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Calcium in PDB 1wv7: Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine

Enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine

All present enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine, PDB code: 1wv7 was solved by S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, K.Yoshihashi, T.Kitazawa, T.Suzuki, T.Koga, K.Hattori, T.Shiraishi, M.Haramura, H.Kodama, Y.Ono, T.Esaki, H.Sato, Y.Watanabe, S.Itoh, M.Ohta, T.Kozono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.340, 82.340, 123.560, 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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine (pdb code 1wv7). 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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine, PDB code: 1wv7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1wv7

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Calcium binding site 1 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1002

b:34.1
occ:1.00
 O L:GLN64 2.6 25.0 1.0
OD2 L:ASP46 2.6 34.0 1.0
O L:GLY47 2.7 32.4 1.0
OE1 L:GLN49 2.8 35.2 1.0
OD2 L:ASP63 2.8 30.3 1.0
OD1 L:ASP63 3.0 29.8 1.0
O L:HOH1108 3.1 30.9 1.0
CG L:ASP63 3.3 29.5 1.0
CG L:ASP46 3.5 35.6 1.0
C L:GLY47 3.6 30.7 1.0
CB L:ASP46 3.7 33.3 1.0
C L:GLN64 3.8 25.2 1.0
CD L:GLN49 3.9 33.8 1.0
N L:GLN66 4.0 30.4 1.0
N L:GLY47 4.2 29.1 1.0
CA L:ASP48 4.2 31.5 1.0
C L:ASP46 4.2 30.1 1.0
CA L:LEU65 4.2 28.7 1.0
N L:ASP48 4.2 30.2 1.0
N L:GLN49 4.2 31.8 1.0
N L:LEU65 4.5 26.4 1.0
CA L:GLY47 4.5 29.4 1.0
O L:ASP46 4.5 31.8 1.0
N L:GLN64 4.6 24.0 1.0
CA L:ASP46 4.6 30.0 1.0
OD1 L:ASP46 4.6 38.2 1.0
NE2 L:GLN49 4.6 33.1 1.0
C L:LEU65 4.7 29.6 1.0
C L:ASP48 4.8 31.4 1.0
CB L:ASP63 4.8 25.6 1.0
CA L:GLN64 4.8 24.9 1.0
CD2 L:LEU65 5.0 31.5 1.0

Calcium binding site 2 out of 9 in 1wv7

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Calcium binding site 2 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1003

b:43.7
occ:1.00
 OE12 L:CGU7 2.7 33.8 1.0
OE22 L:CGU29 2.8 30.1 1.0
OE22 L:CGU7 2.8 32.6 1.0
OE21 L:CGU29 2.9 31.4 1.0
CD2 L:CGU29 3.2 32.3 1.0
OE12 L:CGU26 3.2 23.0 1.0
CD1 L:CGU7 3.4 32.4 1.0
OE11 L:CGU26 3.4 24.1 1.0
CD1 L:CGU26 3.6 25.0 1.0
CD2 L:CGU7 3.8 32.9 1.0
OE11 L:CGU7 3.9 30.5 1.0
CA L:CA1004 3.9 26.8 1.0
CG L:CGU7 4.2 31.9 1.0
OE11 L:CGU25 4.5 33.2 1.0
OD1 L:ASN2 4.6 30.9 1.0
CA L:CA1009 4.6 60.7 1.0
OE11 L:CGU29 4.6 33.0 1.0
CG L:CGU29 4.6 32.3 1.0
CB L:CGU7 4.8 29.4 1.0
OE21 L:CGU7 4.9 38.2 1.0
CG L:CGU26 4.9 26.1 1.0

Calcium binding site 3 out of 9 in 1wv7

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Calcium binding site 3 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1004

b:26.8
occ:1.00
 O L:HOH1085 2.7 20.3 1.0
O L:HOH1084 2.7 12.1 1.0
OE11 L:CGU26 2.8 24.1 1.0
OE22 L:CGU29 2.9 30.1 1.0
OE12 L:CGU7 2.9 33.8 1.0
OE21 L:CGU16 2.9 26.5 1.0
O L:HOH1068 2.9 16.8 1.0
OE11 L:CGU7 3.0 30.5 1.0
CD1 L:CGU7 3.3 32.4 1.0
CD2 L:CGU16 3.8 26.2 1.0
CA L:CA1005 3.8 28.4 1.0
OE22 L:CGU16 3.9 25.1 1.0
CA L:CA1003 3.9 43.7 1.0
CD1 L:CGU26 4.0 25.0 1.0
CD2 L:CGU29 4.1 32.3 1.0
CB L:CGU29 4.5 31.5 1.0
OE12 L:CGU26 4.6 23.0 1.0
OE12 L:CGU6 4.7 24.0 1.0
CA L:GLY11 4.7 31.3 1.0
CG L:CGU7 4.8 31.9 1.0
CA L:CGU26 4.8 26.5 1.0
CB L:CGU26 4.8 26.2 1.0
CG L:CGU29 4.9 32.3 1.0
OE21 L:CGU29 5.0 31.4 1.0
O L:CGU26 5.0 27.9 1.0
CA L:CGU7 5.0 27.1 1.0
O L:ARG9 5.0 28.8 1.0

