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Calcium in PDB 2zp0: Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine

Enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine

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

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine, PDB code: 2zp0 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) 14.94 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.370, 81.990, 123.310, 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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine (pdb code 2zp0). 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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine, PDB code: 2zp0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2zp0

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Calcium binding site 1 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca502

b:21.4
occ:1.00
 OE1 L:GLN49 2.6 21.2 1.0
OD2 L:ASP46 2.7 26.8 1.0
OD2 L:ASP63 2.7 23.1 1.0
O L:GLN64 2.7 22.2 1.0
O L:GLY47 2.8 24.2 1.0
OD1 L:ASP63 2.9 21.0 1.0
CG L:ASP63 3.1 21.3 1.0
O L:HOH1113 3.4 15.6 1.0
C L:GLY47 3.4 22.0 1.0
CG L:ASP46 3.6 25.6 1.0
CD L:GLN49 3.7 20.2 1.0
C L:GLN64 3.7 20.6 1.0
CB L:ASP46 3.8 24.4 1.0
CA L:ASP48 3.8 21.6 1.0
N L:ASP48 3.9 21.9 1.0
NE2 L:GLN49 4.0 19.5 1.0
N L:GLN49 4.1 21.0 1.0
N L:GLY47 4.2 21.6 1.0
N L:GLN66 4.2 23.4 1.0
C L:ASP46 4.3 22.7 1.0
CA L:LEU65 4.3 22.6 1.0
CA L:GLY47 4.4 21.2 1.0
N L:LEU65 4.5 20.9 1.0
N L:GLN64 4.5 19.4 1.0
C L:ASP48 4.5 21.5 1.0
O L:ASP46 4.6 25.3 1.0
CB L:ASP63 4.6 19.3 1.0
CA L:ASP46 4.7 22.6 1.0
CA L:GLN64 4.7 19.8 1.0
OD1 L:ASP46 4.8 27.9 1.0
C L:LEU65 4.8 23.9 1.0
CB L:ASP48 4.9 22.1 1.0
O L:SER67 5.0 21.4 1.0
CG L:GLN49 5.0 21.1 1.0

Calcium binding site 2 out of 9 in 2zp0

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Calcium binding site 2 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca503

b:27.8
occ:1.00
 OE21 L:CGU29 2.7 20.2 1.0
OE22 L:CGU29 2.9 21.6 1.0
OE22 L:CGU7 2.9 16.2 1.0
OE12 L:CGU7 2.9 22.7 1.0
CD1 L:CGU7 3.1 20.8 1.0
OE12 L:CGU26 3.1 24.2 1.0
CD2 L:CGU29 3.1 21.8 1.0
OE11 L:CGU7 3.2 22.4 1.0
O L:HOH1117 3.2 16.0 1.0
OE11 L:CGU26 3.4 21.3 1.0
CD1 L:CGU26 3.6 22.1 1.0
CA L:CA504 3.7 36.9 1.0
CD2 L:CGU7 3.8 18.8 1.0
CG L:CGU7 4.0 19.0 1.0
OE11 L:CGU25 4.3 26.9 1.0
OD1 L:ASN2 4.5 25.1 1.0
CG L:CGU29 4.6 23.1 1.0
ND2 L:ASN2 4.6 27.0 1.0
OE11 L:CGU29 4.6 22.8 1.0
O L:HOH1085 4.7 36.8 1.0
CA L:CA509 4.7 32.6 1.0
CB L:CGU7 4.7 16.9 1.0
CG L:ASN2 4.9 25.7 1.0
O L:HOH1095 5.0 20.1 1.0
OE21 L:CGU7 5.0 22.5 1.0

Calcium binding site 3 out of 9 in 2zp0

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Calcium binding site 3 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca504

b:36.9
occ:1.00
 OE22 L:CGU29 2.7 21.6 1.0
OE12 L:CGU7 2.9 22.7 1.0
OE11 L:CGU7 2.9 22.4 1.0
OE11 L:CGU26 2.9 21.3 1.0
OE21 L:CGU16 2.9 24.8 1.0
O L:HOH1084 2.9 27.2 1.0
O L:HOH1085 3.2 36.8 1.0
CD1 L:CGU7 3.2 20.8 1.0
CA L:CA503 3.7 27.8 1.0
CA L:CA505 3.7 20.4 1.0
CD2 L:CGU29 3.9 21.8 1.0
CD2 L:CGU16 3.9 24.2 1.0
CD1 L:CGU26 4.1 22.1 1.0
OE22 L:CGU16 4.2 27.0 1.0
CB L:CGU29 4.4 22.1 1.0
OE12 L:CGU6 4.6 15.5 1.0
OE21 L:CGU29 4.7 20.2 1.0
CG L:CGU7 4.7 19.0 1.0
OE12 L:CGU26 4.7 24.2 1.0
CA L:CGU26 4.8 21.0 1.0
CA L:GLY11 4.8 18.1 1.0
CG L:CGU29 4.8 23.1 1.0
O L:CGU26 4.9 23.9 1.0
O L:ARG9 4.9 17.3 1.0
CB L:CGU26 4.9 21.9 1.0
OD1 L:ASN2 5.0 25.1 1.0

