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Calcium in PDB 1dan: Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor

Enzymatic activity of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor

All present enzymatic activity of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor:
3.4.21.21;

Protein crystallography data

The structure of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor, PDB code: 1dan was solved by D.W.Banner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.650, 82.550, 126.500, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.8

Other elements in 1dan:

The structure of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor also contains other interesting chemical elements:

Arsenic (As) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor (pdb code 1dan). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor, PDB code: 1dan:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1dan

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Calcium binding site 1 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca155

b:41.0
occ:1.00
 OD2 L:ASP46 2.2 32.4 1.0
OD2 L:ASP63 2.3 57.3 1.0
O L:GLY47 2.4 50.6 1.0
OD1 L:ASP63 2.4 45.6 1.0
O L:GLN64 2.5 35.0 1.0
OE1 L:GLN49 2.5 48.2 1.0
CG L:ASP63 2.7 46.1 1.0
CG L:ASP46 3.4 50.1 1.0
C L:GLN64 3.6 35.2 1.0
C L:GLY47 3.6 48.8 1.0
CD L:GLN49 3.7 49.6 1.0
N L:GLN49 4.1 48.8 1.0
N L:GLN64 4.1 35.3 1.0
CB L:ASP46 4.1 48.4 1.0
N L:GLN66 4.2 40.9 1.0
CA L:ASP48 4.2 48.6 1.0
CB L:ASP63 4.2 41.3 1.0
NE2 L:GLN49 4.3 49.3 1.0
N L:ASP48 4.4 48.0 1.0
CA L:LEU65 4.4 40.2 1.0
N L:LEU65 4.5 37.5 1.0
OD1 L:ASP46 4.5 40.8 1.0
N L:GLY47 4.5 46.2 1.0
CA L:GLN64 4.5 35.5 1.0
C L:ASP46 4.6 47.0 1.0
O L:SER67 4.6 35.9 1.0
CA L:GLY47 4.7 46.8 1.0
C L:ASP48 4.7 50.3 1.0
O L:ASP46 4.8 47.0 1.0
C L:ASP63 4.8 36.0 1.0
C L:LEU65 4.8 41.5 1.0
CG L:GLN49 4.8 42.1 1.0
CB L:GLN49 4.9 42.4 1.0
CA L:ASP63 4.9 37.1 1.0

Calcium binding site 2 out of 9 in 1dan

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Calcium binding site 2 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca156

b:31.3
occ:1.00
 OE21 L:CGU29 2.3 34.7 1.0
OE12 L:CGU7 2.3 25.0 1.0
OE22 L:CGU7 2.4 35.6 1.0
OE12 L:CGU26 2.4 28.8 1.0
O L:HOH205 2.5 49.3 1.0
OE22 L:CGU29 2.6 31.2 1.0
O L:HOH204 2.6 41.0 1.0
CD2 L:CGU29 2.8 36.2 1.0
CD1 L:CGU7 3.2 30.0 1.0
CD1 L:CGU26 3.3 37.8 1.0
CD2 L:CGU7 3.4 36.7 1.0
OE11 L:CGU26 3.5 35.7 1.0
CG L:CGU7 3.8 33.2 1.0
CA L:CA157 3.9 31.3 1.0
OE11 L:CGU7 4.0 23.6 1.0
ND2 L:ASN2 4.3 33.8 1.0
CG L:CGU29 4.3 37.2 1.0
CA L:CA162 4.3 62.8 1.0
OE21 L:CGU7 4.5 40.3 1.0
CB L:CGU7 4.6 31.7 1.0
CG L:CGU26 4.6 36.4 1.0
OD1 L:ASN2 4.7 32.6 1.0
O L:HOH191 4.7 38.0 1.0
OE11 L:CGU25 4.7 68.0 1.0
CG L:ASN2 4.9 36.4 1.0
CA L:CGU26 5.0 34.2 1.0

Calcium binding site 3 out of 9 in 1dan

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Calcium binding site 3 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca157

b:31.3
occ:1.00
 OE11 L:CGU26 2.5 35.7 1.0
O L:HOH192 2.5 28.4 1.0
OE12 L:CGU7 2.5 25.0 1.0
OE21 L:CGU16 2.5 19.1 1.0
OE22 L:CGU29 2.6 31.2 1.0
O L:HOH191 2.6 38.0 1.0
O L:HOH193 2.6 26.2 1.0
OE11 L:CGU7 2.7 23.6 1.0
CD1 L:CGU7 3.0 30.0 1.0
CD2 L:CGU16 3.4 30.6 1.0
CD1 L:CGU26 3.6 37.8 1.0
OE22 L:CGU16 3.6 31.6 1.0
CA L:CA158 3.6 29.6 1.0
CD2 L:CGU29 3.8 36.2 1.0
CA L:CA156 3.9 31.3 1.0
OE12 L:CGU26 4.1 28.8 1.0
CA L:GLY11 4.4 37.7 1.0
CB L:CGU29 4.4 35.0 1.0
OE12 L:CGU6 4.4 29.0 1.0
CG L:CGU7 4.5 33.2 1.0
OE21 L:CGU29 4.6 34.7 1.0
CA L:CGU26 4.7 34.2 1.0
CG L:CGU29 4.7 37.2 1.0
CG L:CGU26 4.7 36.4 1.0
CB L:CGU26 4.8 32.4 1.0
N L:GLY11 4.8 38.9 1.0
O L:CGU26 4.8 33.1 1.0
CG L:CGU16 4.8 31.4 1.0
O L:ARG9 4.9 33.7 1.0
OD1 L:ASN2 5.0 32.6 1.0