Calcium binding site 4 out of 9 in 1wv7

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Calcium binding site 4 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1005

b:28.4
occ:1.00
 OE11 L:CGU7 2.6 30.5 1.0
OE21 L:CGU16 2.6 26.5 1.0
OE22 L:CGU26 2.7 26.1 1.0
OD1 L:ASN2 2.8 30.9 1.0
OE11 L:CGU16 2.8 28.7 1.0
OE11 L:CGU26 2.9 24.1 1.0
O L:ALA1 2.9 29.7 1.0
OE11 L:CGU6 3.0 26.3 1.0
CD1 L:CGU26 3.3 25.0 1.0
CD1 L:CGU16 3.6 27.5 1.0
CD2 L:CGU26 3.6 26.2 1.0
CD2 L:CGU16 3.7 26.2 1.0
C L:ALA1 3.7 29.5 1.0
CA L:CA1004 3.8 26.8 1.0
CG L:ASN2 3.8 29.3 1.0
OE12 L:CGU26 3.8 23.0 1.0
CD1 L:CGU6 3.8 25.9 1.0
CD1 L:CGU7 3.9 32.4 1.0
CG L:CGU26 3.9 26.1 1.0
OE12 L:CGU6 4.0 24.0 1.0
CA L:CA1006 4.1 40.9 1.0
CG L:CGU16 4.1 28.2 1.0
N L:ALA1 4.3 29.0 1.0
CA L:ASN2 4.3 29.7 1.0
OE12 L:CGU16 4.4 28.4 1.0
N L:ASN2 4.4 29.7 1.0
CB L:CGU26 4.4 26.2 1.0
CB L:CGU16 4.5 29.0 1.0
CB L:ASN2 4.6 29.5 1.0
OE12 L:CGU7 4.6 33.8 1.0
CA L:ALA1 4.6 29.3 1.0
OE21 L:CGU26 4.6 28.8 1.0
ND2 L:ASN2 4.7 31.0 1.0
OE22 L:CGU16 4.8 25.1 1.0
CG L:CGU7 4.8 31.9 1.0
O L:HOH1084 4.9 12.1 1.0

Calcium binding site 5 out of 9 in 1wv7

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Calcium binding site 5 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1006

b:40.9
occ:1.00
 OE11 L:CGU6 2.8 26.3 1.0
OE11 L:CGU16 2.8 28.7 1.0
O L:ALA1 2.8 29.7 1.0
OE22 L:CGU20 2.8 40.7 1.0
OE22 L:CGU6 2.8 27.6 1.0
OE21 L:CGU20 2.9 41.5 1.0
CD2 L:CGU20 3.2 40.8 1.0
OE12 L:CGU16 3.2 28.4 1.0
CD2 L:CGU6 3.3 25.9 1.0
CD1 L:CGU6 3.4 25.9 1.0
CD1 L:CGU16 3.4 27.5 1.0
C L:ALA1 3.8 29.5 1.0
CG L:CGU6 3.9 26.2 1.0
OE21 L:CGU6 3.9 28.0 1.0
OE12 L:CGU6 4.1 24.0 1.0
CA L:CA1005 4.1 28.4 1.0
N L:ALA1 4.4 29.0 1.0
CB L:CGU6 4.5 26.2 1.0
O L:ARG15 4.5 26.1 1.0
N L:ASN2 4.6 29.7 1.0
CA L:ALA1 4.6 29.3 1.0
CA L:CA1008 4.7 54.3 1.0
CA L:ASN2 4.7 29.7 1.0
CG L:CGU20 4.7 40.6 1.0
CG L:CGU16 4.9 28.2 1.0
CB L:ALA1 5.0 27.6 1.0
NE L:ARG15 5.0 31.1 1.0

