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Calcium in PDB 2zwl: Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor

Enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor

All present enzymatic activity of Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor, PDB code: 2zwl 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) 30.00 / 2.20
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 (%) 22.6 / 26.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor (pdb code 2zwl). 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 Highly Selective Peptide Inhibitor, PDB code: 2zwl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2zwl

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Calcium binding site 1 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca153

b:30.8
occ:1.00
 O L:GLN64 2.6 29.2 1.0
OD2 L:ASP46 2.6 29.3 1.0
O L:GLY47 2.6 30.9 1.0
OE1 L:GLN49 2.7 32.1 1.0
OD2 L:ASP63 2.7 31.9 1.0
OD1 L:ASP63 2.8 29.8 1.0
O L:HOH242 3.0 44.0 1.0
CG L:ASP63 3.1 31.8 1.0
C L:GLN64 3.7 29.9 1.0
CG L:ASP46 3.7 32.6 1.0
C L:GLY47 3.8 31.3 1.0
CD L:GLN49 3.8 34.0 1.0
N L:GLN66 4.0 35.7 1.0
CB L:ASP46 4.1 31.1 1.0
CA L:ASP48 4.2 32.7 1.0
N L:GLN49 4.2 33.2 1.0
N L:GLN64 4.2 27.7 1.0
CA L:LEU65 4.4 33.9 1.0
NE2 L:GLN49 4.4 32.4 1.0
N L:ASP48 4.4 31.5 1.0
N L:LEU65 4.4 32.4 1.0
CB L:ASP63 4.5 28.6 1.0
CA L:GLN64 4.6 29.5 1.0
C L:ASP46 4.6 30.3 1.0
O L:SER67 4.6 31.3 1.0
N L:GLY47 4.7 29.2 1.0
O L:HOH415 4.7 46.3 1.0
O L:ASP46 4.7 32.6 1.0
OD1 L:ASP46 4.7 33.3 1.0
C L:ASP48 4.8 33.5 1.0
C L:LEU65 4.8 35.1 1.0
C L:ASP63 4.8 27.9 1.0
CA L:GLY47 4.9 28.6 1.0
CA L:GLN66 4.9 35.9 1.0
CG L:GLN49 5.0 31.7 1.0
N L:SER67 5.0 31.8 1.0

Calcium binding site 2 out of 9 in 2zwl

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Calcium binding site 2 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca154

b:32.1
occ:1.00
 OE11 L:CGU7 2.6 23.4 1.0
OE21 L:CGU29 2.6 27.1 1.0
OE22 L:CGU7 2.6 28.4 1.0
OE11 L:CGU26 2.8 26.8 1.0
OE22 L:CGU29 2.9 28.5 1.0
CD2 L:CGU29 3.1 29.6 1.0
CD1 L:CGU7 3.3 25.9 1.0
OE12 L:CGU26 3.4 24.9 1.0
CD1 L:CGU26 3.4 26.8 1.0
CD2 L:CGU7 3.7 27.7 1.0
OE12 L:CGU7 3.9 24.5 1.0
CA L:CA155 3.9 29.1 1.0
CG L:CGU7 4.0 25.8 1.0
OD1 L:ASN2 4.4 26.3 1.0
CA L:CA160 4.4 40.2 1.0
O L:HOH173 4.5 30.6 1.0
CG L:CGU29 4.6 30.9 1.0
CB L:CGU7 4.7 23.1 1.0
OE21 L:CGU7 4.7 28.6 1.0
ND2 L:ASN2 4.8 27.2 1.0
CG L:CGU26 4.9 26.1 1.0
CG L:ASN2 4.9 27.2 1.0

Calcium binding site 3 out of 9 in 2zwl

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Calcium binding site 3 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca155

b:29.1
occ:1.00
 OE22 L:CGU29 2.6 28.5 1.0
OE12 L:CGU26 2.7 24.9 1.0
OE11 L:CGU7 2.8 23.4 1.0
O L:HOH191 2.8 27.9 1.0
OE21 L:CGU16 2.9 20.2 1.0
OE12 L:CGU7 2.9 24.5 1.0
CD1 L:CGU7 3.2 25.9 1.0
CD2 L:CGU16 3.7 23.4 1.0
OE22 L:CGU16 3.7 23.0 1.0
CD2 L:CGU29 3.8 29.6 1.0
CA L:CA156 3.8 26.4 1.0
CD1 L:CGU26 3.9 26.8 1.0
CA L:CA154 3.9 32.1 1.0
CB L:CGU29 4.3 29.0 1.0
OE11 L:CGU26 4.5 26.8 1.0
OE21 L:CGU29 4.6 27.1 1.0
CA L:GLY11 4.6 28.7 1.0
CA L:CGU26 4.7 26.1 1.0
CG L:CGU29 4.7 30.9 1.0
CG L:CGU7 4.7 25.8 1.0
O L:CGU26 4.7 26.8 1.0
OE11 L:CGU6 4.8 22.2 1.0
CB L:CGU26 4.8 24.8 1.0
CG L:CGU26 4.9 26.1 1.0
OD1 L:ASN2 4.9 26.3 1.0

