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Calcium in PDB 2b8o: Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex

Enzymatic activity of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex

All present enzymatic activity of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex, PDB code: 2b8o was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.280, 81.110, 126.860, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 28.5

Other elements in 2b8o:

The structure of Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex (pdb code 2b8o). 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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex, PDB code: 2b8o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2b8o

Go back to Calcium Binding Sites List in 2b8o
Calcium binding site 1 out of 6 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex


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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca503

b:50.9
occ:1.00
 OE11 L:CGU29 2.0 26.4 1.0
O L:HOH514 2.3 19.4 1.0
CD1 L:CGU29 3.0 24.0 1.0
OE12 L:CGU29 3.3 22.6 1.0
OE11 L:CGU25 3.4 33.2 1.0
CD1 L:CGU25 3.5 33.7 1.0
O L:HOH531 3.5 44.6 1.0
OE12 L:CGU25 3.8 35.1 1.0
CG L:CGU25 3.9 33.1 1.0
O L:HOH522 3.9 30.5 1.0
OE22 L:CGU26 4.0 36.0 1.0
CG L:CGU29 4.2 21.9 1.0
OE21 L:CGU26 4.3 37.2 1.0
CD2 L:CGU26 4.4 33.6 1.0
OE21 L:CGU29 4.5 25.9 1.0
CB L:CGU25 4.6 29.9 1.0
CD2 L:CGU29 4.7 25.4 1.0

Calcium binding site 2 out of 6 in 2b8o

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Calcium binding site 2 out of 6 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex


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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca504

b:61.0
occ:1.00
 OE12 L:CGU29 1.9 22.6 1.0
CB L:CGU29 2.7 22.3 1.0
CD1 L:CGU29 2.8 24.0 1.0
O L:HOH522 3.2 30.5 1.0
CG L:CGU29 3.3 21.9 1.0
O L:CGU26 3.7 25.1 1.0
OE11 L:CGU29 3.9 26.4 1.0
CA L:CGU29 4.1 22.3 1.0
N L:ILE30 4.2 15.9 1.0
CG1 L:ILE30 4.3 15.5 1.0
CA L:CGU26 4.4 24.9 1.0
C L:CGU29 4.4 19.3 1.0
CD2 L:CGU29 4.4 25.4 1.0
OE21 L:CGU16 4.5 9.8 1.0
C L:CGU26 4.5 23.8 1.0
OE22 L:CGU29 4.6 26.7 1.0
N L:CGU29 4.9 24.3 1.0
CD1 L:ILE30 4.9 12.3 1.0
CG L:CGU26 5.0 30.9 1.0
OE22 L:CGU26 5.0 36.0 1.0
O L:CGU25 5.0 20.4 1.0

Calcium binding site 3 out of 6 in 2b8o

Go back to Calcium Binding Sites List in 2b8o
Calcium binding site 3 out of 6 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex


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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca506

b:55.1
occ:1.00
 O L:HOH535 2.1 42.2 1.0
OE12 L:CGU16 2.2 17.7 1.0
OE11 L:CGU7 2.7 29.6 1.0
OE11 L:CGU16 2.8 11.2 1.0
CD1 L:CGU16 2.8 12.5 1.0
CD1 L:CGU7 3.6 27.5 1.0
O L:ALA1 3.6 39.3 1.0
OE12 L:CGU7 3.7 24.4 1.0
OE21 L:CGU20 4.0 41.1 1.0
CG L:CGU16 4.3 9.9 1.0
MG L:MG505 4.6 25.6 1.0
CB L:ALA3 4.7 39.1 1.0
C L:ALA1 4.8 39.8 1.0
CD2 L:CGU20 5.0 39.9 1.0
CG L:CGU7 5.0 26.3 1.0

Calcium binding site 4 out of 6 in 2b8o

Go back to Calcium Binding Sites List in 2b8o
Calcium binding site 4 out of 6 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex


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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca507

b:66.6
occ:1.00
 OE21 L:CGU6 1.9 40.9 1.0
CD2 L:CGU6 2.9 39.4 1.0
OE12 L:CGU6 3.2 33.5 1.0
CD1 L:CGU6 3.2 34.3 1.0
CG L:CGU6 3.4 34.0 1.0
OE21 L:CGU20 3.6 41.1 1.0
OE11 L:CGU6 3.8 32.4 1.0
CB L:CGU6 3.9 28.8 1.0
OE22 L:CGU6 4.0 39.4 1.0
O L:HOH573 4.3 25.1 1.0
O L:HOH534 4.4 20.8 1.0
CD2 L:CGU20 4.5 39.9 1.0
CB L:ALA3 4.9 39.1 1.0

