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Calcium in PDB 1nl2: Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine

Enzymatic activity of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine

All present enzymatic activity of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine:
3.4.21.5;

Protein crystallography data

The structure of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine, PDB code: 1nl2 was solved by M.Huang, G.Huang, B.Furie, B.Seaton, B.C.Furie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.98 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.894, 53.217, 128.959, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 27.4

Other elements in 1nl2:

The structure of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine (pdb code 1nl2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine, PDB code: 1nl2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1nl2

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Calcium binding site 1 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:33.9
occ:1.00
 OE11 A:CGU30 2.2 42.7 1.0
OE21 A:CGU26 2.4 39.8 1.0
OE12 A:CGU26 2.4 48.3 1.0
OE22 A:CGU30 2.5 39.6 1.0
CD1 A:CGU30 3.2 43.2 1.0
CD1 A:CGU26 3.4 43.4 1.0
CD2 A:CGU30 3.4 33.5 1.0
CD2 A:CGU26 3.4 46.3 1.0
CG A:CGU30 3.6 36.4 1.0
CG A:CGU26 3.7 44.7 1.0
O A:HOH507 4.0 33.8 1.0
OE12 A:CGU30 4.3 39.7 1.0
OE11 A:CGU26 4.4 53.6 1.0
OE21 A:CGU30 4.5 37.7 1.0
O A:HOH504 4.5 27.4 1.0
OE22 A:CGU26 4.6 56.3 1.0
CA A:CA202 4.8 44.3 1.0

Calcium binding site 2 out of 7 in 1nl2

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Calcium binding site 2 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:44.3
occ:1.00
 O A:HOH507 2.0 33.8 1.0
OE12 A:CGU27 2.5 31.4 1.0
OE21 A:CGU30 2.5 37.7 1.0
OE12 A:CGU8 2.5 57.2 1.0
O A:HOH504 2.5 27.4 1.0
OE21 A:CGU8 2.6 42.0 1.0
OE22 A:CGU30 2.7 39.6 1.0
CD2 A:CGU30 2.9 33.5 1.0
CD2 A:CGU8 3.1 44.9 1.0
CD1 A:CGU27 3.3 40.8 1.0
CD1 A:CGU8 3.3 60.1 1.0
OE11 A:CGU27 3.4 32.6 1.0
CG A:CGU8 3.4 50.9 1.0
CA A:CA203 3.8 38.5 1.0
OE22 A:CGU8 3.9 33.1 1.0
ND2 A:ASN2 4.3 38.1 1.0
O A:HOH514 4.3 33.7 1.0
OE21 A:CGU26 4.4 39.8 1.0
CG A:CGU30 4.4 36.4 1.0
OE11 A:CGU8 4.4 66.0 1.0
OD1 A:ASN2 4.5 54.6 1.0
CB A:CGU8 4.5 51.2 1.0
CG A:CGU27 4.7 35.2 1.0
CD2 A:CGU26 4.7 46.3 1.0
CG A:ASN2 4.8 42.5 1.0
CA A:CA201 4.8 33.9 1.0

