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Calcium in PDB 1w2k: TF7A_4380 Complex

Enzymatic activity of TF7A_4380 Complex

All present enzymatic activity of TF7A_4380 Complex:
3.4.21.21;

Protein crystallography data

The structure of TF7A_4380 Complex, PDB code: 1w2k was solved by D.W.Banner, A.D'arcy, K.Groebke-Zbinden, J.Ackermann, D.Kirchhofer, Y.-H.Ji, T.B.Tschopp, S.Wallbaum, L.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.82 / 3.0
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.874, 82.638, 123.722, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1w2k:

The structure of TF7A_4380 Complex also contains other interesting chemical elements:

Arsenic (As) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the TF7A_4380 Complex (pdb code 1w2k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the TF7A_4380 Complex, PDB code: 1w2k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 1w2k

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Calcium binding site 1 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1259

b:28.9
occ:1.00
 OE1 H:GLU70 2.2 12.8 1.0
O H:ASP72 2.3 6.7 1.0
O H:GLU75 2.5 19.9 1.0
O H:HOH2039 2.6 19.0 1.0
OE2 H:GLU70 2.7 13.5 1.0
CD H:GLU70 2.7 12.2 1.0
OE1 H:GLU80 2.9 17.3 1.0
C H:ASP72 3.1 6.0 1.0
O H:HOH2045 3.6 17.3 1.0
CD H:GLU80 3.7 15.2 1.0
C H:GLU75 3.7 19.0 1.0
N H:LEU73 3.8 5.8 1.0
N H:ASP72 3.8 5.9 1.0
CA H:LEU73 3.8 6.9 1.0
CA H:ASP72 4.0 5.3 1.0
OE2 H:GLU80 4.1 13.9 1.0
CG H:GLU70 4.1 10.8 1.0
N H:GLU75 4.2 17.1 1.0
N H:HIS71 4.2 4.8 1.0
C H:LEU73 4.3 9.1 1.0
CA H:GLU75 4.5 19.2 1.0
CB H:ASP72 4.5 4.5 1.0
N H:SER74 4.6 10.8 1.0
C H:HIS71 4.6 5.6 1.0
CG H:GLU80 4.6 13.6 1.0
N H:HIS76 4.7 19.4 1.0
CD2 H:LEU73 4.8 8.4 1.0
CA H:HIS76 4.8 18.3 1.0
O H:HOH2035 4.8 4.8 1.0
O H:LEU73 4.8 10.9 1.0
CA H:GLU70 4.9 6.7 1.0

Calcium binding site 2 out of 9 in 1w2k

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Calcium binding site 2 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1153

b:29.0
occ:1.00
 OD2 L:ASP63 2.3 26.8 1.0
OD2 L:ASP46 2.4 20.2 1.0
OE1 L:GLN49 2.4 27.6 1.0
O L:GLY47 2.5 27.5 1.0
OD1 L:ASP63 2.5 26.5 1.0
O L:GLN64 2.7 21.0 1.0
CG L:ASP63 2.7 24.9 1.0
C L:GLY47 3.4 26.4 1.0
CD L:GLN49 3.4 26.0 1.0
O L:HOH2030 3.5 18.6 1.0
CG L:ASP46 3.5 22.2 1.0
C L:GLN64 3.7 20.9 1.0
CA L:ASP48 3.9 25.6 1.0
NE2 L:GLN49 3.9 25.2 1.0
N L:GLN49 4.0 23.5 1.0
CB L:ASP46 4.0 24.1 1.0
N L:ASP48 4.0 26.1 1.0
N L:GLN64 4.1 19.2 1.0
N L:GLN66 4.2 27.5 1.0
CB L:ASP63 4.2 22.8 1.0
N L:GLY47 4.3 24.4 1.0
C L:ASP46 4.4 24.2 1.0
C L:ASP48 4.5 25.6 1.0
CA L:GLY47 4.5 25.1 1.0
CA L:GLN64 4.5 20.1 1.0
N L:LEU65 4.5 22.1 1.0
OD1 L:ASP46 4.5 21.1 1.0
CA L:LEU65 4.6 23.8 1.0
CG L:GLN49 4.7 23.6 1.0
O L:ASP46 4.7 24.8 1.0
C L:ASP63 4.8 19.7 1.0
O L:SER67 4.8 27.1 1.0
CA L:ASP46 4.9 23.9 1.0
C L:LEU65 4.9 25.5 1.0
CB L:GLN49 4.9 23.3 1.0
CA L:ASP63 5.0 21.3 1.0

