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Calcium in PDB 1wss: Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4

Enzymatic activity of Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4

All present enzymatic activity of Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4:
3.4.21.21;

Protein crystallography data

The structure of Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4, PDB code: 1wss was solved by S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, 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 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.560, 82.300, 123.520, 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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 (pdb code 1wss). 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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4, PDB code: 1wss:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1wss

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Calcium binding site 1 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1002

b:25.1
occ:1.00
 OE1 L:GLN49 2.6 24.9 1.0
O L:GLN64 2.6 25.8 1.0
OD2 L:ASP46 2.7 25.0 1.0
OD2 L:ASP63 2.7 24.5 1.0
O L:GLY47 2.8 28.3 1.0
OD1 L:ASP63 2.8 23.7 1.0
CG L:ASP63 3.1 22.8 1.0
O L:HOH1113 3.1 20.2 1.0
C L:GLY47 3.6 25.9 1.0
CD L:GLN49 3.6 24.7 1.0
C L:GLN64 3.7 23.9 1.0
CG L:ASP46 3.7 27.0 1.0
CA L:ASP48 3.9 26.2 1.0
N L:GLN49 4.0 25.9 1.0
NE2 L:GLN49 4.1 25.1 1.0
CB L:ASP46 4.1 26.5 1.0
N L:ASP48 4.1 26.4 1.0
N L:GLN64 4.2 21.4 1.0
N L:GLN66 4.3 27.4 1.0
CA L:LEU65 4.4 27.4 1.0
C L:ASP46 4.5 24.0 1.0
N L:LEU65 4.5 25.6 1.0
C L:ASP48 4.5 26.8 1.0
O L:ASP46 4.5 26.8 1.0
N L:GLY47 4.5 23.5 1.0
CB L:ASP63 4.6 21.3 1.0
CA L:GLN64 4.6 22.9 1.0
CA L:GLY47 4.7 23.7 1.0
O L:SER67 4.8 23.0 1.0
OD1 L:ASP46 4.8 30.1 1.0
C L:LEU65 4.8 27.7 1.0
CG L:GLN49 4.8 25.6 1.0
CB L:GLN49 4.9 26.4 1.0
C L:ASP63 5.0 20.9 1.0
CA L:ASP46 5.0 24.1 1.0

Calcium binding site 2 out of 9 in 1wss

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Calcium binding site 2 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1003

b:31.7
occ:1.00
 OE12 L:CGU7 2.7 26.8 1.0
OE21 L:CGU29 2.7 27.4 1.0
OE22 L:CGU7 2.8 22.5 1.0
OE22 L:CGU29 2.9 25.6 1.0
OE12 L:CGU26 3.0 23.0 1.0
CD2 L:CGU29 3.1 26.6 1.0
CD1 L:CGU7 3.5 24.6 1.0
OE11 L:CGU26 3.5 23.4 1.0
CD1 L:CGU26 3.6 23.2 1.0
CD2 L:CGU7 3.8 22.6 1.0
CA L:CA1004 4.1 30.1 1.0
OE11 L:CGU7 4.1 22.6 1.0
CG L:CGU7 4.2 22.9 1.0
OE11 L:CGU25 4.3 33.8 1.0
CA L:CA1009 4.3 30.5 1.0
OD1 L:ASN2 4.4 24.0 1.0
O L:HOH1093 4.4 26.3 1.0
CG L:CGU29 4.6 27.2 1.0
ND2 L:ASN2 4.8 25.0 1.0
OE21 L:CGU7 4.9 24.7 1.0
CB L:CGU7 4.9 19.9 1.0
CD1 L:CGU25 5.0 33.0 1.0
CG L:ASN2 5.0 23.1 1.0
CG L:CGU26 5.0 23.8 1.0
CG L:CGU25 5.0 30.8 1.0

Calcium binding site 3 out of 9 in 1wss

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Calcium binding site 3 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1004

b:30.1
occ:1.00
 OE22 L:CGU29 2.7 25.6 1.0
OE11 L:CGU26 2.8 23.4 1.0
O L:HOH1083 2.8 21.1 1.0
O L:HOH1084 2.8 18.4 1.0
OE11 L:CGU7 2.9 22.6 1.0
O L:HOH1067 2.9 24.3 1.0
OE12 L:CGU7 2.9 26.8 1.0
OE21 L:CGU16 2.9 25.2 1.0
CD1 L:CGU7 3.2 24.6 1.0
CD2 L:CGU16 3.7 24.4 1.0
OE22 L:CGU16 3.7 25.7 1.0
CD2 L:CGU29 3.9 26.6 1.0
CA L:CA1005 3.9 27.2 1.0
CD1 L:CGU26 4.0 23.2 1.0
CA L:CA1003 4.1 31.7 1.0
CB L:CGU29 4.3 26.1 1.0
CA L:GLY11 4.5 24.1 1.0
OE12 L:CGU26 4.6 23.0 1.0
OE21 L:CGU29 4.7 27.4 1.0
OE12 L:CGU6 4.7 22.2 1.0
CG L:CGU29 4.7 27.2 1.0
CA L:CGU26 4.7 22.6 1.0
CG L:CGU7 4.8 22.9 1.0
CB L:CGU26 4.8 21.9 1.0
O L:ARG9 4.9 19.7 1.0
O L:CGU26 4.9 22.6 1.0

