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Calcium in PDB 2zzu: Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine

Enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine

All present enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine, PDB code: 2zzu was solved by S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, T.Koga, K.Hattori, T.Shiraishi, M.Haramura, H.Sato, M.Ohta, T.Kozono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.400, 82.220, 123.470, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine (pdb code 2zzu). 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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine, PDB code: 2zzu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2zzu

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Calcium binding site 1 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1002

b:35.3
occ:1.00
 OD2 L:ASP46 2.6 28.0 1.0
OE1 L:GLN49 2.6 25.2 1.0
O L:GLN64 2.7 26.9 1.0
OD2 L:ASP63 2.8 25.4 1.0
O L:GLY47 2.8 32.5 1.0
OD1 L:ASP63 2.9 26.8 1.0
CG L:ASP63 3.1 26.1 1.0
O L:HOH285 3.2 30.0 1.0
C L:GLY47 3.6 30.5 1.0
CG L:ASP46 3.6 31.8 1.0
C L:GLN64 3.7 25.5 1.0
CD L:GLN49 3.8 26.8 1.0
CB L:ASP46 4.0 30.9 1.0
CA L:ASP48 4.0 28.7 1.0
N L:GLN66 4.1 29.5 1.0
N L:GLN49 4.1 26.9 1.0
N L:ASP48 4.2 30.2 1.0
CA L:LEU65 4.3 28.8 1.0
N L:GLN64 4.3 25.1 1.0
NE2 L:GLN49 4.3 26.5 1.0
N L:LEU65 4.3 27.2 1.0
C L:ASP46 4.4 29.4 1.0
N L:GLY47 4.4 28.7 1.0
O L:ASP46 4.5 31.6 1.0
CA L:GLN64 4.6 25.2 1.0
CB L:ASP63 4.6 24.0 1.0
C L:ASP48 4.6 28.3 1.0
CA L:GLY47 4.6 28.8 1.0
C L:LEU65 4.7 28.9 1.0
OD1 L:ASP46 4.8 34.4 1.0
O L:SER67 4.8 28.0 1.0
CA L:ASP46 4.8 29.3 1.0
CG L:GLN49 5.0 25.5 1.0
C L:ASP63 5.0 24.1 1.0

Calcium binding site 2 out of 9 in 2zzu

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Calcium binding site 2 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1003

b:34.3
occ:1.00
 OE12 L:CGU7 2.7 30.1 1.0
OE22 L:CGU7 2.7 26.5 1.0
OE22 L:CGU29 2.8 32.0 1.0
OE12 L:CGU26 2.9 26.9 1.0
OE21 L:CGU29 2.9 33.2 1.0
CD2 L:CGU29 3.2 31.5 1.0
CD1 L:CGU7 3.3 28.0 1.0
OE11 L:CGU26 3.4 25.2 1.0
CD1 L:CGU26 3.5 25.9 1.0
CA L:CA1004 3.7 31.2 1.0
CD2 L:CGU7 3.8 26.6 1.0
OE11 L:CGU7 3.8 27.9 1.0
CG L:CGU7 4.1 26.7 1.0
OD1 L:ASN2 4.4 22.9 1.0
CG L:CGU29 4.7 31.2 1.0
O L:HOH205 4.7 28.1 1.0
CA L:CA1009 4.7 60.7 1.0
OE11 L:CGU29 4.8 32.2 1.0
CB L:CGU7 4.8 24.1 1.0
OE21 L:CGU7 4.9 28.2 1.0
CG L:CGU26 4.9 25.3 1.0
ND2 L:ASN2 4.9 21.9 1.0
O L:HOH156 5.0 28.6 1.0

Calcium binding site 3 out of 9 in 2zzu

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

b:31.2
occ:1.00
 OE11 L:CGU26 2.8 25.2 1.0
OE22 L:CGU29 2.8 32.0 1.0
O L:HOH155 2.8 19.1 1.0
O L:HOH156 2.8 28.6 1.0
OE12 L:CGU7 2.9 30.1 1.0
O L:HOH161 2.9 19.5 1.0
OE11 L:CGU7 2.9 27.9 1.0
OE21 L:CGU16 3.0 28.2 1.0
CD1 L:CGU7 3.3 28.0 1.0
CA L:CA1003 3.7 34.3 1.0
CD2 L:CGU16 3.9 27.3 1.0
CD1 L:CGU26 3.9 25.9 1.0
CA L:CA1005 3.9 25.9 1.0
CD2 L:CGU29 4.0 31.5 1.0
OE22 L:CGU16 4.0 28.5 1.0
CB L:CGU29 4.4 28.9 1.0
OE12 L:CGU26 4.5 26.9 1.0
OE12 L:CGU6 4.6 23.0 1.0
CA L:GLY11 4.7 25.7 1.0
CA L:CGU26 4.8 24.9 1.0
CG L:CGU7 4.8 26.7 1.0
CG L:CGU29 4.8 31.2 1.0
OE21 L:CGU29 4.8 33.2 1.0
CB L:CGU26 4.9 24.8 1.0
O L:CGU26 4.9 25.1 1.0
OE11 L:CGU29 4.9 32.2 1.0

