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Calcium in PDB 2aer: Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.

Enzymatic activity of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.

All present enzymatic activity of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.:
3.4.21.21;

Protein crystallography data

The structure of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex., PDB code: 2aer was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, A.Liesum, J.Dumas, D.Prevost, H.Schreuder, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.900, 81.200, 125.900, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 25.6

Other elements in 2aer:

The structure of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. (pdb code 2aer). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex., PDB code: 2aer:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2aer

Go back to Calcium Binding Sites List in 2aer
Calcium binding site 1 out of 6 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca3002

b:67.8
occ:1.00
 OE21 L:CGU26 2.0 36.8 1.0
OE11 L:CGU29 2.9 30.6 1.0
O L:HOH3149 3.0 56.2 1.0
CD2 L:CGU26 3.3 33.7 1.0
OE12 L:CGU29 3.3 30.8 1.0
O L:HOH3052 3.4 20.8 1.0
CD1 L:CGU29 3.4 30.0 1.0
CD1 L:CGU25 3.7 31.4 1.0
CG L:CGU25 3.7 30.0 1.0
OE11 L:CGU25 3.8 33.2 1.0
O L:HOH3153 3.9 49.6 1.0
N L:CGU26 4.0 27.0 1.0
CG L:CGU26 4.1 32.4 1.0
CB L:CGU25 4.1 28.8 1.0
OE12 L:CGU25 4.2 33.7 1.0
OE22 L:CGU26 4.2 35.1 1.0
CA L:CGU26 4.2 27.7 1.0
C L:CGU25 4.3 27.1 1.0
O L:HOH3152 4.5 66.3 1.0
O L:HOH3118 4.5 56.7 1.0
O L:CGU25 4.6 26.5 1.0
MG L:MG3001 4.6 33.5 1.0
CB L:CGU26 4.7 29.2 1.0
CG L:CGU29 4.8 29.2 1.0
CA L:CGU25 4.8 27.7 1.0
OG L:SER23 4.9 33.5 1.0

Calcium binding site 2 out of 6 in 2aer

Go back to Calcium Binding Sites List in 2aer
Calcium binding site 2 out of 6 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca3003

b:69.1
occ:1.00
 OE12 L:CGU29 2.5 30.8 1.0
O L:HOH3127 3.3 69.7 1.0
CB L:CGU29 3.5 29.2 1.0
CD1 L:CGU29 3.6 30.0 1.0
OE22 L:CGU26 3.7 35.1 1.0
O L:CGU26 3.8 26.8 1.0
OE21 L:CGU16 3.9 39.4 1.0
CD2 L:CGU26 4.1 33.7 1.0
OE21 L:CGU26 4.1 36.8 1.0
OE22 L:CGU16 4.2 36.8 1.0
CG L:CGU29 4.2 29.2 1.0
CA L:CGU26 4.2 27.7 1.0
C L:CGU26 4.5 26.8 1.0
CD2 L:CGU16 4.5 37.7 1.0
O L:HOH3131 4.7 33.8 1.0
OE11 L:CGU29 4.7 30.6 1.0
CB L:CGU26 4.7 29.2 1.0
CA L:CGU29 4.7 29.5 1.0
CG1 L:ILE30 4.8 31.5 1.0
C L:CGU29 4.9 30.2 1.0
MG L:MG3004 4.9 37.1 1.0
N L:ILE30 5.0 30.9 1.0

Calcium binding site 3 out of 6 in 2aer

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Calcium binding site 3 out of 6 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca3005

b:60.5
occ:1.00
 O L:ALA1 2.0 64.9 1.0
OE11 L:CGU16 2.1 37.2 1.0
OE21 L:CGU20 2.3 65.0 1.0
CD1 L:CGU16 2.8 36.8 1.0
OE12 L:CGU16 2.8 36.6 1.0
O L:HOH3086 2.9 23.0 1.0
OE11 L:CGU7 3.0 35.2 1.0
C L:ALA1 3.3 64.4 1.0
CD2 L:CGU20 3.3 62.9 1.0
MG L:MG3004 3.6 37.1 1.0
OE22 L:CGU20 3.7 64.0 1.0
OD1 L:ASN2 3.9 65.1 1.0
N L:ALA1 4.0 64.9 1.0
OE11 L:CGU26 4.1 31.6 1.0
O L:HOH3131 4.1 33.8 1.0
CA L:ALA1 4.2 65.0 1.0
CD1 L:CGU7 4.2 33.7 1.0
CG L:CGU16 4.2 37.5 1.0
N L:ASN2 4.2 63.2 1.0
CA L:ASN2 4.4 61.4 1.0
OE12 L:CGU7 4.6 33.5 1.0
CG L:CGU20 4.6 61.6 1.0
CB L:ALA1 4.7 65.6 1.0
OE21 L:CGU6 4.7 46.1 1.0
CB L:CGU16 4.7 38.1 1.0
CA L:CGU16 4.8 39.5 1.0
CG L:ASN2 4.9 64.8 1.0
OE21 L:CGU16 4.9 39.4 1.0

