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Calcium in PDB 2c4f: Crystal Structure of Factor VII.Stf Complexed with PD0297121

Enzymatic activity of Crystal Structure of Factor VII.Stf Complexed with PD0297121

All present enzymatic activity of Crystal Structure of Factor VII.Stf Complexed with PD0297121:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Factor VII.Stf Complexed with PD0297121, PDB code: 2c4f was solved by J.T.Kohrt, E.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.72
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.993, 81.302, 125.860, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / n/a

Other elements in 2c4f:

The structure of Crystal Structure of Factor VII.Stf Complexed with PD0297121 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Factor VII.Stf Complexed with PD0297121 (pdb code 2c4f). 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 Factor VII.Stf Complexed with PD0297121, PDB code: 2c4f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2c4f

Go back to Calcium Binding Sites List in 2c4f
Calcium binding site 1 out of 5 in the Crystal Structure of Factor VII.Stf Complexed with PD0297121


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 Factor VII.Stf Complexed with PD0297121 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:29.2
occ:1.00
 O H:GLU75 2.1 23.1 1.0
OE2 H:GLU80 2.1 22.0 1.0
O H:HOH509 2.1 18.8 1.0
O H:HOH430 2.2 23.6 1.0
OE1 H:GLU70 2.2 16.6 1.0
O H:ASP72 2.2 17.5 1.0
CD H:GLU80 3.1 22.5 1.0
CD H:GLU70 3.1 20.4 1.0
C H:GLU75 3.3 24.9 1.0
C H:ASP72 3.3 18.5 1.0
OE2 H:GLU70 3.3 19.8 1.0
OE1 H:GLU80 3.7 23.1 1.0
N H:ASP72 3.8 17.9 1.0
CA H:HIS76 3.9 26.1 1.0
O H:HOH435 4.1 17.4 1.0
N H:HIS76 4.1 24.9 1.0
CA H:ASP72 4.1 18.4 1.0
CG H:GLU80 4.2 23.5 1.0
N H:LEU73 4.3 16.3 1.0
N H:HIS71 4.3 18.2 1.0
N H:GLU75 4.3 22.1 1.0
O H:HOH418 4.4 32.3 1.0
CA H:GLU75 4.4 25.1 1.0
CB H:ASP72 4.4 18.9 1.0
CG H:GLU75 4.5 35.5 1.0
CA H:LEU73 4.5 17.2 1.0
CG H:GLU70 4.5 20.0 1.0
ND1 H:HIS76 4.6 31.0 1.0
N H:ASP77 4.7 23.6 1.0
C H:HIS76 4.8 26.9 1.0
C H:LEU73 4.8 18.9 1.0
C H:HIS71 4.8 17.2 1.0
CA H:GLU70 4.9 19.3 1.0

Calcium binding site 2 out of 5 in 2c4f

Go back to Calcium Binding Sites List in 2c4f
Calcium binding site 2 out of 5 in the Crystal Structure of Factor VII.Stf Complexed with PD0297121


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 Factor VII.Stf Complexed with PD0297121 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca201

b:28.2
occ:1.00
 OD2 L:ASP46 2.2 32.1 1.0
O L:GLY47 2.3 32.9 1.0
O L:GLN64 2.4 29.8 1.0
OE1 L:GLN49 2.4 32.8 1.0
O L:HOH344 2.4 36.5 1.0
OD2 L:ASP63 2.4 32.1 1.0
OD1 L:ASP63 2.6 31.5 1.0
CG L:ASP63 2.9 31.4 1.0
CG L:ASP46 3.4 32.9 1.0
CD L:GLN49 3.5 33.5 1.0
C L:GLN64 3.5 29.0 1.0
C L:GLY47 3.5 32.7 1.0
NE2 L:GLN49 4.0 32.8 1.0
CB L:ASP46 4.0 31.3 1.0
N L:GLN66 4.1 30.4 1.0
N L:GLN49 4.2 32.5 1.0
N L:GLN64 4.2 28.1 1.0
CA L:ASP48 4.2 34.1 1.0
CA L:LEU65 4.2 30.0 1.0
N L:LEU65 4.3 29.2 1.0
N L:ASP48 4.3 33.5 1.0
CB L:ASP63 4.3 28.7 1.0
C L:ASP46 4.4 31.6 1.0
OD1 L:ASP46 4.4 33.9 1.0
N L:GLY47 4.4 31.2 1.0
O L:ASP46 4.5 32.5 1.0
CA L:GLN64 4.5 28.9 1.0
CA L:GLY47 4.6 32.4 1.0
C L:LEU65 4.6 29.7 1.0
O L:SER67 4.7 23.7 1.0
CG L:GLN49 4.7 32.8 1.0
C L:ASP48 4.7 33.3 1.0
C L:ASP63 4.8 28.0 1.0
CA L:ASP46 4.9 31.4 1.0
CB L:GLN49 5.0 32.0 1.0