Calcium binding site 6 out of 9 in 1wv7

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Calcium binding site 6 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1007

b:56.3
occ:1.00
 OE12 L:CGU19 2.7 38.1 1.0
OE21 L:CGU14 2.9 36.0 1.0
OE12 L:CGU14 2.9 33.5 1.0
OE21 L:CGU19 3.0 40.5 1.0
CD2 L:CGU19 3.4 39.2 1.0
CD2 L:CGU14 3.5 34.9 1.0
CD1 L:CGU19 3.5 38.5 1.0
CG L:CGU19 3.6 38.3 1.0
CD1 L:CGU14 3.8 32.5 1.0
CG L:CGU14 3.8 32.4 1.0
OE22 L:CGU19 4.2 40.1 1.0
O L:HOH1115 4.4 39.0 1.0
OE22 L:CGU14 4.4 37.4 1.0
OE11 L:CGU19 4.7 38.0 1.0
OE11 L:CGU14 5.0 32.5 1.0

Calcium binding site 7 out of 9 in 1wv7

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Calcium binding site 7 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1008

b:54.3
occ:1.00
 OE21 L:CGU20 2.8 41.5 1.0
OE11 L:CGU20 2.8 41.8 1.0
CD2 L:CGU20 3.5 40.8 1.0
CD1 L:CGU20 3.6 41.3 1.0
CG L:CGU20 3.8 40.6 1.0
OE22 L:CGU20 4.5 40.7 1.0
CA L:CA1006 4.7 40.9 1.0
OE12 L:CGU20 4.7 40.6 1.0
O L:ARG15 4.7 26.1 1.0
CG L:ARG15 4.8 28.5 1.0
OE22 L:CGU6 4.9 27.6 1.0

Calcium binding site 8 out of 9 in 1wv7

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Calcium binding site 8 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1009

b:60.7
occ:1.00
 OE21 L:CGU29 2.9 31.4 1.0
OE11 L:CGU25 3.0 33.2 1.0
OE22 L:CGU25 3.2 39.1 1.0
CD1 L:CGU25 3.3 32.4 1.0
CG L:CGU25 3.5 32.8 1.0
CD2 L:CGU25 3.6 36.4 1.0
CD2 L:CGU29 4.0 32.3 1.0
OE12 L:CGU25 4.1 30.4 1.0
NH2 L:ARG28 4.2 44.8 1.0
OE11 L:CGU29 4.3 33.0 1.0
CG L:CGU29 4.5 32.3 1.0
CA L:CA1003 4.6 43.7 1.0
CD1 L:CGU29 4.6 32.4 1.0
OE21 L:CGU25 4.7 39.7 1.0
CB L:CGU25 5.0 30.6 1.0

Calcium binding site 9 out of 9 in 1wv7

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Calcium binding site 9 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5-Propoxy-Trp-Gln-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 Ethylsulfonamide-D-5-Propoxy-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1001

b:46.2
occ:1.00
 O H:GLU75 2.6 24.9 1.0
OE1 H:GLU70 2.7 22.1 1.0
O H:ASP72 2.9 11.3 1.0
O H:HOH2090 2.9 37.5 1.0
OE2 H:GLU80 2.9 24.4 1.0
O H:HOH2084 2.9 28.0 1.0
OE2 H:GLU70 3.0 21.1 1.0
CD H:GLU80 3.1 22.9 1.0
CD H:GLU70 3.2 20.5 1.0
OE1 H:GLU80 3.5 25.7 1.0
C H:GLU75 3.6 24.0 1.0
C H:ASP72 3.7 12.5 1.0
CG H:GLU80 3.9 21.4 1.0
O H:HOH2002 4.1 14.2 1.0
N H:ASP72 4.2 14.0 1.0
CA H:HIS76 4.2 23.0 1.0
N H:HIS76 4.3 23.9 1.0
ND1 H:HIS76 4.4 25.8 1.0
N H:GLU75 4.5 20.2 1.0
CA H:ASP72 4.5 13.6 1.0
N H:LEU73 4.5 11.1 1.0
CA H:GLU75 4.6 23.7 1.0
CG H:GLU70 4.6 21.4 1.0
N H:HIS71 4.6 13.6 1.0
CA H:LEU73 4.6 10.4 1.0
N H:ASP77 4.8 20.1 1.0
C H:LEU73 4.9 12.4 1.0
CB H:ASP72 4.9 15.6 1.0

Reference:

S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, K.Yoshihashi, T.Kitazawa, T.Suzuki, T.Koga, K.Hattori, T.Shiraishi, M.Haramura, H.Kodama, Y.Ono, T.Esaki, H.Sato, Y.Watanabe, S.Itoh, M.Ohta, T.Kozono. Structure-Based Design of P3 Moieties in the Peptide Mimetic Factor Viia Inhibitor Biochem.Biophys.Res.Commun. V. 327 589 2005.
ISSN: ISSN 0006-291X
PubMed: 15629154
DOI: 10.1016/J.BBRC.2004.12.042
Page generated: Fri Jul 12 07:20:42 2024

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