Calcium binding site 3 out of 7 in 1nl2

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Calcium binding site 3 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:38.5
occ:1.00
 OE11 A:CGU27 2.1 32.6 1.0
O A:HOH514 2.1 33.7 1.0
OE21 A:CGU8 2.3 42.0 1.0
OE11 A:CGU17 2.4 43.5 1.0
O A:HOH519 2.4 38.2 1.0
OE21 A:CGU30 2.5 37.7 1.0
O A:HOH522 2.6 35.0 1.0
CD2 A:CGU8 3.0 44.9 1.0
OE22 A:CGU8 3.0 33.1 1.0
CD1 A:CGU27 3.2 40.8 1.0
CD1 A:CGU17 3.3 34.0 1.0
OE12 A:CGU17 3.6 34.8 1.0
CA A:CA204 3.6 41.6 1.0
CD2 A:CGU30 3.7 33.5 1.0
CA A:CA202 3.8 44.3 1.0
OE12 A:CGU27 3.9 31.4 1.0
CB A:CGU30 4.1 38.9 1.0
CG A:CGU30 4.3 36.4 1.0
CG A:CGU27 4.4 35.2 1.0
CG A:CGU8 4.4 50.9 1.0
CA A:GLY12 4.5 47.4 1.0
O A:HOH511 4.5 33.2 1.0
CG A:CGU17 4.6 28.0 1.0
O A:HOH507 4.6 33.8 1.0
OE22 A:CGU30 4.7 39.6 1.0
CA A:CGU27 4.7 43.1 1.0
O A:CGU27 4.8 41.6 1.0
OD1 A:ASN2 4.8 54.6 1.0
CB A:CGU27 4.9 39.6 1.0
O A:ARG10 4.9 51.9 1.0
N A:GLY12 4.9 54.0 1.0

Calcium binding site 4 out of 7 in 1nl2

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Calcium binding site 4 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:41.6
occ:1.00
 OE22 A:CGU8 2.3 33.1 1.0
OE22 A:CGU27 2.3 48.3 1.0
OE21 A:CGU17 2.4 43.0 1.0
OD1 A:ASN2 2.4 54.6 1.0
OE11 A:CGU17 2.5 43.5 1.0
OE11 A:CGU27 2.6 32.6 1.0
OE11 A:CGU7 2.6 46.0 1.0
CD2 A:CGU17 3.0 31.5 1.0
O A:ALA1 3.2 47.3 1.0
CD1 A:CGU27 3.2 40.8 1.0
CD2 A:CGU27 3.3 51.8 1.0
CD1 A:CGU17 3.3 34.0 1.0
CG A:CGU17 3.4 28.0 1.0
CD2 A:CGU8 3.4 44.9 1.0
CD1 A:CGU7 3.5 33.9 1.0
CG A:ASN2 3.5 42.5 1.0
CG A:CGU27 3.6 35.2 1.0
CA A:CA203 3.6 38.5 1.0
C A:ALA1 3.9 40.9 1.0
CA A:CA205 3.9 42.5 1.0
O A:HOH511 3.9 33.2 1.0
OE22 A:CGU17 4.0 43.6 1.0
OE12 A:CGU7 4.0 51.0 1.0
OE21 A:CGU8 4.1 42.0 1.0
OE12 A:CGU27 4.1 31.4 1.0
ND2 A:ASN2 4.3 38.1 1.0
CA A:ASN2 4.3 51.6 1.0
CB A:CGU17 4.4 36.9 1.0
N A:ASN2 4.4 51.0 1.0
OE21 A:CGU27 4.4 38.8 1.0
N A:ALA1 4.5 32.2 1.0
OE12 A:CGU17 4.5 34.8 1.0
CG A:CGU8 4.5 50.9 1.0
CB A:ASN2 4.5 46.6 1.0
CG A:CGU7 4.6 51.7 1.0
O A:HOH519 4.6 38.2 1.0
CB A:CGU27 4.8 39.6 1.0
CA A:ALA1 4.8 40.6 1.0

