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

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

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

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-Trp-Gln-P-Aminobenzamidine, PDB code: 1wun 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) 19.97 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.290, 82.530, 123.530, 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-Trp-Gln-P-Aminobenzamidine (pdb code 1wun). 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-Trp-Gln-P-Aminobenzamidine, PDB code: 1wun:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1wun

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

b:30.2
occ:1.00
 OD2 L:ASP46 2.6 27.3 1.0
OD2 L:ASP63 2.7 26.8 1.0
OE1 L:GLN49 2.7 26.0 1.0
O L:GLY47 2.7 31.1 1.0
O L:GLN64 2.8 26.1 1.0
OD1 L:ASP63 2.9 27.4 1.0
CG L:ASP63 3.1 26.3 1.0
O T:HOH282 3.1 36.2 1.0
C L:GLN64 3.6 24.9 1.0
CG L:ASP46 3.6 29.9 1.0
C L:GLY47 3.7 29.4 1.0
CD L:GLN49 3.8 27.0 1.0
CB L:ASP46 3.9 29.3 1.0
CA L:ASP48 4.1 27.7 1.0
N L:GLN66 4.2 31.2 1.0
CA L:LEU65 4.2 29.6 1.0
N L:GLN49 4.2 26.1 1.0
N L:LEU65 4.2 26.7 1.0
N L:GLN64 4.2 23.4 1.0
N L:ASP48 4.3 28.7 1.0
NE2 L:GLN49 4.3 25.9 1.0
C L:ASP46 4.4 27.4 1.0
N L:GLY47 4.4 26.8 1.0
CA L:GLN64 4.5 24.5 1.0
CB L:ASP63 4.6 24.5 1.0
O L:ASP46 4.6 29.0 1.0
C L:LEU65 4.7 30.6 1.0
CA L:GLY47 4.7 27.8 1.0
C L:ASP48 4.7 26.7 1.0
OD1 L:ASP46 4.8 31.7 1.0
O L:SER67 4.8 32.2 1.0
CA L:ASP46 4.8 27.7 1.0
C L:ASP63 4.9 24.0 1.0
CG L:GLN49 5.0 24.8 1.0

Calcium binding site 2 out of 9 in 1wun

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

b:31.8
occ:1.00
 OE12 L:CGU7 2.6 21.8 1.0
OE21 L:CGU29 2.7 23.7 1.0
OE22 L:CGU7 2.7 18.4 1.0
OE12 L:CGU26 2.9 23.5 1.0
OE22 L:CGU29 3.0 26.0 1.0
CD2 L:CGU29 3.2 25.1 1.0
CD1 L:CGU7 3.5 20.0 1.0
CD1 L:CGU26 3.6 22.2 1.0
OE11 L:CGU26 3.6 22.0 1.0
CD2 L:CGU7 3.7 17.9 1.0
CA L:CA1004 4.1 25.2 1.0
CG L:CGU7 4.2 19.7 1.0
OE11 L:CGU7 4.3 20.4 1.0
CA L:CA1009 4.3 52.0 1.0
O L:HOH1099 4.4 25.7 1.0
OD1 L:ASN2 4.4 23.2 1.0
OE11 L:CGU25 4.6 34.9 1.0
CG L:CGU29 4.6 27.2 1.0
OE11 L:CGU29 4.7 32.5 1.0
ND2 L:ASN2 4.8 21.8 1.0
CB L:CGU7 4.8 16.8 1.0
OE21 L:CGU7 4.8 19.8 1.0
CG L:ASN2 4.9 23.2 1.0
CG L:CGU26 4.9 23.2 1.0
CG L:CGU25 5.0 32.2 1.0

Calcium binding site 3 out of 9 in 1wun

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

b:25.2
occ:1.00
 O L:HOH1085 2.7 6.7 1.0
OE22 L:CGU29 2.7 26.0 1.0
OE11 L:CGU26 2.7 22.0 1.0
O L:HOH1086 2.7 15.9 1.0
OE12 L:CGU7 2.8 21.8 1.0
O L:HOH1067 2.8 13.8 1.0
OE21 L:CGU16 2.9 19.6 1.0
OE11 L:CGU7 2.9 20.4 1.0
CD1 L:CGU7 3.2 20.0 1.0
CD2 L:CGU16 3.7 20.8 1.0
OE22 L:CGU16 3.7 22.1 1.0
CD1 L:CGU26 3.9 22.2 1.0
CD2 L:CGU29 3.9 25.1 1.0
CA L:CA1005 3.9 24.9 1.0
CA L:CA1003 4.1 31.8 1.0
CB L:CGU29 4.4 24.6 1.0
OE12 L:CGU26 4.5 23.5 1.0
CA L:GLY11 4.5 23.7 1.0
OE12 L:CGU6 4.6 16.8 1.0
CG L:CGU7 4.7 19.7 1.0
CA L:CGU26 4.8 22.3 1.0
OE21 L:CGU29 4.8 23.7 1.0
CG L:CGU29 4.8 27.2 1.0
CB L:CGU26 4.8 21.8 1.0
O L:CGU26 4.8 23.1 1.0
OD1 L:ASN2 4.9 23.2 1.0
CG L:CGU26 5.0 23.2 1.0
O L:ARG9 5.0 21.1 1.0

