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Calcium in PDB 4o03: Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167

Enzymatic activity of Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167

All present enzymatic activity of Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167, PDB code: 4o03 was solved by N.Pozzi, Z.Chen, D.B.Shropshire, L.A.Pelc, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.75 / 3.38
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.459, 89.431, 87.982, 90.00, 116.36, 90.00
R / Rfree (%) 23.3 / 27.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167 (pdb code 4o03). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167, PDB code: 4o03:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4o03

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Calcium binding site 1 out of 5 in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167


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 CA2+ Bound Prothrombin Deletion Mutant Residues 146-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:0.5
occ:1.00
 OE22 A:CGU29 2.1 0.2 1.0
OE12 A:CGU26 2.3 0.9 1.0
OE21 A:CGU29 2.4 0.0 1.0
OE12 A:CGU7 2.4 99.1 1.0
OE21 A:CGU7 2.5 0.5 1.0
CD2 A:CGU29 2.6 0.4 1.0
CD1 A:CGU7 3.4 99.2 1.0
CD1 A:CGU26 3.4 0.6 1.0
CD2 A:CGU7 3.5 99.4 1.0
CG A:CGU7 3.8 99.1 1.0
CA A:CA603 3.8 86.9 1.0
OE11 A:CGU26 3.8 0.6 1.0
CG A:CGU29 4.1 0.1 1.0
OD1 A:ASN2 4.2 96.5 1.0
OE21 A:CGU25 4.3 0.9 1.0
CB A:CGU7 4.3 99.4 1.0
OE11 A:CGU7 4.5 99.7 1.0
OE22 A:CGU7 4.6 98.9 1.0
CG A:CGU26 4.7 0.6 1.0
CD1 A:CGU29 4.8 0.2 1.0
CB A:CGU29 4.9 0.7 1.0
OE11 A:CGU29 5.0 0.4 1.0

Calcium binding site 2 out of 5 in 4o03

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Calcium binding site 2 out of 5 in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167


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 CA2+ Bound Prothrombin Deletion Mutant Residues 146-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:86.9
occ:1.00
 OE11 A:CGU26 2.2 0.6 1.0
OE21 A:CGU29 2.4 0.0 1.0
OE12 A:CGU16 2.7 97.2 1.0
OE21 A:CGU7 2.8 0.5 1.0
CD1 A:CGU26 3.1 0.6 1.0
OE12 A:CGU26 3.4 0.9 1.0
CD2 A:CGU29 3.5 0.4 1.0
CD1 A:CGU16 3.6 98.2 1.0
OE11 A:CGU16 3.7 97.5 1.0
CD2 A:CGU7 3.8 99.4 1.0
CA A:CA602 3.8 0.5 1.0
CB A:CGU29 3.9 0.7 1.0
CA A:GLY11 3.9 0.7 1.0
OE22 A:CGU7 4.0 98.9 1.0
O A:CGU26 4.1 0.1 1.0
CA A:CA604 4.2 98.0 1.0
CG A:CGU29 4.3 0.1 1.0
CA A:CGU26 4.4 0.1 1.0
CG A:CGU26 4.4 0.6 1.0
OE22 A:CGU29 4.4 0.2 1.0
N A:GLY11 4.4 0.6 1.0
OE22 A:CGU26 4.6 0.3 1.0
CB A:CGU26 4.7 0.6 1.0
C A:CGU26 4.7 0.3 1.0
O A:ARG9 4.9 0.9 1.0
CG A:CGU16 5.0 98.9 1.0
CD2 A:CGU26 5.0 0.2 1.0

Calcium binding site 3 out of 5 in 4o03

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Calcium binding site 3 out of 5 in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167


