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Calcium in PDB 2ec9: Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607

Enzymatic activity of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607

All present enzymatic activity of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607, PDB code: 2ec9 was solved by K.Raman, B.Yarlagadda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.780, 81.410, 125.350, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 (pdb code 2ec9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607, PDB code: 2ec9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2ec9

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Calcium binding site 1 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1002

b:64.0
occ:1.00
 O L:GLY47 2.4 42.7 1.0
OD2 L:ASP46 2.4 52.3 1.0
OD2 L:ASP63 2.5 43.9 1.0
O L:GLN64 2.6 35.8 1.0
OE1 L:GLN49 2.9 42.6 1.0
CG L:ASP46 3.3 51.5 1.0
CG L:ASP63 3.4 41.3 1.0
C L:GLY47 3.6 44.7 1.0
CB L:ASP46 3.6 50.4 1.0
OD1 L:ASP63 3.6 42.9 1.0
C L:GLN64 3.7 34.3 1.0
CD L:GLN49 3.8 43.6 1.0
C L:ASP46 4.0 47.7 1.0
NE2 L:GLN49 4.0 44.2 1.0
N L:GLY47 4.1 45.2 1.0
N L:GLN66 4.2 42.1 1.0
O L:ASP46 4.2 48.9 1.0
CA L:LEU65 4.3 40.5 1.0
OD1 L:ASP46 4.4 51.9 1.0
N L:GLN64 4.4 26.2 1.0
CA L:GLY47 4.5 44.6 1.0
CA L:ASP46 4.5 48.7 1.0
N L:LEU65 4.5 37.9 1.0
N L:ASP48 4.5 43.6 1.0
CA L:ASP48 4.6 42.1 1.0
CD2 L:LEU65 4.7 43.1 1.0
CB L:ASP63 4.7 35.9 1.0
C L:LEU65 4.8 42.0 1.0
CA L:GLN64 4.8 31.3 1.0
N L:GLN49 4.8 38.4 1.0
O L:SER67 5.0 30.7 1.0
O L:SER43 5.0 46.9 1.0

Calcium binding site 2 out of 9 in 2ec9

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Calcium binding site 2 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1003

b:97.0
occ:1.00
 OE11 L:CGU7 3.4 66.5 1.0
OE12 L:CGU26 3.5 49.0 1.0
O L:HOH1080 4.3 36.7 0.6
CB L:ASN2 4.5 70.6 1.0
ND2 L:ASN2 4.6 64.7 1.0
CD1 L:CGU7 4.7 68.0 1.0
CG L:ASN2 4.7 68.6 1.0
CD1 L:CGU26 4.8 45.3 1.0

Calcium binding site 3 out of 9 in 2ec9

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Calcium binding site 3 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1004

b:0.9
occ:1.00
 O L:ARG9 2.9 65.3 1.0
CD1 L:CGU16 3.5 50.1 1.0
O L:CGU6 3.6 58.4 1.0
OE12 L:CGU16 3.7 52.6 1.0
CD2 L:CGU16 3.7 48.5 1.0
OE12 L:CGU7 3.7 67.2 1.0
O L:CGU7 3.8 61.8 1.0
C L:ARG9 3.8 64.4 1.0
ND2 L:ASN2 4.1 64.7 1.0
CA L:CA1005 4.1 70.2 1.0
CG L:CGU16 4.1 50.8 1.0
CB L:ARG9 4.1 66.5 1.0
O L:PRO10 4.2 61.9 1.0
C L:PRO10 4.3 60.8 1.0
OE21 L:CGU16 4.4 47.4 1.0
C L:CGU7 4.4 62.8 1.0
CA L:CGU7 4.5 62.9 1.0
CA L:ARG9 4.5 64.5 1.0
N L:GLY11 4.5 58.1 1.0
OE11 L:CGU16 4.5 50.5 1.0
OE22 L:CGU16 4.5 48.0 1.0
CA L:GLY11 4.7 55.6 1.0
C L:CGU6 4.7 58.4 1.0
N L:PRO10 4.7 63.8 1.0
OE12 L:CGU6 4.7 64.7 1.0
N L:ARG9 4.8 63.8 1.0
CA L:PRO10 4.9 62.6 1.0

Calcium binding site 4 out of 9 in 2ec9

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Calcium binding site 4 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1005

b:70.2
occ:1.00
 OE11 L:CGU16 2.6 50.5 1.0
OE22 L:CGU16 2.7 48.0 1.0
OE11 L:CGU26 2.7 46.2 1.0
OE21 L:CGU26 2.8 41.5 1.0
CD1 L:CGU16 2.9 50.1 1.0
CD2 L:CGU16 3.2 48.5 1.0
CG L:CGU16 3.4 50.8 1.0
CD2 L:CGU26 3.6 45.3 1.0
ND2 L:ASN2 3.6 64.7 1.0
CD1 L:CGU26 3.7 45.3 1.0
OE12 L:CGU26 3.7 49.0 1.0
CB L:CGU16 3.9 52.0 1.0
CA L:CA1004 4.1 0.9 1.0
O L:ALA1 4.1 77.5 1.0
OE12 L:CGU16 4.2 52.6 1.0
CG L:CGU26 4.2 45.8 1.0
CB L:ASN2 4.2 70.6 1.0
CG L:ASN2 4.4 68.6 1.0
C L:ALA1 4.5 76.8 1.0
OE21 L:CGU16 4.5 47.4 1.0
N L:ALA1 4.6 77.0 1.0
OE21 L:CGU29 4.8 64.1 1.0
OE22 L:CGU26 4.8 46.6 1.0
OE12 L:CGU7 4.8 67.2 1.0
N L:ASN2 4.9 74.8 1.0
CB L:CGU26 4.9 44.1 1.0
CA L:ASN2 4.9 72.1 1.0