Calcium binding site 5 out of 6 in 2b8o

Go back to Calcium Binding Sites List in 2b8o
Calcium binding site 5 out of 6 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex


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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca509

b:29.4
occ:1.00
 O L:GLY47 2.0 24.0 1.0
O L:HOH551 2.1 55.7 1.0
OE1 L:GLN49 2.2 31.3 1.0
OD2 L:ASP63 2.4 16.7 1.0
OD2 L:ASP46 2.5 25.3 1.0
O L:GLN64 2.6 8.7 1.0
OD1 L:ASP63 2.8 18.1 1.0
CG L:ASP63 2.9 15.3 1.0
C L:GLY47 3.2 24.6 1.0
CD L:GLN49 3.4 28.6 1.0
CG L:ASP46 3.6 27.3 1.0
C L:GLN64 3.9 12.7 1.0
N L:GLN49 3.9 23.2 1.0
CA L:ASP48 4.1 21.1 1.0
N L:ASP48 4.1 21.9 1.0
N L:GLY47 4.1 25.8 1.0
NE2 L:GLN49 4.1 27.4 1.0
CB L:ASP46 4.1 27.1 1.0
CA L:GLY47 4.2 24.2 1.0
O L:HOH546 4.3 31.8 1.0
N L:GLN64 4.3 12.2 1.0
C L:ASP46 4.4 24.6 1.0
CB L:ASP63 4.4 13.6 1.0
C L:ASP48 4.5 21.2 1.0
N L:GLN66 4.5 21.7 1.0
OD1 L:ASP46 4.6 25.9 1.0
CG L:GLN49 4.6 25.8 1.0
CB L:GLN49 4.6 22.6 1.0
O L:ASP46 4.7 29.3 1.0
CA L:LEU65 4.7 16.9 1.0
N L:LEU65 4.7 14.1 1.0
CA L:GLN64 4.8 12.0 1.0
CA L:GLN49 4.9 21.6 1.0
CA L:ASP46 4.9 25.2 1.0
O L:SER67 4.9 14.1 1.0

Calcium binding site 6 out of 6 in 2b8o

Go back to Calcium Binding Sites List in 2b8o
Calcium binding site 6 out of 6 in the Crystal Structure of Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex


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 Glu-Gly-Arg-Chloromethyl Ketone-Factor Viia/Soluble Tissue Factor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca510

b:35.8
occ:1.00
 O H:GLU75 2.0 15.3 1.0
OE2 H:GLU70 2.2 19.3 1.0
O H:ASP72 2.3 17.9 1.0
OE2 H:GLU80 2.5 25.6 1.0
CD H:GLU70 3.1 18.0 1.0
C H:GLU75 3.2 12.9 1.0
CD H:GLU80 3.3 23.6 1.0
C H:ASP72 3.5 13.4 1.0
OE1 H:GLU70 3.5 21.1 1.0
OE1 H:GLU80 3.8 23.3 1.0
O H:LEU73 3.8 9.3 1.0
CA H:HIS76 4.0 15.2 1.0
N H:HIS76 4.0 13.4 1.0
N H:GLU75 4.1 5.9 1.0
CG H:GLU80 4.2 18.1 1.0
CA H:GLU75 4.2 8.7 1.0
CG H:GLU70 4.3 12.7 1.0
C H:LEU73 4.3 8.8 1.0
N H:LEU73 4.3 10.1 1.0
CA H:LEU73 4.3 9.5 1.0
CA H:ASP72 4.4 13.6 1.0
ND1 H:HIS76 4.5 15.5 1.0
N H:ASP72 4.5 14.0 1.0
CG H:HIS76 4.6 16.9 1.0
CE1 H:HIS76 4.7 17.4 1.0
CB H:ASP72 4.8 11.2 1.0
N H:ASP77 4.8 12.6 1.0
CD2 H:HIS76 4.8 13.3 1.0
NE2 H:HIS76 4.9 11.5 1.0
CB H:HIS76 4.9 17.7 1.0
C H:HIS76 4.9 14.9 1.0
N H:HIS71 5.0 17.1 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, K.Padmanabhan. Crystal Structure of Factor Viia/Soluble Tissue Factor Complexed with Glu-Gly-Arg-Chloromethyl Ketone To Be Published.
Page generated: Fri Jul 12 08:57:12 2024

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