Calcium binding site 4 out of 9 in 2zp0

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Calcium binding site 4 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca505

b:20.4
occ:1.00
 OE11 L:CGU16 2.6 21.7 1.0
OD1 L:ASN2 2.7 25.1 1.0
OE21 L:CGU16 2.7 24.8 1.0
OE11 L:CGU7 2.7 22.4 1.0
OE22 L:CGU26 2.8 22.6 1.0
OE11 L:CGU26 2.8 21.3 1.0
OE11 L:CGU6 2.9 17.1 1.0
CD1 L:CGU16 3.1 22.9 1.0
O L:ALA1 3.1 31.3 1.0
OE12 L:CGU6 3.4 15.5 1.0
OE12 L:CGU16 3.5 24.6 1.0
CD1 L:CGU6 3.6 18.3 1.0
CD1 L:CGU26 3.6 22.1 1.0
CD2 L:CGU26 3.7 21.8 1.0
CA L:CA504 3.7 36.9 1.0
CD2 L:CGU16 3.8 24.2 1.0
CA L:CA506 3.8 39.9 1.0
CD1 L:CGU7 3.9 20.8 1.0
CG L:ASN2 3.9 25.7 1.0
CG L:CGU16 4.0 23.8 1.0
CG L:CGU26 4.1 22.7 1.0
C L:ALA1 4.1 31.1 1.0
OE12 L:CGU26 4.4 24.2 1.0
O L:HOH1084 4.5 27.2 1.0
CB L:CGU26 4.5 21.9 1.0
CA L:ASN2 4.6 28.1 1.0
OE21 L:CGU26 4.6 24.5 1.0
CB L:CGU16 4.7 22.9 1.0
OE12 L:CGU7 4.7 22.7 1.0
CG L:CGU7 4.7 19.0 1.0
N L:ASN2 4.8 29.7 1.0
CB L:ASN2 4.8 26.7 1.0
ND2 L:ASN2 4.8 27.0 1.0
N L:ALA1 4.9 32.4 1.0
OE22 L:CGU16 4.9 27.0 1.0

Calcium binding site 5 out of 9 in 2zp0

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Calcium binding site 5 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca506

b:39.9
occ:1.00
 OE11 L:CGU6 2.7 17.1 1.0
OE22 L:CGU6 2.7 20.1 1.0
O L:ALA1 2.8 31.3 1.0
OE22 L:CGU20 2.8 35.7 1.0
OE12 L:CGU16 2.9 24.6 1.0
OE21 L:CGU20 2.9 35.8 1.0
O L:HOH1107 2.9 19.8 1.0
OE11 L:CGU16 2.9 21.7 1.0
CD2 L:CGU20 3.2 34.2 1.0
CD1 L:CGU16 3.2 22.9 1.0
CD1 L:CGU6 3.4 18.3 1.0
CD2 L:CGU6 3.6 19.2 1.0
CA L:CA505 3.8 20.4 1.0
C L:ALA1 3.9 31.1 1.0
CG L:CGU6 4.1 18.6 1.0
OE12 L:CGU6 4.1 15.5 1.0
N L:ALA1 4.3 32.4 1.0
O L:ARG15 4.5 17.2 1.0
OE21 L:CGU6 4.6 21.9 1.0
CG L:ARG15 4.7 23.1 1.0
CA L:ALA1 4.7 31.7 1.0
CG L:CGU20 4.7 34.2 1.0
N L:ASN2 4.7 29.7 1.0
CG L:CGU16 4.7 23.8 1.0
NE L:ARG15 4.8 28.5 1.0
CA L:ASN2 4.8 28.1 1.0
CB L:CGU6 4.8 18.1 1.0
N L:ALA3 4.8 28.6 1.0
CD L:ARG15 4.9 26.1 1.0
CA L:CA508 4.9 53.5 1.0
OE22 L:CGU26 4.9 22.6 1.0

Calcium binding site 6 out of 9 in 2zp0

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Calcium binding site 6 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca507

b:39.5
occ:1.00
 OE12 L:CGU19 2.7 36.5 1.0
OE21 L:CGU14 2.7 23.9 1.0
OE12 L:CGU14 2.7 23.6 1.0
OE21 L:CGU19 2.9 38.2 1.0
CD2 L:CGU14 3.4 21.7 1.0
CD2 L:CGU19 3.5 36.1 1.0
CD1 L:CGU19 3.5 35.6 1.0
CG L:CGU19 3.5 34.2 1.0
CD1 L:CGU14 3.5 22.5 1.0
CG L:CGU14 3.6 20.9 1.0
OE22 L:CGU14 4.4 22.8 1.0
OE22 L:CGU19 4.6 37.0 1.0
OE11 L:CGU14 4.7 23.2 1.0
OE11 L:CGU19 4.7 36.2 1.0
CB L:CGU19 5.0 32.7 1.0