Calcium binding site 4 out of 9 in 1dan

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Calcium binding site 4 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca158

b:29.6
occ:1.00
 OE11 L:CGU16 2.3 30.9 1.0
OD1 L:ASN2 2.3 32.6 1.0
OE11 L:CGU7 2.4 23.6 1.0
OE21 L:CGU16 2.4 19.1 1.0
OE11 L:CGU26 2.5 35.7 1.0
OE11 L:CGU6 2.6 26.2 1.0
OE22 L:CGU26 2.6 40.4 1.0
O L:ALA1 3.0 34.3 1.0
CD1 L:CGU16 3.1 34.5 1.0
CD1 L:CGU26 3.3 37.8 1.0
CD1 L:CGU6 3.4 32.5 1.0
CD1 L:CGU7 3.4 30.0 1.0
CD2 L:CGU16 3.4 30.6 1.0
OE12 L:CGU6 3.4 29.0 1.0
CD2 L:CGU26 3.5 35.6 1.0
CG L:ASN2 3.6 36.4 1.0
CA L:CA157 3.6 31.3 1.0
C L:ALA1 3.8 38.9 1.0
CG L:CGU16 3.8 31.4 1.0
CA L:CA159 3.8 35.0 1.0
CG L:CGU26 3.9 36.4 1.0
OE12 L:CGU16 4.0 38.1 1.0
OE12 L:CGU26 4.0 28.8 1.0
OE12 L:CGU7 4.1 25.0 1.0
O L:HOH192 4.3 28.4 1.0
CG L:CGU7 4.3 33.2 1.0
N L:ALA1 4.3 34.7 1.0
CA L:ASN2 4.4 41.9 1.0
ND2 L:ASN2 4.4 33.8 1.0
N L:ASN2 4.4 39.4 1.0
CB L:CGU16 4.5 34.7 1.0
OE22 L:CGU16 4.5 31.6 1.0
CB L:ASN2 4.5 35.5 1.0
OE21 L:CGU26 4.6 45.9 1.0
CA L:ALA1 4.6 36.5 1.0
CB L:CGU26 4.7 32.4 1.0
CG L:CGU6 4.8 35.6 1.0
CD2 L:CGU7 5.0 36.7 1.0

Calcium binding site 5 out of 9 in 1dan

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Calcium binding site 5 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca159

b:35.0
occ:1.00
 O L:ALA1 2.4 34.3 1.0
OE12 L:CGU16 2.4 38.1 1.0
OE11 L:CGU16 2.5 30.9 1.0
O L:HOH189 2.5 44.8 1.0
OE11 L:CGU6 2.6 26.2 1.0
OE22 L:CGU20 2.6 41.0 1.0
OE22 L:CGU6 2.7 40.5 1.0
OE21 L:CGU20 2.7 46.0 1.0
CD1 L:CGU16 2.8 34.5 1.0
CD2 L:CGU20 3.0 45.3 1.0
CD1 L:CGU6 3.2 32.5 1.0
CD2 L:CGU6 3.4 40.0 1.0
C L:ALA1 3.5 38.9 1.0
CG L:CGU6 3.8 35.6 1.0
CA L:CA158 3.8 29.6 1.0
N L:ALA1 3.9 34.7 1.0
OE12 L:CGU6 3.9 29.0 1.0
CA L:ALA1 4.3 36.5 1.0
CG L:CGU16 4.3 31.4 1.0
OE21 L:CGU6 4.4 48.6 1.0
N L:ASN2 4.5 39.4 1.0
CB L:CGU6 4.5 35.7 1.0
CG L:CGU20 4.5 46.8 1.0
CA L:ASN2 4.6 41.9 1.0
NE L:ARG15 4.7 37.0 1.0
CA L:CA161 4.8 62.2 1.0
CB L:ALA1 4.8 35.8 1.0
OE22 L:CGU26 4.8 40.4 1.0
O L:ARG15 4.8 38.1 1.0
OE21 L:CGU16 4.9 19.1 1.0
OD1 L:ASN2 4.9 32.6 1.0
CA L:CGU16 4.9 37.6 1.0

Calcium binding site 6 out of 9 in 1dan

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Calcium binding site 6 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca160

b:76.7
occ:1.00
 OE12 L:CGU19 2.3 70.8 1.0
OE21 L:CGU14 2.4 67.4 1.0
OE21 L:CGU19 2.7 59.1 1.0
OE12 L:CGU14 2.7 70.7 1.0
O L:HOH206 2.8 48.7 1.0
CD1 L:CGU19 3.1 68.2 1.0
CD2 L:CGU14 3.2 61.9 1.0
CG L:CGU19 3.3 62.1 1.0
CD2 L:CGU19 3.3 62.0 1.0
CD1 L:CGU14 3.4 67.7 1.0
CG L:CGU14 3.5 61.8 1.0
OE11 L:CGU19 4.3 67.5 1.0
OE22 L:CGU14 4.4 69.4 1.0
OE22 L:CGU19 4.5 64.2 1.0
OE11 L:CGU14 4.6 72.0 1.0
CB L:CGU19 4.8 52.4 1.0
CB L:CGU14 5.0 50.1 1.0

