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Calcium in PDB 1nl1: Bovine Prothrombin Fragment 1 in Complex with Calcium Ion

Enzymatic activity of Bovine Prothrombin Fragment 1 in Complex with Calcium Ion

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

Protein crystallography data

The structure of Bovine Prothrombin Fragment 1 in Complex with Calcium Ion, PDB code: 1nl1 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) 31.60 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.188, 53.443, 128.173, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 25.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Bovine Prothrombin Fragment 1 in Complex with Calcium Ion (pdb code 1nl1). 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 Ion, PDB code: 1nl1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:22.6
occ:1.00
 OE11 A:CGU30 2.2 25.3 1.0
OE21 A:CGU26 2.3 28.9 1.0
O A:HOH394 2.4 38.5 1.0
OE22 A:CGU30 2.4 24.1 1.0
OE12 A:CGU26 2.4 24.7 1.0
O A:HOH458 2.5 26.3 1.0
CD1 A:CGU30 3.2 25.9 1.0
CD2 A:CGU26 3.3 27.6 1.0
CD1 A:CGU26 3.3 26.0 1.0
CD2 A:CGU30 3.3 24.8 1.0
CG A:CGU30 3.5 25.1 1.0
CG A:CGU26 3.6 26.7 1.0
O A:HOH456 4.0 29.5 1.0
O A:HOH457 4.3 24.3 1.0
OE11 A:CGU26 4.4 26.8 1.0
OE12 A:CGU30 4.4 26.2 1.0
OE22 A:CGU26 4.4 28.8 1.0
OE21 A:CGU30 4.5 23.9 1.0
O A:HOH403 4.6 40.6 1.0
CA A:CA202 4.6 25.7 1.0
O A:HOH451 4.9 39.8 1.0
CB A:CGU30 5.0 24.6 1.0

Calcium binding site 2 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:25.7
occ:1.00
 O A:HOH456 2.0 29.5 1.0
OE12 A:CGU8 2.3 26.4 1.0
O A:HOH457 2.4 24.3 1.0
OE21 A:CGU30 2.4 23.9 1.0
OE22 A:CGU30 2.5 24.1 1.0
OE12 A:CGU27 2.5 25.1 1.0
OE21 A:CGU8 2.6 24.2 1.0
CD2 A:CGU30 2.7 24.8 1.0
CD2 A:CGU8 3.3 26.1 1.0
CD1 A:CGU27 3.4 24.0 1.0
CD1 A:CGU8 3.4 27.4 1.0
OE11 A:CGU27 3.5 24.5 1.0
CG A:CGU8 3.7 26.8 1.0
CA A:CA203 3.8 22.8 1.0
CG A:CGU30 4.2 25.1 1.0
OE22 A:CGU8 4.2 27.2 1.0
OE21 A:CGU26 4.2 28.9 1.0
O A:HOH455 4.3 21.3 1.0
O A:HOH392 4.4 31.2 1.0
CB A:CGU8 4.4 27.1 1.0
OE11 A:CGU8 4.5 28.6 1.0
ND2 A:ASN2 4.5 30.5 1.0
CA A:CA201 4.6 22.6 1.0
CD2 A:CGU26 4.7 27.6 1.0
CG A:CGU27 4.8 23.5 1.0
OD1 A:ASN2 4.8 29.7 1.0
O A:HOH391 4.9 45.2 1.0
CD1 A:CGU30 5.0 25.9 1.0

Calcium binding site 3 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:22.8
occ:1.00
 O A:HOH455 2.1 21.3 1.0
OE21 A:CGU8 2.3 24.2 1.0
O A:HOH333 2.3 25.5 1.0
OE11 A:CGU27 2.4 24.5 1.0
O A:HOH313 2.4 15.9 1.0
OE21 A:CGU30 2.6 23.9 1.0
OE11 A:CGU17 2.6 25.6 1.0
OE22 A:CGU8 2.9 27.2 1.0
CD2 A:CGU8 2.9 26.1 1.0
CD1 A:CGU17 3.4 24.9 1.0
CD1 A:CGU27 3.5 24.0 1.0
OE12 A:CGU17 3.6 24.8 1.0
CD2 A:CGU30 3.7 24.8 1.0
CA A:CA204 3.8 23.7 1.0
CA A:CA202 3.8 25.7 1.0
OE12 A:CGU27 4.0 25.1 1.0
CB A:CGU30 4.0 24.6 1.0
CA A:GLY12 4.3 24.7 1.0
CG A:CGU30 4.3 25.1 1.0
O A:HOH325 4.4 25.9 1.0
CG A:CGU8 4.4 26.8 1.0
O A:HOH456 4.6 29.5 1.0
CG A:CGU27 4.6 23.5 1.0
CA A:CGU27 4.7 22.6 1.0
OE22 A:CGU30 4.7 24.1 1.0
O A:CGU27 4.7 22.8 1.0
CB A:CGU27 4.8 23.0 1.0
O A:ARG10 4.8 28.5 1.0
CG A:CGU17 4.8 24.4 1.0
N A:GLY12 4.9 26.1 1.0