Calcium binding site 3 out of 5 in 2c4f

Go back to Calcium Binding Sites List in 2c4f
Calcium binding site 3 out of 5 in the Crystal Structure of Factor VII.Stf Complexed with PD0297121


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 Factor VII.Stf Complexed with PD0297121 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca204

b:46.4
occ:1.00
 OE11 L:CGU26 2.1 29.5 1.0
OE21 L:CGU16 2.1 35.4 1.0
OE11 L:CGU16 2.1 35.3 1.0
OE22 L:CGU26 2.2 33.3 1.0
CD1 L:CGU16 3.1 36.2 1.0
CD2 L:CGU26 3.2 33.4 1.0
CD1 L:CGU26 3.2 32.3 1.0
CD2 L:CGU16 3.2 36.5 1.0
CG L:CGU16 3.6 35.6 1.0
CG L:CGU26 3.7 31.5 1.0
O L:HOH336 4.1 25.9 1.0
OE11 L:CGU7 4.1 32.1 1.0
CB L:CGU16 4.2 35.6 1.0
OE12 L:CGU16 4.2 37.1 1.0
OE21 L:CGU26 4.2 33.6 1.0
OE22 L:CGU16 4.3 36.0 1.0
OE12 L:CGU7 4.3 30.9 1.0
OE12 L:CGU26 4.3 35.5 1.0
CB L:CGU26 4.5 29.5 1.0
CD1 L:CGU7 4.6 32.3 1.0

Calcium binding site 4 out of 5 in 2c4f

Go back to Calcium Binding Sites List in 2c4f
Calcium binding site 4 out of 5 in the Crystal Structure of Factor VII.Stf Complexed with PD0297121


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 Factor VII.Stf Complexed with PD0297121 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca205

b:85.2
occ:1.00
 OE21 L:CGU19 2.2 54.3 1.0
OE12 L:CGU19 2.4 51.9 1.0
OE21 L:CGU14 2.5 48.4 1.0
OE12 L:CGU14 2.7 49.1 1.0
CD2 L:CGU19 2.9 52.8 1.0
CG L:CGU19 2.9 51.9 1.0
CD1 L:CGU19 3.0 52.2 1.0
CD2 L:CGU14 3.2 46.9 1.0
CG L:CGU14 3.4 46.3 1.0
CD1 L:CGU14 3.4 48.0 1.0
OE22 L:CGU19 4.0 54.8 1.0
OE22 L:CGU14 4.2 47.2 1.0
OE11 L:CGU19 4.3 52.4 1.0
CB L:CGU19 4.4 49.1 1.0
OE11 L:CGU14 4.7 48.0 1.0
O L:CGU14 4.8 39.9 1.0
CB L:CGU14 4.9 42.5 1.0

Calcium binding site 5 out of 5 in 2c4f

Go back to Calcium Binding Sites List in 2c4f
Calcium binding site 5 out of 5 in the Crystal Structure of Factor VII.Stf Complexed with PD0297121


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 Factor VII.Stf Complexed with PD0297121 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca206

b:45.5
occ:1.00
 OE11 L:CGU25 2.1 27.8 1.0
OE21 L:CGU29 2.2 29.9 1.0
OE21 L:CGU25 2.2 26.5 1.0
OE11 L:CGU29 2.3 27.7 1.0
CD1 L:CGU25 2.9 28.6 1.0
CD2 L:CGU25 3.0 25.7 1.0
CD2 L:CGU29 3.0 29.5 1.0
CG L:CGU25 3.1 26.8 1.0
CD1 L:CGU29 3.1 27.1 1.0
CG L:CGU29 3.1 27.9 1.0
NH2 L:ARG28 3.9 32.5 1.0
OE22 L:CGU25 4.1 27.9 1.0
OE12 L:CGU25 4.1 29.3 1.0
OE22 L:CGU29 4.2 30.6 1.0
O L:HOH310 4.2 42.0 1.0
OE12 L:CGU29 4.3 27.2 1.0
O L:HOH330 4.4 26.6 1.0
CB L:CGU25 4.6 27.3 1.0
O L:CGU25 4.6 26.6 1.0
CB L:CGU29 4.7 28.0 1.0
CZ L:ARG28 4.9 34.1 1.0
NE L:ARG28 4.9 32.7 1.0

Reference:

J.T.Kohrt, K.J.Filipski, W.L.Cody, C.Cai, D.A.Dudley, C.A.V.Huis, J.A.Willardsen, L.S.Narasimhan, E.Zhang, S.T.Rapundalo, K.Saiya-Cork, R.J.Leadley, J.J.Edmunds. The Discovery of Fluoropyridine-Based Inhibitors of the Factor Viia/Tf Complex--Part 2 Bioorg.Med.Chem.Lett. V. 16 1060 2006.
ISSN: ISSN 0960-894X
PubMed: 16289811
DOI: 10.1016/J.BMCL.2005.10.076
Page generated: Fri Jul 12 09:23:28 2024

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