Calcium binding site 4 out of 9 in 1wss

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Calcium binding site 4 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1005

b:27.2
occ:1.00
 OE11 L:CGU7 2.6 22.6 1.0
OE22 L:CGU26 2.7 24.3 1.0
OE11 L:CGU16 2.7 26.9 1.0
OE21 L:CGU16 2.8 25.2 1.0
OD1 L:ASN2 2.8 24.0 1.0
O L:ALA1 2.9 28.5 1.0
OE11 L:CGU6 2.9 23.2 1.0
OE11 L:CGU26 2.9 23.4 1.0
CD1 L:CGU26 3.4 23.2 1.0
CD1 L:CGU16 3.5 25.7 1.0
CD2 L:CGU26 3.7 25.7 1.0
CG L:ASN2 3.7 23.1 1.0
CD1 L:CGU7 3.7 24.6 1.0
CD1 L:CGU6 3.8 24.1 1.0
C L:ALA1 3.8 28.5 1.0
CD2 L:CGU16 3.8 24.4 1.0
CA L:CA1006 3.8 38.7 1.0
OE12 L:CGU6 3.9 22.2 1.0
CA L:CA1004 3.9 30.1 1.0
OE12 L:CGU26 4.0 23.0 1.0
CG L:CGU26 4.1 23.8 1.0
OE12 L:CGU16 4.2 25.2 1.0
CG L:CGU16 4.2 26.0 1.0
CA L:ASN2 4.3 27.2 1.0
ND2 L:ASN2 4.4 25.0 1.0
N L:ASN2 4.4 28.2 1.0
N L:ALA1 4.5 29.0 1.0
OE12 L:CGU7 4.5 26.8 1.0
CG L:CGU7 4.6 22.9 1.0
CB L:CGU26 4.6 21.9 1.0
CB L:ASN2 4.6 25.3 1.0
OE21 L:CGU26 4.7 29.0 1.0
CB L:CGU16 4.7 25.8 1.0
O L:HOH1083 4.7 21.1 1.0
CA L:ALA1 4.8 28.6 1.0
OE22 L:CGU16 4.9 25.7 1.0

Calcium binding site 5 out of 9 in 1wss

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Calcium binding site 5 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1006

b:38.7
occ:1.00
 OE11 L:CGU6 2.8 23.2 1.0
OE21 L:CGU20 2.8 36.8 1.0
O L:ALA1 2.8 28.5 1.0
OE11 L:CGU16 2.8 26.9 1.0
OE22 L:CGU6 2.8 29.1 1.0
O L:HOH1106 2.9 29.9 1.0
OE22 L:CGU20 3.0 36.5 1.0
OE12 L:CGU16 3.1 25.2 1.0
CD2 L:CGU6 3.2 26.2 1.0
CD2 L:CGU20 3.2 35.9 1.0
CD1 L:CGU6 3.3 24.1 1.0
CD1 L:CGU16 3.3 25.7 1.0
OE21 L:CGU6 3.7 29.1 1.0
CG L:CGU6 3.8 25.5 1.0
CA L:CA1005 3.8 27.2 1.0
C L:ALA1 3.9 28.5 1.0
OE12 L:CGU6 4.0 22.2 1.0
CB L:CGU6 4.5 22.4 1.0
O L:ARG15 4.6 19.4 1.0
N L:ALA1 4.6 29.0 1.0
CA L:ASN2 4.7 27.2 1.0
N L:ASN2 4.7 28.2 1.0
CA L:CA1008 4.7 44.2 1.0
N L:ALA3 4.7 26.9 1.0
CA L:ALA1 4.7 28.6 1.0
CG L:CGU20 4.8 34.4 1.0
NE L:ARG15 4.8 20.4 1.0
CG L:CGU16 4.8 26.0 1.0
CG L:ARG15 4.9 20.4 1.0

Calcium binding site 6 out of 9 in 1wss

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Calcium binding site 6 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1007

b:40.4
occ:1.00
 OE21 L:CGU14 2.7 28.0 1.0
OE12 L:CGU19 2.8 38.6 1.0
OE12 L:CGU14 2.9 25.5 1.0
OE21 L:CGU19 3.0 37.3 1.0
CD2 L:CGU19 3.1 37.0 1.0
CG L:CGU19 3.3 35.0 1.0
CD2 L:CGU14 3.4 26.2 1.0
CD1 L:CGU19 3.5 36.1 1.0
CG L:CGU14 3.5 24.0 1.0
CD1 L:CGU14 3.6 25.2 1.0
OE22 L:CGU19 3.7 41.8 1.0
OE22 L:CGU14 4.6 26.7 1.0
OE11 L:CGU19 4.7 37.6 1.0
OE11 L:CGU14 4.8 26.7 1.0
CB L:CGU19 4.8 33.2 1.0