Calcium binding site 5 out of 7 in 1nl2

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Calcium binding site 5 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:42.5
occ:1.00
 OE21 A:CGU17 2.3 43.0 1.0
O A:ALA1 2.3 47.3 1.0
O A:HOH527 2.4 34.5 1.0
OE12 A:CGU7 2.5 51.0 1.0
OE11 A:CGU7 2.5 46.0 1.0
OE11 A:CGU21 2.5 41.1 1.0
OE22 A:CGU17 2.5 43.6 1.0
CD2 A:CGU17 2.7 31.5 1.0
CD1 A:CGU7 2.7 33.9 1.0
OE12 A:CGU21 3.0 57.0 1.0
OT2 A:LPS451 3.1 57.2 0.7
CD1 A:CGU21 3.1 38.8 1.0
C A:ALA1 3.5 40.9 1.0
CA A:CA204 3.9 41.6 1.0
C A:LPS451 4.1 66.9 0.7
CG A:CGU7 4.1 51.7 1.0
O12 A:LPS451 4.1 75.5 0.7
N A:ALA1 4.2 32.2 1.0
CG A:CGU17 4.2 28.0 1.0
CA A:ALA1 4.3 40.6 1.0
C12 A:LPS451 4.3 72.2 0.7
N A:ASN2 4.5 51.0 1.0
O A:HOH511 4.5 33.2 1.0
OE22 A:CGU27 4.6 48.3 1.0
CG A:CGU21 4.6 45.3 1.0
CA A:ASN2 4.6 51.6 1.0
O14 A:LPS451 4.6 69.7 0.7
CB A:CGU7 4.6 46.3 1.0
C11 A:LPS451 4.7 69.8 0.7
CB A:ALA1 4.7 33.3 1.0
CD A:ARG16 4.8 44.9 1.0
CA A:CGU17 4.9 32.5 1.0
N A:LYS3 4.9 49.9 1.0

Calcium binding site 6 out of 7 in 1nl2

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Calcium binding site 6 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:68.7
occ:1.00
 OT1 A:LPS451 2.2 65.8 0.7
OE22 A:CGU21 2.4 62.0 1.0
OE12 A:CGU21 2.4 57.0 1.0
C A:LPS451 2.6 66.9 0.7
O A:HOH557 2.7 57.9 1.0
OT2 A:LPS451 3.2 57.2 0.7
C12 A:LPS451 3.3 72.2 0.7
N A:LPS451 3.3 67.3 0.7
O A:HOH550 3.3 50.9 1.0
CD2 A:CGU21 3.4 55.9 1.0
CD1 A:CGU21 3.4 38.8 1.0
CG A:CGU21 3.6 45.3 1.0
OE21 A:CGU21 4.5 62.8 1.0
OE11 A:CGU21 4.6 41.1 1.0
O A:HOH527 4.7 34.5 1.0
O A:ARG16 4.8 35.2 1.0
OE12 A:CGU20 4.8 50.6 1.0
C11 A:LPS451 4.8 69.8 0.7
CG A:ARG16 4.9 38.7 1.0

Calcium binding site 7 out of 7 in 1nl2

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Calcium binding site 7 out of 7 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:42.8
occ:1.00
 OE21 A:CGU15 2.0 34.4 1.0
OE11 A:CGU20 2.3 48.2 1.0
OE12 A:CGU15 2.4 42.4 1.0
OE21 A:CGU20 2.4 51.0 1.0
O A:HOH537 2.8 42.3 1.0
CD2 A:CGU15 3.0 30.4 1.0
CD1 A:CGU15 3.2 28.5 1.0
CD1 A:CGU20 3.3 50.2 1.0
CD2 A:CGU20 3.3 52.6 1.0
CG A:CGU15 3.4 32.6 1.0
CG A:CGU20 3.5 40.5 1.0
O A:HOH530 4.1 39.8 1.0
NH1 A:ARG55 4.2 31.6 1.0
OE22 A:CGU15 4.2 34.8 1.0
OE11 A:CGU15 4.3 38.8 1.0
OE12 A:CGU20 4.4 50.6 1.0
OE22 A:CGU20 4.5 37.5 1.0
CB A:CGU15 4.8 31.8 1.0
CB A:CGU20 5.0 46.0 1.0

Reference:

M.Huang, A.C.Rigby, X.Morelli, M.A.Grant, G.Huang, B.Furie, B.Seaton, B.C.Furie. Structural Basis of Membrane Binding By Gla Domains of Vitamin K-Dependent Proteins. Nat.Struct.Biol. V. 10 751 2003.
ISSN: ISSN 1072-8368
PubMed: 12923575
DOI: 10.1038/NSB971
Page generated: Thu Jul 11 12:53:08 2024

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