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Calcium in PDB 1wqv: Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine

Enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine

All present enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine, PDB code: 1wqv was solved by S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, T.Koga, K.Hattori, T.Shiraishi, M.Haramura, H.Kodama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.390, 82.420, 123.510, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine (pdb code 1wqv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine, PDB code: 1wqv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1wqv

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Calcium binding site 1 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca502

b:25.5
occ:1.00
 O L:GLY47 2.6 28.2 1.0
OD2 L:ASP46 2.6 27.2 1.0
O L:GLN64 2.6 22.9 1.0
OE1 L:GLN49 2.7 31.8 1.0
OD2 L:ASP63 2.7 22.4 1.0
OD1 L:ASP63 2.8 20.7 1.0
O L:HOH1109 3.0 11.1 1.0
CG L:ASP63 3.1 21.5 1.0
CG L:ASP46 3.5 28.4 1.0
C L:GLN64 3.5 21.6 1.0
C L:GLY47 3.8 27.4 1.0
CD L:GLN49 3.9 31.7 1.0
CB L:ASP46 4.0 27.5 1.0
N L:GLN66 4.1 26.4 1.0
N L:GLN64 4.2 20.4 1.0
N L:GLN49 4.2 26.4 1.0
CA L:LEU65 4.2 24.6 1.0
CA L:ASP48 4.3 27.1 1.0
N L:LEU65 4.3 23.0 1.0
CA L:GLN64 4.5 22.2 1.0
C L:ASP46 4.5 24.8 1.0
O L:ASP46 4.5 25.9 1.0
OD1 L:ASP46 4.5 27.9 1.0
N L:ASP48 4.5 27.6 1.0
NE2 L:GLN49 4.6 32.7 1.0
CB L:ASP63 4.6 19.3 1.0
N L:GLY47 4.6 24.7 1.0
C L:LEU65 4.7 25.8 1.0
O L:SER67 4.8 25.1 1.0
C L:ASP48 4.8 27.1 1.0
CA L:GLY47 4.8 25.2 1.0
C L:ASP63 4.9 19.3 1.0
CA L:ASP46 4.9 25.2 1.0
CG L:GLN49 5.0 30.4 1.0

Calcium binding site 2 out of 9 in 1wqv

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Calcium binding site 2 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca503

b:30.2
occ:1.00
 OE12 L:CGU7 2.7 26.2 1.0
OE21 L:CGU29 2.7 27.3 1.0
OE22 L:CGU7 2.7 20.9 1.0
OE22 L:CGU29 2.8 24.6 1.0
OE12 L:CGU26 3.1 24.1 1.0
CD2 L:CGU29 3.1 25.7 1.0
CD1 L:CGU7 3.4 23.0 1.0
OE11 L:CGU26 3.5 21.2 1.0
CD1 L:CGU26 3.6 21.5 1.0
CD2 L:CGU7 3.8 20.9 1.0
CA L:CA504 4.0 21.2 1.0
OE11 L:CGU7 4.1 22.8 1.0
CG L:CGU7 4.2 20.9 1.0
OD1 L:ASN2 4.4 23.1 1.0
OE11 L:CGU25 4.5 39.6 1.0
CG L:CGU29 4.5 26.2 1.0
O L:HOH1093 4.6 22.9 1.0
CA L:CA509 4.6 65.1 1.0
CB L:CGU7 4.8 17.7 1.0
OE21 L:CGU7 4.9 22.1 1.0
CG L:CGU26 5.0 23.0 1.0

Calcium binding site 3 out of 9 in 1wqv

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Calcium binding site 3 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca504

b:21.2
occ:1.00
 OE11 L:CGU26 2.7 21.2 1.0
OE22 L:CGU29 2.7 24.6 1.0
O L:HOH1082 2.7 14.5 1.0
OE12 L:CGU7 2.8 26.2 1.0
O L:HOH1066 2.8 20.5 1.0
O L:HOH1083 2.9 23.1 1.0
OE21 L:CGU16 2.9 25.6 1.0
OE11 L:CGU7 3.0 22.8 1.0
CD1 L:CGU7 3.3 23.0 1.0
CD2 L:CGU16 3.8 23.9 1.0
OE22 L:CGU16 3.9 23.0 1.0
CA L:CA505 3.9 23.5 1.0
CD1 L:CGU26 3.9 21.5 1.0
CD2 L:CGU29 4.0 25.7 1.0
CA L:CA503 4.0 30.2 1.0
CB L:CGU29 4.3 23.3 1.0
OE12 L:CGU26 4.5 24.1 1.0
CA L:CGU26 4.7 20.7 1.0
OE12 L:CGU6 4.7 19.4 1.0
CB L:CGU26 4.7 20.2 1.0
CA L:GLY11 4.7 21.8 1.0
CG L:CGU29 4.7 26.2 1.0
CG L:CGU7 4.8 20.9 1.0
OE21 L:CGU29 4.8 27.3 1.0
O L:CGU26 4.8 19.8 1.0
CG L:CGU26 4.9 23.0 1.0
OD1 L:ASN2 5.0 23.1 1.0