Calcium binding site 7 out of 9 in 1wss

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Calcium binding site 7 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1008

b:44.2
occ:1.00
 OE21 L:CGU20 2.8 36.8 1.0
OE11 L:CGU20 3.0 35.1 1.0
CD2 L:CGU20 3.5 35.9 1.0
CD1 L:CGU20 3.7 34.2 1.0
CG L:CGU20 3.7 34.4 1.0
O L:ARG15 4.3 19.4 1.0
CG L:ARG15 4.4 20.4 1.0
OE22 L:CGU20 4.5 36.5 1.0
OE22 L:CGU6 4.7 29.1 1.0
CA L:CA1006 4.7 38.7 1.0
OE12 L:CGU20 4.8 34.5 1.0
O L:HOH1106 4.9 29.9 1.0

Calcium binding site 8 out of 9 in 1wss

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Calcium binding site 8 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1009

b:30.5
occ:1.00
 OE21 L:CGU29 2.6 27.4 1.0
OE11 L:CGU25 2.7 33.8 1.0
OE22 L:CGU25 2.9 31.4 1.0
OE11 L:CGU29 2.9 31.0 1.0
CD1 L:CGU25 3.4 33.0 1.0
CD2 L:CGU29 3.4 26.6 1.0
CG L:CGU25 3.4 30.8 1.0
CD2 L:CGU25 3.5 31.8 1.0
NH2 L:ARG28 3.5 29.5 1.0
CD1 L:CGU29 3.7 28.5 1.0
CG L:CGU29 3.7 27.2 1.0
CA L:CA1003 4.3 31.7 1.0
OE22 L:CGU29 4.4 25.6 1.0
OE12 L:CGU25 4.5 34.9 1.0
OE21 L:CGU25 4.6 36.1 1.0
CZ L:ARG28 4.8 29.9 1.0
OE12 L:CGU29 4.8 31.4 1.0
CB L:CGU25 4.9 27.6 1.0
O L:CGU25 4.9 22.3 1.0

Calcium binding site 9 out of 9 in 1wss

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Calcium binding site 9 out of 9 in the Human Factor Viia-Tissue Factor in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4


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 in Complex with Peptide-Mimetic Inhibitor That Has Two Charged Groups in P2 and P4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1001

b:32.5
occ:1.00
 O H:GLU75 2.7 25.4 1.0
O H:ASP72 2.7 11.9 1.0
OE1 H:GLU70 2.7 23.6 1.0
O H:HOH2105 2.8 19.7 1.0
O H:HOH2094 2.9 24.1 1.0
OE2 H:GLU80 2.9 21.8 1.0
OE2 H:GLU70 3.0 23.6 1.0
CD H:GLU80 3.2 19.7 1.0
CD H:GLU70 3.2 21.4 1.0
OE1 H:GLU80 3.3 24.4 1.0
C H:GLU75 3.4 21.3 1.0
C H:ASP72 3.7 10.0 1.0
CA H:HIS76 3.9 17.7 1.0
N H:HIS76 4.0 19.0 1.0
CG H:GLU80 4.1 19.6 1.0
N H:GLU75 4.3 17.5 1.0
ND1 H:HIS76 4.3 20.9 1.0
N H:ASP72 4.4 9.7 1.0
CA H:GLU75 4.5 20.6 1.0
CA H:LEU73 4.5 9.4 1.0
O H:HOH2002 4.5 8.1 1.0
N H:LEU73 4.5 8.7 1.0
CA H:ASP72 4.6 9.6 1.0
CG H:GLU70 4.6 20.0 1.0
C H:LEU73 4.7 11.1 1.0
O H:HOH2118 4.8 37.4 1.0
N H:ASP77 4.8 13.9 1.0
N H:HIS71 4.8 10.0 1.0
C H:HIS76 4.8 16.1 1.0
CG H:HIS76 4.8 20.8 1.0
CE1 H:HIS76 4.9 20.9 1.0
CB H:HIS76 4.9 18.2 1.0
N H:SER74 4.9 11.9 1.0
CB H:ASP72 5.0 7.8 1.0

Reference:

S.Kadono, A.Sakamoto, Y.Kikuchi, M.Oh-Eda, N.Yabuta, 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 of Human Factor Viia/Tissue Factor in Complex with A Peptide-Mimetic Inhibitor: High Selectivity Against Thrombin By Introducing Two Charged Groups in P2 and P4. Acta Crystallogr.,Sect.F V. 61 169 2005.
ISSN: ISSN 1744-3091
PubMed: 16510984
DOI: 10.1107/S1744309105000047
Page generated: Fri Jul 12 07:17:52 2024

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