Calcium binding site 3 out of 9 in 1w2k

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Calcium binding site 3 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1154

b:30.2
occ:1.00
 OE12 L:CGU7 1.8 27.0 1.0
OE12 L:CGU26 2.2 18.4 1.0
OE21 L:CGU29 2.3 26.7 1.0
OE22 L:CGU29 2.6 27.4 1.0
OE22 L:CGU7 2.7 26.3 1.0
CD2 L:CGU29 2.8 28.3 1.0
CD1 L:CGU7 2.9 27.8 1.0
CD1 L:CGU26 3.1 21.0 1.0
OE11 L:CGU26 3.4 22.2 1.0
CD2 L:CGU7 3.6 27.0 1.0
OE11 L:CGU7 3.6 26.2 1.0
OE11 L:CGU25 3.7 28.8 1.0
CA L:CA1155 3.8 28.2 1.0
CG L:CGU7 3.8 26.8 1.0
OD1 L:ASN2 4.2 30.6 1.0
CA L:CA1160 4.3 50.4 1.0
CG L:CGU29 4.3 28.9 1.0
CG L:CGU26 4.4 21.8 1.0
ND2 L:ASN2 4.4 30.6 1.0
CG L:ASN2 4.5 29.7 1.0
CD1 L:CGU25 4.6 29.7 1.0
O L:HOH2015 4.6 16.7 1.0
CB L:CGU7 4.7 23.9 1.0
CA L:CGU26 4.8 20.3 1.0
OE21 L:CGU7 4.8 27.8 1.0
CG L:CGU25 4.8 28.2 1.0

Calcium binding site 4 out of 9 in 1w2k

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Calcium binding site 4 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1155

b:28.2
occ:1.00
 O L:HOH2008 2.1 33.9 1.0
OE11 L:CGU26 2.3 22.2 1.0
O L:HOH2019 2.5 33.0 1.0
OE11 L:CGU7 2.5 26.2 1.0
OE22 L:CGU29 2.5 27.4 1.0
OE21 L:CGU16 2.8 15.9 1.0
OE12 L:CGU7 3.0 27.0 1.0
CD1 L:CGU7 3.1 27.8 1.0
O L:HOH2022 3.3 14.4 1.0
CD1 L:CGU26 3.4 21.0 1.0
CA L:CA1156 3.6 15.2 1.0
CD2 L:CGU16 3.6 17.6 1.0
OE22 L:CGU16 3.7 16.7 1.0
CD2 L:CGU29 3.8 28.3 1.0
CA L:CA1154 3.8 30.2 1.0
OE12 L:CGU26 3.9 18.4 1.0
CB L:CGU29 4.2 27.9 1.0
OD1 L:ASN2 4.4 30.6 1.0
CG L:CGU7 4.6 26.8 1.0
CA L:CGU26 4.6 20.3 1.0
OE21 L:CGU29 4.6 26.7 1.0
OE12 L:CGU6 4.6 29.0 1.0
CG L:CGU29 4.7 28.9 1.0
CG L:CGU26 4.7 21.8 1.0
O L:CGU26 4.7 19.1 1.0
CB L:CGU26 4.7 19.5 1.0
CA L:GLY11 4.8 27.6 1.0
OE22 L:CGU26 4.9 23.7 1.0
CG L:CGU16 4.9 18.7 1.0