Calcium binding site 4 out of 9 in 1wqv

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Calcium binding site 4 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca505

b:23.5
occ:1.00
 OE11 L:CGU7 2.5 22.8 1.0
OE11 L:CGU16 2.6 25.7 1.0
OE22 L:CGU26 2.6 23.2 1.0
OE21 L:CGU16 2.8 25.6 1.0
O L:ALA1 2.8 24.0 1.0
OE11 L:CGU6 2.8 17.1 1.0
OD1 L:ASN2 2.8 23.1 1.0
OE11 L:CGU26 2.9 21.2 1.0
CD1 L:CGU26 3.4 21.5 1.0
CD1 L:CGU16 3.4 24.5 1.0
CD2 L:CGU26 3.6 24.5 1.0
CD1 L:CGU6 3.6 19.1 1.0
OE12 L:CGU6 3.7 19.4 1.0
CG L:ASN2 3.7 20.1 1.0
CD1 L:CGU7 3.7 23.0 1.0
CD2 L:CGU16 3.8 23.9 1.0
C L:ALA1 3.8 23.6 1.0
CA L:CA506 3.9 36.4 1.0
CA L:CA504 3.9 21.2 1.0
OE12 L:CGU26 4.0 24.1 1.0
CG L:CGU26 4.0 23.0 1.0
CG L:CGU16 4.1 24.3 1.0
OE12 L:CGU16 4.2 27.1 1.0
CA L:ASN2 4.3 23.9 1.0
ND2 L:ASN2 4.3 23.7 1.0
N L:ALA1 4.4 20.6 1.0
N L:ASN2 4.4 24.5 1.0
OE12 L:CGU7 4.5 26.2 1.0
CB L:CGU26 4.5 20.2 1.0
CB L:ASN2 4.6 22.0 1.0
CG L:CGU7 4.6 20.9 1.0
CB L:CGU16 4.6 24.6 1.0
OE21 L:CGU26 4.7 28.7 1.0
CA L:ALA1 4.7 22.8 1.0
OE22 L:CGU16 4.8 23.0 1.0
O L:HOH1082 4.8 14.5 1.0

Calcium binding site 5 out of 9 in 1wqv

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Calcium binding site 5 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca506

b:36.4
occ:1.00
 OE22 L:CGU6 2.6 23.3 1.0
O L:ALA1 2.7 24.0 1.0
OE11 L:CGU6 2.7 17.1 1.0
OE21 L:CGU20 2.7 26.4 1.0
OE11 L:CGU16 2.8 25.7 1.0
OE22 L:CGU20 2.8 29.8 1.0
OE12 L:CGU16 3.0 27.1 1.0
CD2 L:CGU20 3.2 27.3 1.0
CD1 L:CGU16 3.3 24.5 1.0
CD1 L:CGU6 3.3 19.1 1.0
C L:ALA1 3.7 23.6 1.0
CD2 L:CGU6 3.7 22.2 1.0
CA L:CA505 3.9 23.5 1.0
CG L:CGU6 4.0 20.3 1.0
OE12 L:CGU6 4.1 19.4 1.0
N L:ALA1 4.3 20.6 1.0
N L:ASN2 4.5 24.5 1.0
CA L:ALA1 4.5 22.8 1.0
CA L:ASN2 4.5 23.9 1.0
CB L:CGU6 4.6 19.4 1.0
N L:ALA3 4.6 24.6 1.0
O L:ARG15 4.7 20.2 1.0
CG L:CGU20 4.7 27.2 1.0
CG L:CGU16 4.8 24.3 1.0
CB L:ALA1 4.8 19.8 1.0
OE21 L:CGU6 4.8 25.1 1.0
CA L:CA508 4.8 38.0 1.0

Calcium binding site 6 out of 9 in 1wqv

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Calcium binding site 6 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca507

b:58.8
occ:1.00
 OE12 L:CGU19 2.7 34.8 1.0
OE12 L:CGU14 2.8 25.8 1.0
OE21 L:CGU14 2.9 29.5 1.0
OE21 L:CGU19 3.0 35.3 1.0
CD2 L:CGU14 3.4 27.0 1.0
CD1 L:CGU14 3.5 25.8 1.0
CD1 L:CGU19 3.5 33.3 1.0
CD2 L:CGU19 3.6 34.4 1.0
CG L:CGU14 3.6 24.7 1.0
CG L:CGU19 3.7 32.5 1.0
OE22 L:CGU14 4.3 27.5 1.0
OE11 L:CGU14 4.6 26.7 1.0
OE22 L:CGU19 4.7 36.3 1.0
OE11 L:CGU19 4.7 34.4 1.0