Calcium binding site 4 out of 9 in 2zzu

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Calcium binding site 4 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1005

b:25.9
occ:1.00
 OE11 L:CGU7 2.6 27.9 1.0
OE11 L:CGU16 2.7 27.4 1.0
OE22 L:CGU26 2.7 24.4 1.0
OE11 L:CGU6 2.8 26.0 1.0
OE21 L:CGU16 2.8 28.2 1.0
OE11 L:CGU26 2.8 25.2 1.0
OD1 L:ASN2 2.9 22.9 1.0
O L:ALA1 2.9 27.0 1.0
CD1 L:CGU16 3.5 27.6 1.0
CD1 L:CGU26 3.5 25.9 1.0
CD1 L:CGU6 3.6 25.6 1.0
OE12 L:CGU6 3.6 23.0 1.0
CG L:ASN2 3.7 22.0 1.0
CD2 L:CGU26 3.7 26.4 1.0
C L:ALA1 3.8 26.9 1.0
CA L:CA1006 3.8 32.2 1.0
CD1 L:CGU7 3.8 28.0 1.0
CD2 L:CGU16 3.9 27.3 1.0
CA L:CA1004 3.9 31.2 1.0
CG L:CGU26 4.1 25.3 1.0
OE12 L:CGU16 4.2 27.9 1.0
CG L:CGU16 4.2 28.6 1.0
OE12 L:CGU26 4.2 26.9 1.0
ND2 L:ASN2 4.3 21.9 1.0
CA L:ASN2 4.3 25.4 1.0
N L:ASN2 4.4 26.4 1.0
N L:ALA1 4.5 27.2 1.0
O L:HOH155 4.5 19.1 1.0
CB L:ASN2 4.6 22.5 1.0
CB L:CGU16 4.7 28.6 1.0
OE12 L:CGU7 4.7 30.1 1.0
CG L:CGU7 4.7 26.7 1.0
CB L:CGU26 4.7 24.8 1.0
CA L:ALA1 4.8 27.2 1.0
OE21 L:CGU26 4.8 30.9 1.0
OE22 L:CGU16 5.0 28.5 1.0

Calcium binding site 5 out of 9 in 2zzu

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Calcium binding site 5 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1006

b:32.2
occ:1.00
 OE11 L:CGU16 2.7 27.4 1.0
OE11 L:CGU6 2.8 26.0 1.0
O L:HOH262 2.8 33.2 1.0
O L:ALA1 2.8 27.0 1.0
OE21 L:CGU20 2.9 36.9 1.0
OE22 L:CGU20 2.9 39.3 1.0
OE22 L:CGU6 2.9 32.3 1.0
OE12 L:CGU16 3.0 27.9 1.0
CD2 L:CGU6 3.2 27.8 1.0
CD1 L:CGU16 3.2 27.6 1.0
CD1 L:CGU6 3.2 25.6 1.0
CD2 L:CGU20 3.2 37.0 1.0
OE21 L:CGU6 3.6 31.9 1.0
CG L:CGU6 3.7 26.6 1.0
CA L:CA1005 3.8 25.9 1.0
C L:ALA1 3.9 26.9 1.0
OE12 L:CGU6 3.9 23.0 1.0
CB L:CGU6 4.5 24.2 1.0
NE L:ARG15 4.5 26.9 1.0
O L:ARG15 4.6 23.0 1.0
N L:ALA1 4.6 27.2 1.0
N L:ASN2 4.7 26.4 1.0
CG L:CGU16 4.7 28.6 1.0
CA L:ASN2 4.7 25.4 1.0
CA L:ALA1 4.7 27.2 1.0
CG L:CGU20 4.7 36.6 1.0
CA L:CA1008 4.8 45.5 1.0
CG L:ARG15 4.9 27.2 1.0

Calcium binding site 6 out of 9 in 2zzu

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Calcium binding site 6 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1007

b:61.4
occ:1.00
 OE12 L:CGU19 2.7 42.6 1.0
OE12 L:CGU14 2.8 31.4 1.0
OE21 L:CGU14 2.9 30.4 1.0
OE21 L:CGU19 3.1 41.5 1.0
CD2 L:CGU19 3.4 40.2 1.0
CD1 L:CGU19 3.6 40.2 1.0
CD1 L:CGU14 3.6 30.0 1.0
CD2 L:CGU14 3.6 28.8 1.0
CG L:CGU19 3.6 38.6 1.0
CG L:CGU14 3.7 28.8 1.0
OE22 L:CGU19 4.2 43.2 1.0
OE22 L:CGU14 4.7 27.4 1.0
OE11 L:CGU14 4.7 31.1 1.0
OE11 L:CGU19 4.8 40.6 1.0