Calcium binding site 7 out of 9 in 2zp0

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Calcium binding site 7 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca508

b:53.5
occ:1.00
 OE21 L:CGU20 2.8 35.8 1.0
OE11 L:CGU20 3.2 36.1 1.0
CD2 L:CGU20 3.8 34.2 1.0
CD1 L:CGU20 3.9 34.3 1.0
CG L:CGU20 4.1 34.2 1.0
O L:HOH1107 4.5 19.8 1.0
OE22 L:CGU6 4.6 20.1 1.0
CG L:ARG15 4.6 23.1 1.0
OE22 L:CGU19 4.7 37.0 1.0
O L:ARG15 4.7 17.2 1.0
OE22 L:CGU20 4.9 35.7 1.0
OE12 L:CGU20 4.9 34.2 1.0
CA L:CA506 4.9 39.9 1.0

Calcium binding site 8 out of 9 in 2zp0

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Calcium binding site 8 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca509

b:32.6
occ:1.00
 OE21 L:CGU29 2.5 20.2 1.0
OE11 L:CGU25 2.8 26.9 1.0
OE22 L:CGU25 3.0 27.4 1.0
NH2 L:ARG28 3.0 29.2 1.0
CD1 L:CGU25 3.3 26.5 1.0
CG L:CGU25 3.3 25.4 1.0
CD2 L:CGU25 3.4 26.4 1.0
CD2 L:CGU29 3.5 21.8 1.0
CD1 L:CGU29 3.5 23.7 1.0
OE11 L:CGU29 3.5 22.8 1.0
CG L:CGU29 3.6 23.1 1.0
OE12 L:CGU29 4.0 27.1 1.0
O L:HOH1117 4.1 16.0 1.0
CZ L:ARG28 4.3 30.6 1.0
OE12 L:CGU25 4.3 23.8 1.0
OE21 L:CGU25 4.4 30.4 1.0
OE22 L:CGU29 4.6 21.6 1.0
CA L:CA503 4.7 27.8 1.0
CB L:CGU25 4.8 22.2 1.0
NE L:ARG28 4.8 30.7 1.0
O L:CGU25 5.0 21.1 1.0

Calcium binding site 9 out of 9 in 2zp0

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Calcium binding site 9 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Benzylsulfonamide-D- Ile-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 Benzylsulfonamide-D- Ile-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca501

b:20.7
occ:1.00
 O H:GLU75 2.7 20.2 1.0
O H:ASP72 2.8 10.4 1.0
OE1 H:GLU70 2.9 17.2 1.0
OE2 H:GLU70 2.9 18.7 1.0
O H:HOH1096 3.0 12.0 1.0
O H:HOH1086 3.1 26.1 1.0
CD H:GLU70 3.2 15.3 1.0
OE2 H:GLU80 3.2 10.4 1.0
CD H:GLU80 3.3 9.4 1.0
OE1 H:GLU80 3.4 10.9 1.0
C H:ASP72 3.6 8.5 1.0
C H:GLU75 3.6 17.3 1.0
CG H:GLU80 4.1 8.9 1.0
N H:ASP72 4.1 9.7 1.0
CA H:HIS76 4.2 13.8 1.0
N H:HIS76 4.3 16.0 1.0
N H:LEU73 4.3 7.2 1.0
N H:GLU75 4.4 14.2 1.0
CA H:ASP72 4.4 8.2 1.0
CA H:LEU73 4.4 5.7 1.0
O H:HOH1002 4.5 6.4 1.0
N H:HIS71 4.5 11.4 1.0
ND1 H:HIS76 4.6 14.9 1.0
CA H:GLU75 4.6 16.9 1.0
CG H:GLU70 4.7 14.5 1.0
C H:LEU73 4.8 7.8 1.0
O H:HOH1109 4.9 12.4 1.0
CA H:GLU70 4.9 12.4 1.0
N H:SER74 4.9 8.4 1.0
CB H:ASP72 4.9 8.6 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, S.Watanabe, S.Itoh, M.Ohta, T.Kozono. Peptide Mimetic Factor Viia Inhibitor: Importance of Hydrophilic Pocket in S2 Site to Improve Selectivity Aganist Thrombin Lett.Drug Des.Discovery V. 2 177 2005.
ISSN: ISSN 1570-1808
Page generated: Sat Dec 12 04:01:52 2020

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