Calcium binding site 5 out of 9 in 2ec9

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Calcium binding site 5 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1006

b:68.8
occ:1.00
 CD2 L:CGU6 3.1 62.7 1.0
CG L:CGU6 3.4 63.0 1.0
CB L:CGU6 3.5 59.5 1.0
CD1 L:CGU6 3.5 65.7 1.0
OE22 L:CGU6 3.8 60.9 1.0
OE21 L:CGU20 4.0 61.7 1.0
OE21 L:CGU6 4.0 61.2 1.0
OE11 L:CGU6 4.4 65.4 1.0
OE12 L:CGU6 4.5 64.7 1.0
CD2 L:CGU20 4.8 61.2 1.0
OE12 L:CGU20 4.8 61.8 1.0
CA L:CGU6 5.0 57.4 1.0

Calcium binding site 6 out of 9 in 2ec9

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Calcium binding site 6 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1007

b:84.1
occ:1.00
 OE12 L:CGU14 2.7 63.7 1.0
OE22 L:CGU14 2.8 66.4 1.0
CD1 L:CGU19 2.9 65.6 1.0
OE11 L:CGU14 2.9 65.3 1.0
OE21 L:CGU19 3.0 68.5 1.0
OE11 L:CGU19 3.2 65.0 1.0
CD1 L:CGU14 3.3 64.3 1.0
OE12 L:CGU19 3.7 64.3 1.0
CD2 L:CGU19 3.7 68.0 1.0
CG L:CGU19 3.8 66.4 1.0
OE22 L:CGU19 3.8 69.7 1.0
CG L:CGU14 3.8 64.2 1.0
CD2 L:CGU14 3.9 64.8 1.0
OE21 L:CGU14 4.7 68.1 1.0

Calcium binding site 7 out of 9 in 2ec9

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Calcium binding site 7 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1008

b:97.2
occ:1.00
 OE22 L:CGU19 2.7 69.7 1.0
CD2 L:CGU19 3.1 68.0 1.0
CB L:CGU19 3.2 63.8 1.0
OE11 L:CGU20 3.4 61.8 1.0
CG L:CGU19 3.6 66.4 1.0
CD L:ARG15 4.0 65.2 1.0
CA L:CGU19 4.2 61.1 1.0
O L:ARG15 4.3 55.0 1.0
OE21 L:CGU19 4.4 68.5 1.0
C L:CGU19 4.4 61.2 1.0
NE L:ARG15 4.4 69.4 1.0
OE11 L:CGU19 4.5 65.0 1.0
N L:CGU20 4.6 60.1 1.0
CD1 L:CGU19 4.6 65.6 1.0
CD1 L:CGU20 4.8 61.6 1.0
O L:CGU19 5.0 61.9 1.0

Calcium binding site 8 out of 9 in 2ec9

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Calcium binding site 8 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca1009

b:68.1
occ:1.00
 O L:HOH1077 2.8 33.6 1.0
OE11 L:CGU29 3.1 63.9 1.0
OE22 L:CGU29 3.4 63.1 1.0
O L:HOH1063 3.7 45.3 1.0
OE12 L:CGU25 3.8 57.0 1.0
NH1 L:ARG28 4.3 44.2 1.0
CD1 L:CGU29 4.4 62.6 1.0
CD2 L:CGU29 4.5 63.3 1.0
NH2 L:ARG28 4.6 50.8 1.0
CG L:CGU29 4.6 63.4 1.0
OE22 L:CGU25 4.8 49.3 1.0
CZ L:ARG28 4.8 54.6 1.0

Calcium binding site 9 out of 9 in 2ec9

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Calcium binding site 9 out of 9 in the Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure Analysis of Human Factor Viia , Souluble Tissue Factor Complexed with Bcx-3607 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1001

b:60.3
occ:1.00
 OE2 H:GLU70 2.6 19.7 1.0
O H:GLU75 2.9 35.1 1.0
OE1 H:GLU70 3.0 23.8 1.0
ND1 H:HIS76 3.0 48.2 1.0
OE2 H:GLU80 3.0 32.5 1.0
CD H:GLU70 3.1 22.4 1.0
CE1 H:HIS76 3.2 48.5 1.0
O H:ASP72 3.4 18.6 1.0
C H:GLU75 3.7 36.3 1.0
CG H:HIS76 3.8 47.4 1.0
O H:LEU73 4.0 24.4 1.0
CD H:GLU80 4.0 35.2 1.0
NE2 H:HIS76 4.1 49.4 1.0
CA H:LEU73 4.1 21.2 1.0
CA H:HIS76 4.1 39.3 1.0
N H:HIS76 4.2 35.4 1.0
C H:LEU73 4.3 22.7 1.0
C H:ASP72 4.3 19.6 1.0
CD2 H:HIS76 4.4 46.4 1.0
CG H:GLU80 4.5 31.9 1.0
N H:GLU75 4.5 32.1 1.0
CB H:HIS76 4.5 41.3 1.0
CG H:GLU70 4.6 19.7 1.0
O H:HOH1010 4.6 18.1 1.0
CA H:GLU75 4.7 36.4 1.0
N H:LEU73 4.7 17.1 1.0

Reference:

R.Krishnan, P.L.Kotian, P.Chand, S.Bantia, S.Rowland, Y.S.Babu. Probing the S2 Site of Factor Viia to Generate Potent and Selective Inhibitors: the Structure of Bcx-3607 in Complex with Tissue Factor-Factor Viia. Acta Crystallogr.,Sect.D V. 63 689 2007.
ISSN: ISSN 0907-4449
PubMed: 17505107
DOI: 10.1107/S0907444907014187
Page generated: Fri Jul 12 10:11:21 2024

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