Calcium binding site 7 out of 9 in 2zzu

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Calcium binding site 7 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1008

b:45.5
occ:1.00
 OE21 L:CGU20 2.8 36.9 1.0
O L:HOH287 2.9 59.0 1.0
OE11 L:CGU20 3.0 38.8 1.0
CD2 L:CGU20 3.6 37.0 1.0
CD1 L:CGU20 3.8 37.5 1.0
CG L:CGU20 3.8 36.6 1.0
O L:ARG15 4.5 23.0 1.0
CG L:ARG15 4.6 27.2 1.0
OE22 L:CGU20 4.6 39.3 1.0
CA L:CA1006 4.8 32.2 1.0
O L:HOH262 4.8 33.2 1.0
OE22 L:CGU6 4.9 32.3 1.0
OE12 L:CGU20 4.9 39.6 1.0

Calcium binding site 8 out of 9 in 2zzu

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Calcium binding site 8 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-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 2.8 33.2 1.0
OE11 L:CGU25 3.1 41.3 1.0
OE22 L:CGU25 3.1 41.2 1.0
NH2 L:ARG28 3.3 39.4 1.0
CG L:CGU25 3.4 37.4 1.0
CD1 L:CGU25 3.5 39.3 1.0
CD2 L:CGU25 3.6 39.7 1.0
CD2 L:CGU29 3.9 31.5 1.0
CD1 L:CGU29 4.3 31.2 1.0
OE12 L:CGU29 4.3 33.8 1.0
CG L:CGU29 4.4 31.2 1.0
OE12 L:CGU25 4.6 39.9 1.0
CZ L:ARG28 4.6 38.7 1.0
OE11 L:CGU29 4.7 32.2 1.0
OE21 L:CGU25 4.7 43.0 1.0
CA L:CA1003 4.7 34.3 1.0
CB L:CGU25 4.9 31.5 1.0

Calcium binding site 9 out of 9 in 2zzu

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Calcium binding site 9 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Ethylsulfonamide-D-5- (3-Carboxybenzyloxy)-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- (3-Carboxybenzyloxy)-Trp-Gln-P-Aminobenzamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1001

b:31.1
occ:1.00
 O H:ASP72 2.7 12.7 1.0
O H:GLU75 2.7 25.7 1.0
OE1 H:GLU80 2.7 22.3 1.0
OE1 H:GLU70 2.8 28.8 1.0
O H:HOH405 2.8 21.5 1.0
O H:HOH396 2.8 21.2 1.0
OE2 H:GLU70 2.9 27.4 1.0
CD H:GLU70 3.2 26.4 1.0
CD H:GLU80 3.3 18.1 1.0
C H:GLU75 3.5 22.3 1.0
C H:ASP72 3.6 12.6 1.0
OE2 H:GLU80 3.7 18.8 1.0
CA H:HIS76 4.1 19.1 1.0
N H:HIS76 4.2 20.8 1.0
CG H:GLU80 4.2 17.4 1.0
N H:ASP72 4.3 12.3 1.0
N H:GLU75 4.3 19.2 1.0
O H:HOH258 4.4 4.5 1.0
CA H:LEU73 4.4 12.8 1.0
N H:LEU73 4.4 12.6 1.0
O H:HOH417 4.4 26.4 1.0
ND1 H:HIS76 4.4 18.0 1.0
CA H:ASP72 4.5 12.9 1.0
CA H:GLU75 4.5 22.2 1.0
C H:LEU73 4.7 13.0 1.0
CG H:GLU70 4.7 23.2 1.0
N H:HIS71 4.7 12.0 1.0
N H:SER74 4.9 14.1 1.0
CB H:ASP72 4.9 13.3 1.0
N H:ASP77 4.9 16.4 1.0
CG H:HIS76 5.0 19.0 1.0

Reference:

T.Shiraishi, S.Kadono, M.Haramura, H.Kodama, Y.Ono, H.Iikura, T.Esaki, T.Koga, K.Hattori, Y.Watanabe, A.Sakamoto, K.Yoshihashi, T.Kitazawa, K.Esaki, M.Ohta, H.Sato, T.Kozono. Design and Synthesis of Peptidomimetic Factor Viia Inhibitors Chem.Pharm.Bull. V. 58 38 2010.
ISSN: ISSN 0009-2363
PubMed: 20045964
DOI: 10.1248/CPB.58.38
Page generated: Sat Jul 13 07:00:31 2024

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