Calcium binding site 7 out of 9 in 1dan

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Calcium binding site 7 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca161

b:62.2
occ:1.00
 OE21 L:CGU20 2.5 46.0 1.0
OE11 L:CGU20 2.6 43.4 1.0
CD2 L:CGU20 3.3 45.3 1.0
CD1 L:CGU20 3.4 47.5 1.0
CG L:CGU20 3.4 46.8 1.0
OE22 L:CGU20 4.4 41.0 1.0
O L:ARG15 4.5 38.1 1.0
OE22 L:CGU19 4.5 64.2 1.0
OE22 L:CGU6 4.6 40.5 1.0
OE12 L:CGU20 4.6 55.8 1.0
CG L:ARG15 4.7 41.3 1.0
CA L:CA159 4.8 35.0 1.0
O L:HOH189 4.8 44.8 1.0
CB L:CGU20 4.9 44.0 1.0

Calcium binding site 8 out of 9 in 1dan

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Calcium binding site 8 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca162

b:62.8
occ:1.00
 OE11 L:CGU25 2.4 68.0 1.0
OE21 L:CGU29 2.5 34.7 1.0
OE11 L:CGU29 2.9 47.3 1.0
OE21 L:CGU25 3.1 72.4 1.0
CG L:CGU25 3.2 63.6 1.0
CD1 L:CGU25 3.2 70.4 1.0
CD2 L:CGU29 3.4 36.2 1.0
CG L:CGU29 3.5 37.2 1.0
CD2 L:CGU25 3.6 68.8 1.0
CD1 L:CGU29 3.6 44.8 1.0
O L:HOH204 3.9 41.0 1.0
O L:HOH205 4.0 49.3 1.0
NH2 L:ARG28 4.1 76.5 1.0
CA L:CA156 4.3 31.3 1.0
OE12 L:CGU25 4.4 72.2 1.0
OE22 L:CGU29 4.5 31.2 1.0
CB L:CGU25 4.5 48.4 1.0
O L:CGU25 4.6 36.0 1.0
NE L:ARG28 4.7 71.9 1.0
OE12 L:CGU29 4.8 50.0 1.0
OE22 L:CGU25 4.9 71.4 1.0
CZ L:ARG28 4.9 78.0 1.0

Calcium binding site 9 out of 9 in 1dan

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Calcium binding site 9 out of 9 in the Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Complex of Active Site Inhibited Human Blood Coagulation Factor Viia with Human Recombinant Soluble Tissue Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca258

b:30.8
occ:1.00
 OE2 H:GLU80 2.2 39.6 1.0
O H:HOH354 2.2 38.1 1.0
O H:GLU75 2.3 41.4 1.0
OE1 H:GLU70 2.3 23.1 1.0
O H:HOH303 2.4 22.6 1.0
O H:ASP72 2.4 22.4 1.0
CD H:GLU80 3.3 41.0 1.0
CD H:GLU70 3.3 23.1 1.0
C H:GLU75 3.5 42.0 1.0
C H:ASP72 3.5 23.3 1.0
OE2 H:GLU70 3.5 28.0 1.0
N H:ASP72 4.1 23.1 1.0
OE1 H:GLU80 4.1 47.8 1.0
CG H:GLU80 4.1 34.1 1.0
CA H:HIS76 4.1 46.7 1.0
O H:HOH304 4.2 25.0 1.0
N H:HIS76 4.2 45.0 1.0
CA H:ASP72 4.3 23.0 1.0
N H:GLU75 4.4 35.2 1.0
N H:LEU73 4.5 22.2 1.0
CA H:GLU75 4.5 40.0 1.0
N H:HIS71 4.6 20.4 1.0
CA H:LEU73 4.6 24.8 1.0
CB H:ASP72 4.6 24.8 1.0
N H:ASP77 4.7 46.0 1.0
CG H:GLU70 4.7 19.3 1.0
ND1 H:HIS76 4.8 60.2 1.0
CG H:GLU75 4.9 62.7 1.0
C H:LEU73 4.9 29.8 1.0
C H:HIS76 4.9 47.5 1.0
OD2 H:ASP77 4.9 50.4 1.0

Reference:

D.W.Banner, A.D'arcy, C.Chene, F.K.Winkler, A.Guha, W.H.Konigsberg, Y.Nemerson, D.Kirchhofer. The Crystal Structure of the Complex of Blood Coagulation Factor Viia with Soluble Tissue Factor. Nature V. 380 41 1996.
ISSN: ISSN 0028-0836
PubMed: 8598903
DOI: 10.1038/380041A0
Page generated: Thu Jul 11 07:27:44 2024

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