Calcium binding site 4 out of 9 in 2zwl

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Calcium binding site 4 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca156

b:26.4
occ:1.00
 OE21 L:CGU16 2.6 20.2 1.0
OE12 L:CGU7 2.6 24.5 1.0
OE22 L:CGU26 2.6 26.9 1.0
OE12 L:CGU16 2.6 27.3 1.0
OD1 L:ASN2 2.8 26.3 1.0
OE12 L:CGU6 2.8 19.1 1.0
O L:ALA1 2.9 27.6 1.0
OE12 L:CGU26 2.9 24.9 1.0
CD1 L:CGU16 3.3 24.5 1.0
OE11 L:CGU6 3.5 22.2 1.0
CD1 L:CGU6 3.5 23.7 1.0
CD1 L:CGU26 3.6 26.8 1.0
CD2 L:CGU16 3.6 23.4 1.0
CA L:CA157 3.7 31.8 1.0
CD2 L:CGU26 3.7 26.7 1.0
CD1 L:CGU7 3.7 25.9 1.0
CG L:ASN2 3.8 27.2 1.0
C L:ALA1 3.8 28.6 1.0
CA L:CA155 3.8 29.1 1.0
OE11 L:CGU16 4.0 24.7 1.0
CG L:CGU16 4.0 23.9 1.0
CG L:CGU26 4.2 26.1 1.0
OE11 L:CGU26 4.3 26.8 1.0
CA L:ASN2 4.4 29.8 1.0
N L:ALA1 4.4 26.9 1.0
N L:ASN2 4.5 29.2 1.0
OE11 L:CGU7 4.5 23.4 1.0
ND2 L:ASN2 4.6 27.2 1.0
CG L:CGU7 4.6 25.8 1.0
CB L:CGU16 4.6 27.4 1.0
CB L:ASN2 4.7 27.1 1.0
OE22 L:CGU16 4.7 23.0 1.0
CB L:CGU26 4.7 24.8 1.0
OE21 L:CGU26 4.7 28.6 1.0
CA L:ALA1 4.8 27.4 1.0
OE22 L:CGU20 5.0 30.4 1.0

Calcium binding site 5 out of 9 in 2zwl

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Calcium binding site 5 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca157

b:31.8
occ:1.00
 OE22 L:CGU6 2.6 26.5 1.0
O L:ALA1 2.7 27.6 1.0
OE12 L:CGU6 2.7 19.1 1.0
OE12 L:CGU16 2.8 27.3 1.0
OE22 L:CGU20 2.8 30.4 1.0
OE21 L:CGU20 2.8 29.5 1.0
OE11 L:CGU16 2.9 24.7 1.0
CD2 L:CGU20 3.1 30.2 1.0
CD1 L:CGU16 3.2 24.5 1.0
CD1 L:CGU6 3.2 23.7 1.0
CD2 L:CGU6 3.6 26.9 1.0
CA L:CA156 3.7 26.4 1.0
C L:ALA1 3.7 28.6 1.0
OE11 L:CGU6 3.8 22.2 1.0
CG L:CGU6 3.9 25.5 1.0
N L:ALA1 4.3 26.9 1.0
O L:HOH182 4.5 37.6 1.0
CA L:ALA1 4.5 27.4 1.0
N L:ASN2 4.5 29.2 1.0
CB L:CGU6 4.6 26.2 1.0
CA L:ASN2 4.6 29.8 1.0
CG L:CGU20 4.6 30.6 1.0
CG L:CGU16 4.7 23.9 1.0
OE21 L:CGU6 4.7 27.4 1.0
O L:ARG15 4.7 25.9 1.0
N L:ALA3 4.7 31.9 1.0
NE L:ARG15 4.8 23.8 1.0
CB L:ALA1 4.9 27.3 1.0
CA L:CA159 5.0 43.2 1.0
OE21 L:CGU16 5.0 20.2 1.0