Calcium binding site 4 out of 9 in 1wun

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

b:24.9
occ:1.00
 OE11 L:CGU7 2.6 20.4 1.0
OE22 L:CGU26 2.7 21.0 1.0
OE11 L:CGU16 2.7 23.2 1.0
OE11 L:CGU6 2.7 15.3 1.0
OE21 L:CGU16 2.7 19.6 1.0
OD1 L:ASN2 2.7 23.2 1.0
OE11 L:CGU26 2.9 22.0 1.0
O L:ALA1 2.9 25.2 1.0
CD1 L:CGU6 3.5 18.8 1.0
OE12 L:CGU6 3.5 16.8 1.0
CD1 L:CGU26 3.5 22.2 1.0
CD1 L:CGU16 3.6 22.5 1.0
CA L:CA1006 3.6 29.2 1.0
CD1 L:CGU7 3.7 20.0 1.0
CG L:ASN2 3.7 23.2 1.0
C L:ALA1 3.7 25.3 1.0
CD2 L:CGU26 3.7 23.0 1.0
CD2 L:CGU16 3.8 20.8 1.0
CA L:CA1004 3.9 25.2 1.0
OE12 L:CGU26 4.1 23.5 1.0
CG L:CGU26 4.1 23.2 1.0
CA L:ASN2 4.2 25.0 1.0
CG L:CGU16 4.3 22.7 1.0
N L:ASN2 4.3 24.9 1.0
N L:ALA1 4.4 23.7 1.0
OE12 L:CGU16 4.4 23.6 1.0
OE12 L:CGU7 4.4 21.8 1.0
CB L:ASN2 4.5 22.8 1.0
ND2 L:ASN2 4.6 21.8 1.0
CG L:CGU7 4.6 19.7 1.0
CB L:CGU16 4.7 23.4 1.0
CA L:ALA1 4.7 24.1 1.0
CB L:CGU26 4.7 21.8 1.0
O L:HOH1085 4.7 6.7 1.0
OE21 L:CGU26 4.8 28.0 1.0
OE22 L:CGU16 4.9 22.1 1.0
CG L:CGU6 4.9 20.1 1.0
OE22 L:CGU20 5.0 30.7 1.0

Calcium binding site 5 out of 9 in 1wun

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

b:29.2
occ:1.00
 OE22 L:CGU6 2.6 18.8 1.0
O L:ALA1 2.6 25.2 1.0
OE11 L:CGU16 2.6 23.2 1.0
OE11 L:CGU6 2.7 15.3 1.0
OE21 L:CGU20 2.7 24.1 1.0
O L:HOH1111 2.8 25.1 1.0
OE22 L:CGU20 2.9 30.7 1.0
OE12 L:CGU16 3.1 23.6 1.0
CD2 L:CGU20 3.2 27.6 1.0
CD1 L:CGU6 3.2 18.8 1.0
CD1 L:CGU16 3.2 22.5 1.0
CD2 L:CGU6 3.5 20.3 1.0
CA L:CA1005 3.6 24.9 1.0
C L:ALA1 3.8 25.3 1.0
OE12 L:CGU6 3.8 16.8 1.0
CG L:CGU6 3.9 20.1 1.0
N L:ALA1 4.4 23.7 1.0
CB L:CGU6 4.5 20.2 1.0
O L:ARG15 4.5 22.8 1.0
OE21 L:CGU6 4.6 23.8 1.0
CA L:ALA1 4.6 24.1 1.0
N L:ASN2 4.6 24.9 1.0
CA L:ASN2 4.6 25.0 1.0
NE L:ARG15 4.7 18.6 1.0
CG L:CGU20 4.7 28.1 1.0
CG L:CGU16 4.7 22.7 1.0
OE21 L:CGU16 4.8 19.6 1.0
CA L:CA1008 4.9 34.4 1.0
N L:ALA3 4.9 25.4 1.0
CG L:ARG15 4.9 22.4 1.0
CB L:ALA1 5.0 21.8 1.0