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 CA2+ Bound Prothrombin Deletion Mutant Residues 146-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:98.0
occ:1.00
 O A:ALA1 2.3 96.4 1.0
OE11 A:CGU6 2.3 94.5 1.0
OE21 A:CGU16 2.4 95.0 1.0
CD2 A:CGU16 2.7 97.2 1.0
OE22 A:CGU7 2.8 98.9 1.0
OE11 A:CGU26 3.1 0.6 1.0
OE22 A:CGU26 3.1 0.3 1.0
OE22 A:CGU16 3.2 96.6 1.0
CD1 A:CGU6 3.2 96.9 1.0
CD1 A:CGU16 3.2 98.2 1.0
OD1 A:ASN2 3.3 96.5 1.0
OE11 A:CGU16 3.4 97.5 1.0
CG A:CGU16 3.5 98.9 1.0
C A:ALA1 3.5 96.5 1.0
OE12 A:CGU16 3.5 97.2 1.0
CD2 A:CGU7 3.6 99.4 1.0
CD2 A:CGU26 3.6 0.2 1.0
CA A:CA605 3.6 0.3 1.0
CD1 A:CGU26 3.7 0.6 1.0
OE21 A:CGU7 3.9 0.5 1.0
OE12 A:CGU6 3.9 96.6 1.0
CG A:CGU6 4.1 98.7 1.0
CG A:ASN2 4.1 96.8 1.0
CA A:ASN2 4.1 96.8 1.0
OE21 A:CGU26 4.2 0.5 1.0
CA A:CA603 4.2 86.9 1.0
N A:ASN2 4.3 96.7 1.0
OE12 A:CGU26 4.3 0.9 1.0
CG A:CGU26 4.3 0.6 1.0
CB A:CGU16 4.4 0.6 1.0
N A:ALA1 4.4 96.0 1.0
CD2 A:CGU6 4.5 0.4 1.0
OE22 A:CGU6 4.6 0.2 1.0
CA A:ALA1 4.6 96.3 1.0
CB A:ASN2 4.6 96.8 1.0
CG A:CGU7 4.7 99.1 1.0
ND2 A:ASN2 4.9 96.8 1.0
OE12 A:CGU7 5.0 99.1 1.0

Calcium binding site 4 out of 5 in 4o03

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Calcium binding site 4 out of 5 in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167


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 CA2+ Bound Prothrombin Deletion Mutant Residues 146-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:0.3
occ:1.00
 OE22 A:CGU16 2.3 96.6 1.0
OE12 A:CGU6 2.4 96.6 1.0
OE21 A:CGU16 2.7 95.0 1.0
CD2 A:CGU16 2.9 97.2 1.0
OE12 A:CGU20 3.0 0.6 1.0
CD1 A:CGU6 3.1 96.9 1.0
OE11 A:CGU20 3.2 0.2 1.0
O A:ALA1 3.2 96.4 1.0
CD1 A:CGU20 3.4 0.8 1.0
OE11 A:CGU6 3.4 94.5 1.0
C A:ALA1 3.6 96.5 1.0
CA A:CA604 3.6 98.0 1.0
CB A:ALA1 3.7 96.3 1.0
CA A:ALA1 4.0 96.3 1.0
OG1 A:THR3 4.2 98.1 1.0
N A:ALA1 4.2 96.0 1.0
N A:ASN2 4.3 96.7 1.0
CA A:CA606 4.3 68.2 1.0
CG A:CGU6 4.3 98.7 1.0
OE21 A:CGU6 4.3 0.1 1.0
CG A:CGU16 4.3 98.9 1.0
CD2 A:CGU6 4.4 0.4 1.0
CD A:ARG15 4.6 0.9 1.0
N A:THR3 4.6 97.0 1.0
CA A:ASN2 4.7 96.8 1.0
CG A:CGU20 4.8 0.4 1.0

Calcium binding site 5 out of 5 in 4o03

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Calcium binding site 5 out of 5 in the Crystal Structure of CA2+ Bound Prothrombin Deletion Mutant Residues 146-167


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 CA2+ Bound Prothrombin Deletion Mutant Residues 146-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:68.2
occ:1.00
 OE12 A:CGU20 2.2 0.6 1.0
OE22 A:CGU20 2.6 99.3 1.0
CD1 A:CGU20 3.3 0.8 1.0
CD2 A:CGU20 3.4 0.2 1.0
CG A:CGU20 3.9 0.4 1.0
CA A:CA605 4.3 0.3 1.0
OE21 A:CGU20 4.4 0.3 1.0
OE11 A:CGU20 4.4 0.2 1.0
O A:ARG15 4.7 0.3 1.0
CG A:ARG15 5.0 0.1 1.0

Reference:

N.Pozzi, Z.Chen, L.A.Pelc, D.B.Shropshire, E.Di Cera. The Linker Connecting the Two Kringles Plays A Key Role in Prothrombin Activation. Proc.Natl.Acad.Sci.Usa V. 111 7630 2014.
ISSN: ISSN 0027-8424
PubMed: 24821807
DOI: 10.1073/PNAS.1403779111
Page generated: Sun Jul 14 11:16:40 2024

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