Calcium binding site 5 out of 9 in 1w2k

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Calcium binding site 5 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1156

b:15.2
occ:1.00
 OE11 L:CGU16 2.1 18.5 1.0
OE21 L:CGU16 2.2 15.9 1.0
OD1 L:ASN2 2.3 30.6 1.0
OE22 L:CGU26 2.4 23.7 1.0
OE11 L:CGU7 2.5 26.2 1.0
OE11 L:CGU6 2.7 29.2 1.0
OE11 L:CGU26 2.7 22.2 1.0
O L:ALA1 2.7 29.4 1.0
CD1 L:CGU16 2.9 17.5 1.0
OE12 L:CGU6 3.1 29.0 1.0
CD2 L:CGU16 3.2 17.6 1.0
CD1 L:CGU6 3.2 29.8 1.0
CD1 L:CGU26 3.3 21.0 1.0
CA L:CA1157 3.4 17.5 1.0
CG L:ASN2 3.5 29.7 1.0
CD2 L:CGU26 3.5 22.8 1.0
CG L:CGU16 3.6 18.7 1.0
CA L:CA1155 3.6 28.2 1.0
OE12 L:CGU16 3.6 14.2 1.0
CD1 L:CGU7 3.7 27.8 1.0
C L:ALA1 3.8 29.3 1.0
OE12 L:CGU26 4.0 18.4 1.0
CG L:CGU26 4.0 21.8 1.0
CB L:CGU16 4.2 20.5 1.0
O L:HOH2008 4.2 33.9 1.0
CA L:ASN2 4.2 30.8 1.0
OE22 L:CGU16 4.3 16.7 1.0
ND2 L:ASN2 4.3 30.6 1.0
CB L:ASN2 4.4 29.7 1.0
N L:ASN2 4.5 30.3 1.0
OE12 L:CGU7 4.5 27.0 1.0
CG L:CGU7 4.5 26.8 1.0
OE21 L:CGU26 4.6 26.2 1.0
N L:ALA1 4.7 27.3 1.0
CB L:CGU26 4.7 19.5 1.0
CG L:CGU6 4.7 29.9 1.0
OE22 L:CGU20 4.8 30.4 1.0
O L:HOH2019 4.8 33.0 1.0
CA L:ALA1 4.9 28.5 1.0

Calcium binding site 6 out of 9 in 1w2k

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Calcium binding site 6 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1157

b:17.5
occ:1.00
 OE11 L:CGU16 2.3 18.5 1.0
O L:HOH2001 2.3 28.0 1.0
OE11 L:CGU6 2.4 29.2 1.0
OE22 L:CGU20 2.5 30.4 1.0
O L:ALA1 2.6 29.4 1.0
OE12 L:CGU16 2.6 14.2 1.0
CD1 L:CGU6 2.7 29.8 1.0
CD2 L:CGU6 2.7 32.4 1.0
OE22 L:CGU6 2.7 33.6 1.0
CD1 L:CGU16 2.8 17.5 1.0
OE21 L:CGU20 2.9 26.2 1.0
CD2 L:CGU20 3.0 27.9 1.0
CG L:CGU6 3.2 29.9 1.0
OE21 L:CGU6 3.2 35.4 1.0
OE12 L:CGU6 3.4 29.0 1.0
CA L:CA1156 3.4 15.2 1.0
C L:ALA1 3.5 29.3 1.0
CA L:ASN2 4.1 30.8 1.0
N L:ASN2 4.1 30.3 1.0
CB L:CGU6 4.3 28.4 1.0
CG L:CGU16 4.3 18.7 1.0
N L:ALA3 4.3 32.1 1.0
CA L:ALA1 4.4 28.5 1.0
CB L:ALA1 4.5 26.8 1.0
CG L:CGU20 4.5 27.7 1.0
OE22 L:CGU26 4.6 23.7 1.0
OD1 L:ASN2 4.7 30.6 1.0
NE L:ARG15 4.7 24.3 1.0
N L:ALA1 4.7 27.3 1.0
OE21 L:CGU16 4.7 15.9 1.0
C L:ASN2 4.8 31.5 1.0
CB L:CGU16 4.9 20.5 1.0
CA L:CGU16 5.0 21.1 1.0
CD2 L:CGU16 5.0 17.6 1.0