Calcium binding site 4 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:23.7
occ:1.00
 OE22 A:CGU8 2.2 27.2 1.0
OD1 A:ASN2 2.4 29.7 1.0
OE21 A:CGU17 2.4 23.4 1.0
OE22 A:CGU27 2.4 22.9 1.0
OE11 A:CGU7 2.5 27.9 1.0
OE11 A:CGU17 2.5 25.6 1.0
OE11 A:CGU27 2.6 24.5 1.0
O A:ALA1 3.0 27.0 1.0
CD2 A:CGU17 3.2 24.6 1.0
CD1 A:CGU27 3.3 24.0 1.0
CD2 A:CGU8 3.3 26.1 1.0
CD2 A:CGU27 3.5 22.6 1.0
CD1 A:CGU7 3.5 28.6 1.0
CD1 A:CGU17 3.6 24.9 1.0
CG A:ASN2 3.6 30.5 1.0
C A:ALA1 3.7 28.0 1.0
CG A:CGU17 3.8 24.4 1.0
CA A:CA203 3.8 22.8 1.0
CG A:CGU27 3.8 23.5 1.0
CA A:CA205 3.9 26.2 1.0
O A:HOH325 3.9 25.9 1.0
OE22 A:CGU17 4.0 25.2 1.0
OE21 A:CGU8 4.1 24.2 1.0
OE12 A:CGU27 4.2 25.1 1.0
OE12 A:CGU7 4.3 27.8 1.0
O A:HOH333 4.3 25.5 1.0
CA A:ASN2 4.3 30.5 1.0
N A:ALA1 4.3 27.2 1.0
N A:ASN2 4.3 28.7 1.0
CG A:CGU8 4.4 26.8 1.0
ND2 A:ASN2 4.4 30.5 1.0
CG A:CGU7 4.5 29.1 1.0
CB A:CGU17 4.5 22.8 1.0
CB A:ASN2 4.5 30.4 1.0
OE21 A:CGU27 4.6 23.2 1.0
CA A:ALA1 4.6 27.3 1.0
OE12 A:CGU17 4.7 24.8 1.0
CB A:CGU27 4.7 23.0 1.0
OE22 A:CGU21 4.9 27.2 1.0

Calcium binding site 5 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:26.2
occ:1.00
 OE22 A:CGU21 2.4 27.2 1.0
O A:ALA1 2.4 27.0 1.0
O A:HOH459 2.4 28.0 1.0
O A:HOH463 2.5 26.9 1.0
OE21 A:CGU17 2.5 23.4 1.0
OE12 A:CGU7 2.5 27.8 1.0
OE11 A:CGU7 2.6 27.9 1.0
OE22 A:CGU17 2.6 25.2 1.0
OE21 A:CGU21 2.8 27.1 1.0
CD1 A:CGU7 2.9 28.6 1.0
CD2 A:CGU17 2.9 24.6 1.0
CD2 A:CGU21 2.9 27.4 1.0
C A:ALA1 3.5 28.0 1.0
CA A:CA204 3.9 23.7 1.0
N A:ALA1 4.0 27.2 1.0
O A:HOH460 4.2 37.7 1.0
CA A:ALA1 4.3 27.3 1.0
CG A:CGU7 4.3 29.1 1.0
CG A:CGU21 4.3 27.7 1.0
CG A:CGU17 4.4 24.4 1.0
N A:ASN2 4.5 28.7 1.0
N A:LYS3 4.6 31.8 0.5
CD A:ARG16 4.6 24.4 1.0
O A:HOH325 4.7 25.9 1.0
CA A:ASN2 4.7 30.5 1.0
CB A:ALA1 4.7 27.4 1.0
N A:LYS3 4.7 33.4 0.6
CB A:CGU7 4.8 29.5 1.0
OE22 A:CGU27 4.9 22.9 1.0
CA A:CGU17 4.9 22.2 1.0
O A:HOH462 5.0 40.4 1.0
OE11 A:CGU17 5.0 25.6 1.0

Calcium binding site 6 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:29.3
occ:0.90
 OE12 A:CGU21 2.2 29.1 1.0
O A:HOH464 2.3 27.7 1.0
O A:HOH460 2.4 37.7 1.0
O A:HOH461 2.5 40.0 1.0
OE21 A:CGU21 2.5 27.1 1.0
O A:HOH462 2.6 40.4 1.0
O A:HOH465 2.6 39.0 1.0
CD1 A:CGU21 3.2 28.6 1.0
CD2 A:CGU21 3.4 27.4 1.0
CG A:CGU21 3.5 27.7 1.0
OE11 A:CGU21 4.4 29.0 1.0
O A:HOH463 4.4 26.9 1.0
O A:HOH459 4.4 28.0 1.0
O A:ARG16 4.5 22.2 1.0
O A:HOH466 4.6 52.1 1.0
O A:HOH467 4.6 46.4 1.0
OE22 A:CGU21 4.6 27.2 1.0
OE12 A:CGU20 4.7 25.1 1.0
CG A:ARG16 4.8 23.3 1.0
CB A:CGU21 5.0 26.7 1.0

Calcium binding site 7 out of 7 in 1nl1

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


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 Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:23.8
occ:0.89
 OE21 A:CGU20 1.7 26.3 1.0
OE21 A:CGU15 1.9 21.1 1.0
O A:HOH469 2.3 30.9 1.0
OE11 A:CGU20 2.3 26.2 1.0
OE12 A:CGU15 2.4 21.8 1.0
CD2 A:CGU20 2.8 27.1 1.0
CD2 A:CGU15 3.0 21.0 1.0
CD1 A:CGU15 3.2 21.6 1.0
O A:HOH443 3.2 43.8 1.0
CD1 A:CGU20 3.2 26.3 1.0
CG A:CGU20 3.3 26.0 1.0
CG A:CGU15 3.3 21.3 1.0
OE22 A:CGU20 3.9 25.6 1.0
OE22 A:CGU15 4.1 21.0 1.0
O A:HOH338 4.2 27.1 1.0
OE11 A:CGU15 4.3 21.7 1.0
NH1 A:ARG55 4.3 26.5 1.0
OE12 A:CGU20 4.4 25.1 1.0
CB A:CGU20 4.8 25.9 1.0
CB A:CGU15 4.8 21.1 1.0
O A:HOH375 4.9 37.0 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: Mon Jul 7 17:34:09 2025

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