Atomistry » Calcium » PDB 2f59-2foc » 2fir
Atomistry »
  Calcium »
    PDB 2f59-2foc »
      2fir »

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

Go back to Calcium Binding Sites List in 2fir
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

Go back to Calcium Binding Sites List in 2fir
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

Go back to Calcium Binding Sites List in 2fir
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

Go back to Calcium Binding Sites List in 2fir
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: Fri Jul 12 10:31:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy