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Calcium in PDB 2pf2: The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1

Protein crystallography data

The structure of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1, PDB code: 2pf2 was solved by M.Soriano-Garcia, K.Padmanabhan, A.M.De Vos, A.Tulinsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.390, 53.880, 129.640, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 (pdb code 2pf2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1, PDB code: 2pf2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2pf2

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Calcium binding site 1 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca171

b:24.8
occ:1.00
 OE12 A:CGU26 2.3 26.0 1.0
OE11 A:CGU30 2.4 25.0 1.0
OE21 A:CGU26 2.5 26.4 1.0
OE21 A:CGU30 2.5 25.0 1.0
CD1 A:CGU30 3.4 24.8 1.0
CD2 A:CGU26 3.5 25.9 1.0
CD2 A:CGU30 3.5 23.1 1.0
CD1 A:CGU26 3.5 26.6 1.0
CG A:CGU30 3.7 22.1 1.0
CG A:CGU26 4.0 26.2 1.0
OE12 A:CGU30 4.4 22.7 1.0
OE11 A:CGU26 4.4 27.3 1.0
CA A:CA172 4.4 25.6 1.0
OE22 A:CGU26 4.5 27.0 1.0
O A:HOH266 4.5 24.1 0.7
OE22 A:CGU30 4.7 25.1 1.0
O A:CGU26 4.9 24.6 1.0

Calcium binding site 2 out of 7 in 2pf2

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Calcium binding site 2 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca172

b:25.6
occ:1.00
 OE21 A:CGU30 2.4 25.0 1.0
OE22 A:CGU30 2.5 25.1 1.0
OE22 A:CGU8 2.6 27.2 1.0
O A:HOH266 2.7 24.1 0.7
OE12 A:CGU8 2.7 27.3 1.0
CD2 A:CGU30 2.7 23.1 1.0
OE12 A:CGU27 2.8 24.5 1.0
CD2 A:CGU8 3.2 27.5 1.0
CG A:CGU8 3.3 26.8 1.0
CD1 A:CGU8 3.5 27.9 1.0
CD1 A:CGU27 3.6 22.6 1.0
OE11 A:CGU27 3.6 23.8 1.0
CA A:CA173 4.0 26.4 1.0
OE21 A:CGU26 4.0 26.4 1.0
OE21 A:CGU8 4.2 25.6 1.0
CG A:CGU30 4.2 22.1 1.0
ND2 A:ASN2 4.3 22.0 1.0
CA A:CA171 4.4 24.8 1.0
OE11 A:CGU8 4.6 26.7 1.0
O A:HOH273 4.6 17.1 0.6
CB A:CGU8 4.7 29.8 1.0
O A:HOH237 4.7 28.0 1.0
OD1 A:ASN2 4.7 22.8 1.0
CD1 A:CGU30 4.8 24.8 1.0
CD2 A:CGU26 4.9 25.9 1.0
OE11 A:CGU30 4.9 25.0 1.0
CG A:CGU27 5.0 21.9 1.0
CG A:ASN2 5.0 24.0 1.0

Calcium binding site 3 out of 7 in 2pf2

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Calcium binding site 3 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca173

b:26.4
occ:1.00
 O A:HOH231 2.4 22.3 1.0
OE22 A:CGU8 2.4 27.2 1.0
O A:HOH273 2.4 17.1 0.6
OE11 A:CGU17 2.5 27.6 1.0
OE22 A:CGU30 2.6 25.1 1.0
OE12 A:CGU17 2.7 28.1 1.0
OE11 A:CGU27 2.7 23.8 1.0
CD1 A:CGU17 2.9 27.4 1.0
CD2 A:CGU8 3.4 27.5 1.0
OE21 A:CGU8 3.6 25.6 1.0
CD2 A:CGU30 3.7 23.1 1.0
CD1 A:CGU27 3.8 22.6 1.0
CA A:GLY12 3.8 25.1 1.0
CA A:CA174 3.8 23.4 1.0
CA A:CA172 4.0 25.6 1.0
CB A:CGU30 4.0 22.4 1.0
CG A:CGU17 4.2 27.5 1.0
OE12 A:CGU27 4.4 24.5 1.0
O A:CGU27 4.4 17.4 1.0
CG A:CGU30 4.4 22.1 1.0
CA A:CGU27 4.5 20.3 1.0
N A:GLY12 4.6 27.9 1.0
OE21 A:CGU30 4.6 25.0 1.0
O A:HOH190 4.7 15.1 0.7
CG A:CGU8 4.7 26.8 1.0
CB A:CGU27 4.8 21.4 1.0
CD2 A:CGU17 4.9 28.6 1.0
CG A:CGU27 4.9 21.9 1.0
OE21 A:CGU17 4.9 27.1 1.0
OD1 A:ASN2 5.0 22.8 1.0
C A:CGU27 5.0 20.1 1.0
O A:ARG10 5.0 33.2 1.0