Calcium binding site 6 out of 9 in 2zwl

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Calcium binding site 6 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca158

b:52.4
occ:1.00
 OE12 L:CGU19 2.7 36.4 1.0
OE12 L:CGU14 2.7 37.6 1.0
OE21 L:CGU14 2.8 37.3 1.0
O L:HOH268 3.1 52.1 1.0
OE21 L:CGU19 3.1 38.9 1.0
O L:HOH379 3.3 58.5 1.0
CD2 L:CGU19 3.4 39.1 1.0
CD2 L:CGU14 3.4 36.1 1.0
CD1 L:CGU14 3.5 36.6 1.0
CD1 L:CGU19 3.5 37.8 1.0
CG L:CGU14 3.5 35.3 1.0
CG L:CGU19 3.5 37.0 1.0
OE22 L:CGU19 4.2 41.5 1.0
OE22 L:CGU14 4.5 37.3 1.0
OE11 L:CGU14 4.6 40.4 1.0
OE11 L:CGU19 4.7 39.6 1.0

Calcium binding site 7 out of 9 in 2zwl

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Calcium binding site 7 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca159

b:43.2
occ:1.00
 OE21 L:CGU20 2.7 29.5 1.0
OE12 L:CGU20 2.7 33.2 1.0
O L:HOH241 3.0 33.3 1.0
O L:HOH182 3.0 37.6 1.0
CD1 L:CGU20 3.5 31.5 1.0
CD2 L:CGU20 3.6 30.2 1.0
CG L:CGU20 3.8 30.6 1.0
OE11 L:CGU20 4.5 33.6 1.0
O L:ARG15 4.6 25.9 1.0
CG L:ARG15 4.6 29.0 1.0
OE22 L:CGU6 4.7 26.5 1.0
OE22 L:CGU20 4.8 30.4 1.0
CA L:CA157 5.0 31.8 1.0

Calcium binding site 8 out of 9 in 2zwl

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Calcium binding site 8 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca160

b:40.2
occ:1.00
 OE21 L:CGU29 2.6 27.1 1.0
OE22 L:CGU25 2.8 43.0 1.0
OE12 L:CGU29 2.9 37.5 1.0
CD2 L:CGU25 3.4 40.8 1.0
CG L:CGU25 3.5 38.5 1.0
CD2 L:CGU29 3.6 29.6 1.0
CD1 L:CGU29 3.7 34.0 1.0
CD1 L:CGU25 3.8 40.6 1.0
OE12 L:CGU25 3.9 41.2 1.0
CG L:CGU29 3.9 30.9 1.0
NH2 L:ARG28 4.0 39.3 1.0
CA L:CA154 4.4 32.1 1.0
OE21 L:CGU25 4.4 41.6 1.0
OE11 L:CGU25 4.5 43.5 1.0
OE22 L:CGU29 4.7 28.5 1.0
OE11 L:CGU29 4.8 36.8 1.0
CB L:CGU25 4.9 33.4 1.0

Calcium binding site 9 out of 9 in 2zwl

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Calcium binding site 9 out of 9 in the Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor


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 Highly Selective Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca258

b:33.9
occ:1.00
 O H:GLU75 2.4 25.8 1.0
OE2 H:GLU70 2.5 23.2 1.0
O H:ASP72 2.6 14.2 1.0
OE1 H:GLU80 2.8 27.8 1.0
O H:HOH321 2.9 22.1 1.0
OE1 H:GLU70 3.1 24.4 1.0
CD H:GLU70 3.1 25.4 1.0
C H:GLU75 3.5 25.1 1.0
C H:ASP72 3.7 14.9 1.0
CD H:GLU80 3.7 29.9 1.0
CA H:HIS76 4.0 24.2 1.0
OE2 H:GLU80 4.0 32.2 1.0
N H:HIS76 4.2 25.0 1.0
N H:ASP72 4.3 12.8 1.0
O H:HOH271 4.4 13.6 1.0
ND1 H:HIS76 4.4 28.6 1.0
CA H:LEU73 4.5 16.4 1.0
N H:GLU75 4.5 22.6 1.0
N H:LEU73 4.5 16.6 1.0
CA H:ASP72 4.5 14.8 1.0
CG H:GLU70 4.6 22.7 1.0
CA H:GLU75 4.6 24.8 1.0
N H:HIS71 4.7 12.7 1.0
N H:ASP77 4.8 20.8 1.0
C H:LEU73 4.8 18.3 1.0
C H:HIS76 4.8 23.4 1.0
CB H:ASP72 5.0 17.3 1.0
CG H:HIS76 5.0 29.2 1.0

Reference:

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. Human Factor Viia-Tissue Factor Complexed with Highly Selective Peptide Inhibitor To Be Published.
Page generated: Sat Jul 13 06:52:11 2024

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