Calcium binding site 6 out of 9 in 1wun

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

b:54.9
occ:1.00
 OE12 L:CGU19 2.7 33.4 1.0
OE12 L:CGU14 2.8 31.7 1.0
OE21 L:CGU14 2.8 33.6 1.0
OE21 L:CGU19 3.0 31.1 1.0
CD2 L:CGU19 3.5 31.5 1.0
CD1 L:CGU14 3.6 31.1 1.0
CD1 L:CGU19 3.6 32.6 1.0
CD2 L:CGU14 3.6 30.9 1.0
CG L:CGU14 3.7 29.4 1.0
CG L:CGU19 3.7 30.1 1.0
OE22 L:CGU19 4.4 32.9 1.0
OE11 L:CGU14 4.7 32.6 1.0
OE22 L:CGU14 4.8 29.8 1.0
OE11 L:CGU19 4.8 33.6 1.0

Calcium binding site 7 out of 9 in 1wun

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

b:34.4
occ:1.00
 OE21 L:CGU20 2.6 24.1 1.0
OE11 L:CGU20 2.8 30.0 1.0
CD1 L:CGU20 3.4 29.1 1.0
CD2 L:CGU20 3.5 27.6 1.0
CG L:CGU20 3.6 28.1 1.0
O L:ARG15 4.4 22.8 1.0
OE12 L:CGU20 4.5 30.6 1.0
CG L:ARG15 4.6 22.4 1.0
OE22 L:CGU20 4.7 30.7 1.0
OE22 L:CGU6 4.8 18.8 1.0
CA L:CA1006 4.9 29.2 1.0
OE22 L:CGU19 5.0 32.9 1.0
O L:HOH1111 5.0 25.1 1.0

Calcium binding site 8 out of 9 in 1wun

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

b:52.0
occ:1.00
 OE21 L:CGU29 2.8 23.7 1.0
OE22 L:CGU25 3.0 35.4 1.0
OE11 L:CGU25 3.0 34.9 1.0
OE11 L:CGU29 3.1 32.5 1.0
CG L:CGU25 3.5 32.2 1.0
CD1 L:CGU25 3.5 33.4 1.0
CD2 L:CGU25 3.6 34.4 1.0
NH2 L:ARG28 3.6 37.8 1.0
CD2 L:CGU29 3.8 25.1 1.0
CD1 L:CGU29 4.0 28.7 1.0
CG L:CGU29 4.2 27.2 1.0
CA L:CA1003 4.3 31.8 1.0
OE12 L:CGU25 4.6 33.6 1.0
OE21 L:CGU25 4.7 36.0 1.0
CZ L:ARG28 4.8 38.2 1.0
OE22 L:CGU29 4.9 26.0 1.0
CB L:CGU25 4.9 28.0 1.0

Calcium binding site 9 out of 9 in 1wun

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

b:23.6
occ:1.00
 O H:GLU75 2.6 21.3 1.0
OE1 H:GLU80 2.7 17.2 1.0
O H:ASP72 2.7 11.8 1.0
OE1 H:GLU70 2.7 17.2 1.0
O H:HOH2092 2.8 30.6 1.0
OE2 H:GLU70 2.9 17.3 1.0
O H:HOH2105 2.9 26.7 1.0
CD H:GLU70 3.2 16.1 1.0
CD H:GLU80 3.4 13.9 1.0
C H:GLU75 3.5 19.6 1.0
C H:ASP72 3.6 11.5 1.0
OE2 H:GLU80 4.0 15.7 1.0
CA H:HIS76 4.1 16.4 1.0
N H:HIS76 4.2 18.4 1.0
CG H:GLU80 4.3 14.6 1.0
N H:ASP72 4.3 10.3 1.0
CA H:LEU73 4.3 11.0 1.0
ND1 H:HIS76 4.3 14.6 1.0
N H:GLU75 4.3 17.7 1.0
N H:LEU73 4.3 11.8 1.0
O H:HOH2002 4.4 1.8 1.0
O H:HOH2120 4.5 20.1 1.0
CA H:ASP72 4.5 10.9 1.0
CA H:GLU75 4.5 19.6 1.0
C H:LEU73 4.6 12.0 1.0
CG H:GLU70 4.7 14.1 1.0
N H:HIS71 4.7 9.5 1.0
CE1 H:HIS76 4.9 13.4 1.0
CG H:HIS76 4.9 15.8 1.0
N H:SER74 4.9 12.6 1.0
N H:ASP77 4.9 14.4 1.0
O H:HOH2114 4.9 15.6 1.0
CB H:ASP72 4.9 10.4 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 07:20:31 2024

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