Calcium binding site 7 out of 9 in 1wqv

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Calcium binding site 7 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca508

b:38.0
occ:1.00
 OE21 L:CGU20 2.7 26.4 1.0
OE11 L:CGU20 2.9 29.3 1.0
CD2 L:CGU20 3.6 27.3 1.0
CD1 L:CGU20 3.7 27.1 1.0
CG L:CGU20 3.8 27.2 1.0
O L:ARG15 4.3 20.2 1.0
OE22 L:CGU6 4.6 23.3 1.0
CG L:ARG15 4.7 20.4 1.0
OE22 L:CGU19 4.7 36.3 1.0
OE22 L:CGU20 4.8 29.8 1.0
CA L:CA506 4.8 36.4 1.0
OE12 L:CGU20 4.9 28.2 1.0
O L:CGU19 5.0 27.2 1.0

Calcium binding site 8 out of 9 in 1wqv

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Calcium binding site 8 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca509

b:65.1
occ:1.00
 OE21 L:CGU29 2.8 27.3 1.0
OE11 L:CGU25 2.9 39.6 1.0
OE22 L:CGU25 3.0 39.9 1.0
CG L:CGU25 3.4 36.5 1.0
CD1 L:CGU25 3.4 38.1 1.0
CD2 L:CGU25 3.5 38.8 1.0
OE11 L:CGU29 3.6 27.6 1.0
NH2 L:ARG28 3.7 38.0 1.0
CD2 L:CGU29 3.9 25.7 1.0
CG L:CGU29 4.3 26.2 1.0
CD1 L:CGU29 4.3 26.5 1.0
OE21 L:CGU25 4.4 43.1 1.0
OE12 L:CGU25 4.5 37.8 1.0
CA L:CA503 4.6 30.2 1.0
CZ L:ARG28 4.9 37.3 1.0
CB L:CGU25 4.9 31.1 1.0
OE22 L:CGU29 5.0 24.6 1.0

Calcium binding site 9 out of 9 in 1wqv

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Calcium binding site 9 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Human Factor Viia-Tissue Factor Complexed with Propylsulfonamide-D- Thr-Met-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca501

b:26.2
occ:1.00
 O H:ASP72 2.6 12.3 1.0
O H:GLU75 2.7 22.7 1.0
OE1 H:GLU80 2.7 19.5 1.0
OE1 H:GLU70 2.7 17.0 1.0
O H:HOH1108 2.8 14.8 1.0
O H:HOH1095 2.8 18.7 1.0
OE2 H:GLU70 2.9 19.3 1.0
CD H:GLU70 3.2 17.9 1.0
C H:GLU75 3.5 19.9 1.0
C H:ASP72 3.5 12.1 1.0
CD H:GLU80 3.5 15.7 1.0
CA H:HIS76 4.0 16.6 1.0
N H:HIS76 4.1 18.8 1.0
N H:ASP72 4.2 11.5 1.0
OE2 H:GLU80 4.2 18.0 1.0
N H:LEU73 4.3 11.4 1.0
CA H:LEU73 4.3 11.1 1.0
N H:GLU75 4.3 16.3 1.0
CG H:GLU80 4.3 14.5 1.0
ND1 H:HIS76 4.3 15.2 1.0
CA H:ASP72 4.4 11.2 1.0
O H:HOH1002 4.4 3.2 1.0
CA H:GLU75 4.5 18.9 1.0
C H:LEU73 4.6 11.6 1.0
O H:HOH1122 4.6 30.1 1.0
CG H:GLU70 4.7 15.7 1.0
N H:HIS71 4.7 9.3 1.0
CB H:ASP72 4.8 11.5 1.0
CG H:HIS76 4.9 17.3 1.0
C H:HIS76 4.9 15.7 1.0
N H:ASP77 4.9 14.1 1.0
O H:LEU73 4.9 11.7 1.0
CE1 H:HIS76 4.9 15.6 1.0
O H:HOH1116 4.9 19.8 1.0
N H:SER74 5.0 10.9 1.0

Reference:

S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, T.Koga, K.Hattori, T.Shiraishi, M.Haramura, H.Kodama, T.Esaki, H.Sato, Y.Watanabe, S.Itoh, M.Ohta, T.Kozono. Crystal Structure of Human Factor Viia/Tissue Factor in Complex with Peptide Mimetic Inhibitor Biochem.Biophys.Res.Commun. V. 324 1227 2004.
ISSN: ISSN 0006-291X
PubMed: 15504346
DOI: 10.1016/J.BBRC.2004.09.182
Page generated: Fri Jul 12 07:14:59 2024

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