OE2 B:GLU86 2.3 22.8 1.0 OE22 D:CGU7 2.4 21.9 1.0 OE12 D:CGU26 2.4 21.9 1.0 OE22 D:CGU29 2.5 19.0 1.0 OE21 D:CGU29 2.5 22.9 1.0 CD2 D:CGU29 2.8 17.3 1.0 CD1 D:CGU7 3.1 20.0 1.0 CD B:GLU86 3.2 21.7 1.0 CD1 D:CGU26 3.3 20.6 1.0 CD2 D:CGU7 3.3 21.5 1.0 OE11 D:CGU26 3.5 20.1 1.0 OE1 B:GLU86 3.6 20.2 1.0 CG D:CGU7 3.6 21.2 1.0 CA D:CA41 3.8 20.5 1.0 CA D:CA40 4.1 32.6 1.0 OE12 D:CGU7 4.1 21.4 1.0 O B:HOH666 4.1 31.7 1.0 O D:HOH49 4.1 26.3 1.0 O D:HOH76 4.2 31.4 1.0 CG D:CGU29 4.3 23.2 1.0 OE22 D:CGU25 4.3 20.9 1.0 CB D:CGU7 4.4 23.1 1.0 CG B:GLU86 4.5 23.0 1.0 OE21 D:CGU7 4.5 25.6 1.0 O D:HOH56 4.5 22.0 1.0 ND2 D:ASN2 4.7 25.7 1.0 CG D:CGU26 4.7 18.4 1.0 OD1 D:ASN2 4.8 22.2 1.0 CD2 D:CGU25 4.8 21.5 1.0 OE12 D:CGU29 4.9 20.1 1.0 CD1 D:CGU29 5.0 25.6 1.0

Calcium binding site 9 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca38 b:21.7 occ:1.00 O D:ALA1 2.3 22.9 1.0 OE21 D:CGU20 2.3 26.1 1.0 OE21 D:CGU16 2.4 21.0 1.0 OE22 D:CGU6 2.4 24.9 1.0 O D:HOH77 2.4 23.6 1.0 OE11 D:CGU6 2.4 22.4 1.0 OE22 D:CGU16 2.5 21.4 1.0 OE22 D:CGU20 2.7 24.3 1.0 CD2 D:CGU16 2.7 21.4 1.0 CD2 D:CGU20 2.8 21.5 1.0 CD1 D:CGU6 3.1 29.2 1.0 CD2 D:CGU6 3.4 32.9 1.0 C D:ALA1 3.4 21.1 1.0 CG D:CGU6 3.6 26.9 1.0 CA D:CA47 3.7 20.1 1.0 OE12 D:CGU6 3.8 26.9 1.0 O D:HOH75 4.0 33.7 1.0 N D:ALA1 4.1 19.4 1.0 CG D:CGU16 4.2 21.6 1.0 CA D:ALA1 4.3 18.2 1.0 CG D:CGU20 4.3 23.5 1.0 N D:ASN2 4.3 21.0 1.0 CA D:ASN2 4.4 22.2 1.0 O D:HOH70 4.5 30.3 1.0 OE21 D:CGU6 4.6 28.6 1.0 CA D:CA44 4.6 36.5 1.0 O D:ARG15 4.7 27.3 1.0 CB D:CGU6 4.7 22.6 1.0 NE D:ARG15 4.7 27.3 1.0 CB D:ALA1 4.7 24.0 1.0 CA D:CGU16 4.8 21.7 1.0 OE22 D:CGU26 4.8 19.9 1.0 N D:SER3 4.9 21.9 1.0 O D:HOH78 4.9 50.4 1.0 OE12 D:CGU16 4.9 22.4 1.0 OD1 D:ASN2 4.9 22.2 1.0 CB D:CGU16 5.0 19.3 1.0

Calcium binding site 10 out of 14 in the Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of the Endothelial Protein C Receptor with Phospholipid in the Groove in Complex with Gla Domain of Protein C. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca39 b:26.7 occ:0.40 OE22 D:CGU14 2.0 29.5 1.0 OE11 D:CGU14 2.1 32.4 1.0 O D:HOH87 2.1 39.0 1.0 OE21 D:CGU19 2.1 39.2 1.0 O D:HOH68 2.2 28.2 0.5 OE11 D:CGU19 2.2 39.1 1.0 CD2 D:CGU14 2.9 26.9 1.0 CD1 D:CGU14 2.9 31.8 1.0 CD2 D:CGU19 3.0 37.9 1.0 CG D:CGU14 3.1 30.3 1.0 CD1 D:CGU19 3.1 38.0 1.0 CG D:CGU19 3.3 36.5 1.0 OE21 D:CGU14 4.1 31.8 1.0 OE12 D:CGU14 4.1 28.5 1.0 OE22 D:CGU19 4.2 30.4 1.0 O D:HOH84 4.2 34.0 1.0 OE12 D:CGU19 4.3 35.1 1.0 CB D:CGU14 4.6 24.4 1.0 CB D:CGU19 4.8 35.6 1.0 O D:CGU14 4.9 27.8 1.0

V.Oganesyan, N.Oganesyan, S.Terzyan, D.Qu, Z.Dauter, N.L.Esmon, C.T.Esmon. The Crystal Structure of the Endothelial Protein C Receptor and A Bound Phospholipid. J.Biol.Chem. V. 277 24851 2002.
ISSN: ISSN 0021-9258
PubMed: 12034704
DOI: 10.1074/JBC.C200163200