Calcium binding site 7 out of 9 in 1w2k

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Calcium binding site 7 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1158

b:40.5
occ:1.00
 OE21 L:CGU14 1.9 31.6 1.0
OE12 L:CGU14 2.1 31.4 1.0
OE12 L:CGU19 2.1 33.0 1.0
OE21 L:CGU19 2.2 32.3 1.0
CD1 L:CGU19 2.7 31.8 1.0
CG L:CGU19 2.8 30.0 1.0
CD2 L:CGU14 2.8 30.9 1.0
CD2 L:CGU19 2.9 31.2 1.0
CD1 L:CGU14 3.0 30.5 1.0
CG L:CGU14 3.1 29.7 1.0
OE22 L:CGU14 3.9 31.4 1.0
OE11 L:CGU19 3.9 31.6 1.0
OE22 L:CGU19 4.0 30.4 1.0
OE11 L:CGU14 4.2 32.8 1.0
CB L:CGU19 4.3 27.4 1.0
CB L:CGU14 4.6 28.0 1.0
CA L:CGU19 5.0 26.8 1.0

Calcium binding site 8 out of 9 in 1w2k

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Calcium binding site 8 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1159

b:29.7
occ:1.00
 O L:HOH2012 2.5 43.6 1.0
OE11 L:CGU20 2.5 28.0 1.0
O L:HOH2010 2.7 34.2 1.0
OE21 L:CGU20 3.0 26.2 1.0
CD1 L:CGU20 3.4 28.3 1.0
CD2 L:CGU20 3.6 27.9 1.0
O L:HOH2014 3.6 17.2 1.0
CG L:CGU20 3.6 27.7 1.0
OE22 L:CGU6 4.1 33.6 1.0
OE12 L:CGU20 4.5 29.6 1.0
O L:HOH2001 4.5 28.0 1.0
CG L:ARG15 4.6 26.0 1.0
OE22 L:CGU20 4.6 30.4 1.0
O L:ARG15 4.8 24.6 1.0
OE21 L:CGU6 4.9 35.4 1.0
CD2 L:CGU6 4.9 32.4 1.0

Calcium binding site 9 out of 9 in 1w2k

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Calcium binding site 9 out of 9 in the TF7A_4380 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of TF7A_4380 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1160

b:50.4
occ:1.00
 OE11 L:CGU25 1.9 28.8 1.0
OE21 L:CGU29 2.3 26.7 1.0
OE21 L:CGU25 2.4 30.9 1.0
OE11 L:CGU29 2.5 34.6 1.0
CD1 L:CGU25 2.6 29.7 1.0
CG L:CGU25 3.0 28.2 1.0
CD2 L:CGU25 3.1 29.8 1.0
CD2 L:CGU29 3.3 28.3 1.0
CD1 L:CGU29 3.4 31.1 1.0
CG L:CGU29 3.5 28.9 1.0
OE12 L:CGU25 3.6 31.2 1.0
OE22 L:CGU25 4.2 30.7 1.0
NH1 L:ARG28 4.2 24.5 1.0
CA L:CA1154 4.3 30.2 1.0
OE22 L:CGU29 4.4 27.4 1.0
CB L:CGU25 4.5 23.2 1.0
OE12 L:CGU29 4.6 32.3 1.0

Reference:

K.Groebke-Zbinden, D.W.Banner, J.Ackermann, A.D'arcy, D.Kirchhofer, Y.-H.Ji, T.B.Tschopp, S.Wallbaum, L.Weber. Design of Selective Phenylglycine Amide Tissue Factor/Factor Viia Inhibitors Bioorg.Med.Chem.Lett. V. 15 817 2005.
ISSN: ISSN 0960-894X
PubMed: 15664864
DOI: 10.1016/J.BMCL.2004.10.092
Page generated: Tue Jul 8 03:04:32 2025

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