Calcium binding site 4 out of 7 in 2pf2

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Calcium binding site 4 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca174

b:23.4
occ:1.00
 OE21 A:CGU17 2.0 27.1 1.0
OD1 A:ASN2 2.1 22.8 1.0
OE22 A:CGU27 2.6 22.5 1.0
OE11 A:CGU27 2.6 23.8 1.0
OE21 A:CGU8 2.7 25.6 1.0
OE11 A:CGU7 2.8 28.6 1.0
CD2 A:CGU17 2.9 28.6 1.0
OE11 A:CGU17 3.1 27.6 1.0
CG A:ASN2 3.2 24.0 1.0
CD1 A:CGU27 3.3 22.6 1.0
N A:ASN2 3.3 25.8 1.0
CG A:CGU17 3.3 27.5 1.0
CD1 A:CGU17 3.5 27.4 1.0
CD1 A:CGU7 3.6 29.8 1.0
CD2 A:CGU27 3.6 22.7 1.0
CD2 A:CGU8 3.6 27.5 1.0
N A:ALA1 3.8 25.0 1.0
CA A:CA175 3.8 27.9 1.0
CA A:CA173 3.8 26.4 1.0
CA A:ASN2 3.9 26.5 1.0
OE22 A:CGU17 3.9 29.7 1.0
OE22 A:CGU8 4.0 27.2 1.0
CG A:CGU27 4.0 21.9 1.0
OE12 A:CGU7 4.1 28.5 1.0
CB A:ASN2 4.1 23.8 1.0
C A:ALA1 4.1 25.1 1.0
OE12 A:CGU27 4.1 24.5 1.0
ND2 A:ASN2 4.2 22.0 1.0
O A:HOH190 4.2 15.1 0.7
O A:HOH231 4.3 22.3 1.0
OE12 A:CGU17 4.4 28.1 1.0
CA A:ALA1 4.5 25.0 1.0
OE12 A:CGU8 4.6 27.3 1.0
OE21 A:CGU27 4.7 21.6 1.0
CB A:CGU27 4.7 21.4 1.0
CB A:CGU17 4.7 24.7 1.0
OE22 A:CGU7 4.8 32.8 1.0
CG A:CGU7 4.8 31.8 1.0
CG A:CGU8 4.9 26.8 1.0
CD1 A:CGU8 5.0 27.9 1.0

Calcium binding site 5 out of 7 in 2pf2

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Calcium binding site 5 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca175

b:27.9
occ:1.00
 OE12 A:CGU7 2.5 28.5 1.0
OE11 A:CGU7 2.5 28.6 1.0
OE21 A:CGU17 2.5 27.1 1.0
OE22 A:CGU21 2.8 27.7 1.0
CD1 A:CGU7 2.8 29.8 1.0
N A:ALA1 2.8 25.0 1.0
OE22 A:CGU17 2.9 29.7 1.0
CD2 A:CGU17 3.0 28.6 1.0
O A:HOH239 3.1 26.7 0.8
O A:HOH224 3.2 21.8 0.8
N A:ASN2 3.3 25.8 1.0
CD2 A:CGU21 3.7 30.4 1.0
CA A:CA174 3.8 23.4 1.0
CA A:ALA1 3.8 25.0 1.0
C A:ALA1 4.0 25.1 1.0
OE21 A:CGU21 4.0 32.6 1.0
CG A:CGU7 4.2 31.8 1.0
CB A:ALA1 4.3 25.5 1.0
CA A:ASN2 4.3 26.5 1.0
N A:LYS3 4.4 31.7 1.0
CG A:CGU17 4.5 27.5 1.0
O A:HOH190 4.7 15.1 0.7
CB A:CGU7 4.7 31.5 1.0
CD A:ARG16 4.8 21.5 1.0
OE22 A:CGU27 4.8 22.5 1.0
C A:ASN2 4.8 28.1 1.0
CA A:CGU17 4.9 19.8 1.0
OD1 A:ASN2 4.9 22.8 1.0

Calcium binding site 6 out of 7 in 2pf2

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Calcium binding site 6 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca176

b:34.6
occ:0.90
 OE21 A:CGU21 2.4 32.6 1.0
OE12 A:CGU20 2.5 32.3 1.0
OE12 A:CGU21 2.7 34.1 1.0
CD2 A:CGU21 2.8 30.4 1.0
CG A:CGU21 3.2 31.6 1.0
CD1 A:CGU21 3.3 32.5 1.0
OE22 A:CGU21 3.8 27.7 1.0
CD1 A:CGU20 3.8 28.5 1.0
O A:HOH239 3.9 26.7 0.8
O A:ARG16 4.4 20.9 1.0
CG A:CGU20 4.5 26.2 1.0
OE11 A:CGU21 4.5 35.1 1.0
O A:HOH224 4.6 21.8 0.8
CG A:ARG16 4.7 21.2 1.0
CB A:CGU21 4.7 28.3 1.0
OE11 A:CGU20 4.7 30.0 1.0
O A:CGU20 4.8 27.9 1.0
CB A:CGU20 4.9 25.7 1.0

Calcium binding site 7 out of 7 in 2pf2

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Calcium binding site 7 out of 7 in the The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Ca+2 Ion and Membrane Binding Structure of the Gla Domain of Ca- Prothrombin Fragment 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca177

b:26.3
occ:0.89
 OE21 A:CGU20 2.4 25.8 1.0
OE22 A:CGU20 2.7 24.1 1.0
OE22 A:CGU15 2.8 28.0 1.0
CD2 A:CGU20 2.9 24.8 1.0
CD2 A:CGU15 3.6 28.1 1.0
OE21 A:CGU15 4.2 29.2 1.0
OE11 A:CGU20 4.3 30.0 1.0
CG A:CGU15 4.4 28.6 1.0
CG A:CGU20 4.4 26.2 1.0
NH1 A:ARG55 4.6 32.6 1.0
NH2 A:ARG55 4.6 33.1 1.0
CB A:CGU15 4.8 23.0 1.0
CD1 A:CGU20 4.8 28.5 1.0
CZ A:ARG55 4.9 33.6 1.0

Reference:

M.Soriano-Garcia, K.Padmanabhan, A.M.De Vos, A.Tulinsky. The CA2+ Ion and Membrane Binding Structure of the Gla Domain of Ca-Prothrombin Fragment 1. Biochemistry V. 31 2554 1992.
ISSN: ISSN 0006-2960
PubMed: 1547238
DOI: 10.1021/BI00124A016
Page generated: Sat Dec 12 03:49:53 2020

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