Atomistry » Calcium » PDB 2a2z-2ago » 2aer
Atomistry »
  Calcium »
    PDB 2a2z-2ago »
      2aer »

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

Go back to Calcium Binding Sites List in 2aer
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

Go back to Calcium Binding Sites List in 2aer
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

Go back to Calcium Binding Sites List in 2aer
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: Wed Oct 28 07:35:44 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy