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Calcium in PDB 2fir: Crystal Structure of Dfpr-Viia/Stf

Enzymatic activity of Crystal Structure of Dfpr-Viia/Stf

All present enzymatic activity of Crystal Structure of Dfpr-Viia/Stf:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, D.Prevost, H.Schreuder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.020, 80.980, 126.330, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 28.1

Other elements in 2fir:

The structure of Crystal Structure of Dfpr-Viia/Stf also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dfpr-Viia/Stf (pdb code 2fir). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2fir

Go back to Calcium Binding Sites List in 2fir
Calcium binding site 1 out of 6 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1002

b:43.8
occ:1.00
 O L:HOH1116 1.9 40.5 1.0
OE21 L:CGU26 2.2 36.0 1.0
O L:HOH1042 2.5 43.2 1.0
OE12 L:CGU29 2.8 26.1 1.0
OE11 L:CGU29 3.1 25.5 1.0
O L:HOH1016 3.2 90.7 1.0
CD2 L:CGU26 3.3 34.9 1.0
CD1 L:CGU29 3.3 25.0 1.0
O L:HOH1055 3.7 60.9 1.0
OE22 L:CGU26 3.8 33.3 1.0
CA L:CA1003 3.8 77.6 1.0
CG L:CGU26 4.6 37.0 1.0
O L:HOH1172 4.7 34.0 1.0
CG L:CGU29 4.9 24.5 1.0
OE12 L:CGU25 4.9 37.2 1.0
CA L:CGU26 5.0 32.3 1.0

Calcium binding site 2 out of 6 in 2fir

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Calcium binding site 2 out of 6 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1003

b:77.6
occ:1.00
 OE12 L:CGU29 2.1 26.1 1.0
O L:HOH1171 2.3 43.0 1.0
O L:HOH1172 2.6 34.0 1.0
O L:HOH1042 3.0 43.2 1.0
O L:HOH1036 3.0 50.9 1.0
CD1 L:CGU29 3.1 25.0 1.0
O L:HOH1173 3.1 50.7 1.0
CB L:CGU29 3.2 25.8 1.0
OE22 L:CGU26 3.7 33.3 1.0
CG L:CGU29 3.7 24.5 1.0
CA L:CA1002 3.8 43.8 1.0
OE21 L:CGU26 4.0 36.0 1.0
OE11 L:CGU29 4.0 25.5 1.0
CD2 L:CGU26 4.1 34.9 1.0
O L:CGU26 4.4 31.8 1.0
O L:HOH1061 4.5 36.0 1.0
CA L:CGU26 4.5 32.3 1.0
OE21 L:CGU16 4.5 33.6 1.0
CD2 L:CGU29 4.6 23.9 1.0
OE22 L:CGU29 4.6 23.4 1.0
CA L:CGU29 4.6 28.1 1.0
C L:CGU26 4.9 31.8 1.0
O L:HOH1067 4.9 41.9 1.0
C L:CGU29 5.0 29.2 1.0

Calcium binding site 3 out of 6 in 2fir

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Calcium binding site 3 out of 6 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1005

b:61.3
occ:1.00
 O L:ALA1 1.9 69.8 1.0
OE21 L:CGU20 2.0 57.9 1.0
O L:HOH1056 2.3 23.0 1.0
OE11 L:CGU16 2.7 30.6 1.0
CD2 L:CGU20 2.8 55.6 1.0
C L:ALA1 2.9 70.8 1.0
O L:HOH1057 3.0 46.3 1.0
CB L:ALA1 3.1 71.4 1.0
OE12 L:CGU16 3.2 32.3 1.0
CD1 L:CGU16 3.3 31.5 1.0
OE22 L:CGU20 3.4 57.0 1.0
CA L:ALA1 3.4 71.3 1.0
O L:HOH1028 3.6 24.4 1.0
OE11 L:CGU7 3.8 43.0 1.0
CG L:CGU20 3.8 53.2 1.0
N L:ALA1 3.8 71.0 1.0
CA L:CA1006 3.9 69.0 1.0
O L:HOH1059 3.9 35.5 1.0
N L:ASN2 4.1 70.5 1.0
MG L:MG1004 4.2 36.9 1.0
OE11 L:CGU26 4.2 41.1 1.0
CB L:CGU20 4.4 50.1 1.0
CA L:CGU16 4.6 34.0 1.0
CG L:CGU16 4.6 32.4 1.0
O L:HOH1058 4.7 68.9 1.0
CB L:CGU16 4.7 32.7 1.0
CA L:ASN2 4.7 69.3 1.0
O L:CGU16 4.8 33.5 1.0
CD1 L:CGU7 4.8 41.8 1.0

Calcium binding site 4 out of 6 in 2fir

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Calcium binding site 4 out of 6 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1006

b:69.0
occ:1.00
 O L:HOH1057 2.2 46.3 1.0
OE21 L:CGU6 2.3 55.4 1.0
OE22 L:CGU20 2.5 57.0 1.0
OE21 L:CGU20 2.6 57.9 1.0
CD2 L:CGU20 2.8 55.6 1.0
O L:HOH1049 2.8 47.3 1.0
O L:HOH1058 3.1 68.9 1.0
CD2 L:CGU6 3.3 52.9 1.0
CB L:CGU6 3.9 42.3 1.0
O L:HOH1059 3.9 35.5 1.0
CA L:CA1005 3.9 61.3 1.0
OE22 L:CGU6 4.0 55.8 1.0
CG L:CGU6 4.1 49.9 1.0
CG L:CGU20 4.2 53.2 1.0
OE12 L:CGU16 4.4 32.3 1.0
OE12 L:CGU20 4.5 50.9 1.0
CD1 L:CGU20 4.6 52.6 1.0
OE11 L:CGU6 4.6 52.8 1.0
O L:ALA1 4.7 69.8 1.0
OE11 L:CGU7 4.7 43.0 1.0
CB L:ALA3 4.7 62.3 1.0
CD1 L:CGU6 4.9 51.5 1.0
O L:CGU6 5.0 34.8 1.0

Calcium binding site 5 out of 6 in 2fir

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Calcium binding site 5 out of 6 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1008

b:23.7
occ:1.00
 OD2 L:ASP63 2.2 25.1 1.0
O L:GLN64 2.3 20.7 1.0
OD2 L:ASP46 2.4 21.8 1.0
OE1 L:GLN49 2.5 20.0 1.0
O L:GLY47 2.6 24.3 1.0
OD1 L:ASP63 2.8 23.0 1.0
O T:HOH1025 2.8 17.0 1.0
CG L:ASP63 2.8 25.1 1.0
O L:HOH1011 3.0 25.8 1.0
C L:GLN64 3.5 18.8 1.0
CG L:ASP46 3.5 22.8 1.0
CD L:GLN49 3.6 20.2 1.0
C L:GLY47 3.8 24.5 1.0
CB L:ASP46 4.1 26.0 1.0
NE2 L:GLN49 4.1 14.9 1.0
N L:GLN64 4.2 19.0 1.0
N L:GLN66 4.2 24.6 1.0
CA L:LEU65 4.2 23.2 1.0
CB L:ASP63 4.3 22.7 1.0
N L:LEU65 4.3 20.3 1.0
N L:GLN49 4.4 26.4 1.0
CA L:ASP48 4.5 27.1 1.0
CA L:GLN64 4.5 18.4 1.0
O L:SER67 4.6 20.0 1.0
N L:ASP48 4.6 23.9 1.0
OD1 L:ASP46 4.6 19.6 1.0
O L:HOH1060 4.6 32.9 1.0
N L:GLY47 4.6 26.3 1.0
C L:ASP46 4.6 27.1 1.0
C L:LEU65 4.7 25.4 1.0
O L:ASP46 4.8 31.5 1.0
C L:ASP63 4.8 20.6 1.0
CA L:GLY47 4.8 24.1 1.0
CG L:GLN49 4.8 20.0 1.0
O L:HOH1050 4.8 32.1 1.0
C L:ASP48 4.9 27.7 1.0
OE1 T:GLN110 5.0 20.4 1.0

Calcium binding site 6 out of 6 in 2fir

Go back to Calcium Binding Sites List in 2fir
Calcium binding site 6 out of 6 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1009

b:28.4
occ:1.00
 O H:HOH1133 1.9 15.2 1.0
O H:GLU75 2.0 21.4 1.0
OE2 H:GLU80 2.1 25.3 1.0
OE2 H:GLU70 2.2 13.3 1.0
O H:ASP72 2.2 10.8 1.0
O H:HOH1134 2.4 23.4 1.0
CD H:GLU80 3.1 26.5 1.0
C H:GLU75 3.2 21.3 1.0
CD H:GLU70 3.2 15.5 1.0
C H:ASP72 3.3 12.6 1.0
OE1 H:GLU70 3.6 18.6 1.0
OE1 H:GLU80 3.7 26.8 1.0
N H:ASP72 3.9 11.5 1.0
CA H:HIS76 3.9 22.7 1.0
N H:HIS76 4.0 20.7 1.0
O H:HOH1057 4.0 18.6 1.0
CA H:ASP72 4.1 12.0 1.0
CG H:GLU80 4.2 20.6 1.0
N H:GLU75 4.2 20.8 1.0
CA H:GLU75 4.3 20.3 1.0
N H:LEU73 4.3 10.8 1.0
N H:HIS71 4.4 12.2 1.0
O H:HOH1081 4.4 12.1 1.0
CB H:ASP72 4.5 12.1 1.0
CA H:LEU73 4.5 15.2 1.0
N H:ASP77 4.5 19.2 1.0
CG H:GLU70 4.5 15.7 1.0
C H:HIS76 4.7 22.9 1.0
C H:LEU73 4.7 17.3 1.0
ND1 H:HIS76 4.9 26.7 1.0
C H:HIS71 4.9 11.6 1.0
CB H:GLU75 4.9 21.2 1.0
CA H:GLU70 4.9 13.2 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan. High Resolution Structures of P-Aminobenzamidine- and Benzamidine-Viia/Soluble Tissue Factor: Unpredicted Conformation of the 192-193 Peptide Bond and Mapping of CA2+, MG2+, Na+ and ZN2+ Sites in Factor Viia J.Biol.Chem. V. 281 24873 2006.
ISSN: ISSN 0021-9258
PubMed: 16757484
DOI: 10.1074/JBC.M509971200
Page generated: Tue Jul 8 05:34:48 2025

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