Calcium binding site 4 out of 6 in 2aer

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Calcium binding site 4 out of 6 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca3006

b:76.5
occ:1.00
 OE11 L:CGU6 2.0 45.9 1.0
OE21 L:CGU6 2.4 46.1 1.0
OE22 L:CGU20 2.8 64.0 1.0
CD L:ARG15 3.0 45.7 1.0
CD1 L:CGU6 3.1 43.7 1.0
NE L:ARG15 3.2 46.4 1.0
CG L:ARG15 3.2 44.7 1.0
CD2 L:CGU6 3.2 44.0 1.0
CG L:CGU6 3.6 42.2 1.0
CD2 L:CGU20 4.0 62.9 1.0
CB L:CGU6 4.1 35.6 1.0
OE12 L:CGU6 4.2 44.3 1.0
OE12 L:CGU16 4.2 36.6 1.0
OE22 L:CGU6 4.3 45.7 1.0
OE12 L:CGU20 4.3 64.0 1.0
CZ L:ARG15 4.5 46.8 1.0
OE21 L:CGU20 4.6 65.0 1.0
OE22 L:CGU19 4.6 62.2 1.0
CB L:ARG15 4.6 43.5 1.0
O L:ARG15 4.8 40.4 1.0

Calcium binding site 5 out of 6 in 2aer

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Calcium binding site 5 out of 6 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca3008

b:25.4
occ:1.00
 OD2 L:ASP46 2.2 26.3 1.0
OE1 L:GLN49 2.2 27.2 1.0
OD2 L:ASP63 2.3 25.1 1.0
O L:GLY47 2.3 29.6 1.0
O L:GLN64 2.3 22.7 1.0
O T:HOH3040 2.7 29.7 1.0
CG L:ASP63 2.9 24.9 1.0
OD1 L:ASP63 2.9 25.6 1.0
O L:HOH3061 2.9 39.0 1.0
CG L:ASP46 3.4 29.4 1.0
CD L:GLN49 3.4 27.4 1.0
C L:GLY47 3.5 28.9 1.0
C L:GLN64 3.5 22.2 1.0
NE2 L:GLN49 4.0 26.6 1.0
CB L:ASP46 4.1 29.8 1.0
N L:GLN66 4.1 25.4 1.0
CA L:LEU65 4.2 25.1 1.0
N L:GLN49 4.2 26.9 1.0
N L:GLN64 4.2 21.0 1.0
N L:LEU65 4.3 23.3 1.0
CA L:ASP48 4.4 28.0 1.0
OD1 L:ASP46 4.4 30.7 1.0
CB L:ASP63 4.4 22.8 1.0
C L:ASP46 4.4 30.2 1.0
O L:ASP46 4.4 30.7 1.0
N L:ASP48 4.4 28.2 1.0
N L:GLY47 4.4 29.3 1.0
O L:SER67 4.5 18.3 1.0
CA L:GLN64 4.5 21.7 1.0
CA L:GLY47 4.5 29.3 1.0
C L:LEU65 4.6 25.3 1.0
CG L:GLN49 4.6 26.3 1.0
C L:ASP48 4.8 27.5 1.0
CB L:GLN49 4.9 25.5 1.0
C L:ASP63 4.9 21.4 1.0
CA L:ASP46 4.9 30.1 1.0

Calcium binding site 6 out of 6 in 2aer

Go back to Calcium Binding Sites List in 2aer
Calcium binding site 6 out of 6 in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca3009

b:29.4
occ:1.00
 O H:GLU75 1.9 15.6 1.0
O H:HOH3227 2.1 8.5 1.0
OE2 H:GLU80 2.1 16.7 1.0
O H:HOH3073 2.2 14.2 1.0
O H:ASP72 2.2 12.8 1.0
OE2 H:GLU70 2.3 12.3 1.0
C H:GLU75 3.1 16.9 1.0
CD H:GLU80 3.2 16.2 1.0
CD H:GLU70 3.2 10.9 1.0
C H:ASP72 3.3 12.6 1.0
OE1 H:GLU70 3.5 11.3 1.0
OE1 H:GLU80 3.8 18.4 1.0
CA H:HIS76 3.9 17.5 1.0
N H:ASP72 3.9 10.6 1.0
N H:HIS76 3.9 16.3 1.0
O H:HOH3104 4.0 18.8 1.0
CA H:ASP72 4.1 11.9 1.0
N H:GLU75 4.2 16.5 1.0
CA H:GLU75 4.2 16.9 1.0
O H:HOH3088 4.2 34.6 1.0
CG H:GLU80 4.2 15.1 1.0
O H:HOH3041 4.2 9.1 1.0
N H:LEU73 4.2 13.1 1.0
N H:HIS71 4.4 10.0 1.0
CA H:LEU73 4.4 13.7 1.0
ND1 H:HIS76 4.5 20.3 1.0
CB H:ASP72 4.5 12.7 1.0
CG H:GLU70 4.6 11.0 1.0
N H:ASP77 4.6 16.2 1.0
C H:HIS76 4.7 17.4 1.0
C H:LEU73 4.7 14.1 1.0
CB H:GLU75 4.8 18.6 1.0
C H:HIS71 4.9 10.4 1.0
O H:LEU73 5.0 15.7 1.0

Reference:

S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, K.Padmanabhan. High Resolution Structures of P-Aminobenzamidine- and Benzamidine-Viia/Soluble Tissue Factor: Unpredicted Conformation of the 192-193 Peptide Bond and Mapping of CA2+, MG2+, Na+ and ZN2+ Sites in Factor Viia J.Biol.Chem. V. 281 24873 2006.
ISSN: ISSN 0021-9258
PubMed: 16757484
DOI: 10.1074/JBC.M509971200
Page generated: Fri Jul 12 08:41:09 2024

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