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Zinc 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
Calcium (Ca) 6 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Benzamidine-Factor Viia/Soluble Tissue Factor Complex., PDB code: 2aer:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2aer

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
H:Zn3011

b:62.5
occ:1.00
O H:HOH3262 2.3 73.7 1.0
O H:HOH3136 2.6 37.8 1.0
OE1 H:GLU80 2.6 18.4 1.0
O H:HOH3101 2.8 22.1 1.0
O H:HOH3139 2.9 31.2 1.0
ND1 H:HIS76 3.4 20.3 1.0
CE1 H:HIS76 3.6 21.8 1.0
CB H:GLU80 3.7 13.3 1.0
CD H:GLU80 3.7 16.2 1.0
OG H:SER82 3.8 18.7 1.0
O H:HOH3171 3.9 25.9 1.0
O H:HOH3197 4.0 20.9 1.0
CG1 H:VAL67 4.2 8.4 1.0
CG H:GLU80 4.2 15.1 1.0
CG H:HIS76 4.5 20.9 1.0
O H:HOH3154 4.5 27.1 1.0
O H:HOH3199 4.5 25.0 1.0
O H:HOH3237 4.6 52.3 1.0
NE2 H:HIS76 4.7 23.5 1.0
OE1 H:GLU70 4.7 11.3 1.0
OE2 H:GLU80 4.8 16.7 1.0
O H:HOH3334 4.8 35.2 1.0
CA H:GLU80 4.9 12.9 1.0
C H:GLU80 5.0 12.7 1.0

Zinc binding site 2 out of 2 in 2aer

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
H:Zn3012

b:55.8
occ:1.00
O H:HOH3029 2.3 16.8 1.0
O H:GLY69 2.6 12.2 1.0
NZ H:LYS24 2.7 15.9 1.0
ND1 H:HIS117 3.2 12.7 1.0
O H:HOH3041 3.3 9.1 1.0
C H:GLY69 3.5 11.1 1.0
CG H:LYS24 3.5 11.9 1.0
CE H:LYS24 3.7 14.5 1.0
CB H:HIS117 3.9 10.9 1.0
CG H:HIS117 3.9 11.5 1.0
CA H:GLY69 4.0 11.0 1.0
CB H:ASP79 4.0 14.4 1.0
O H:GLU70 4.1 10.9 1.0
CD H:LYS24 4.1 13.5 1.0
CB H:HIS71 4.1 10.7 1.0
OD2 H:ASP79 4.2 14.0 1.0
CE1 H:HIS117 4.2 10.9 1.0
O H:HOH3030 4.2 14.4 1.0
N H:GLY25 4.3 10.8 1.0
C H:GLU70 4.3 10.5 1.0
N H:GLU70 4.4 10.2 1.0
CG H:ASP79 4.6 15.3 1.0
O H:HIS117 4.7 10.4 1.0
N H:HIS71 4.7 10.0 1.0
CB H:LYS24 4.8 11.4 1.0
CA H:GLU70 4.8 10.0 1.0
CA H:GLY25 4.9 10.0 1.0
C H:LYS24 4.9 11.6 1.0
CA H:HIS117 5.0 11.7 1.0
CA H:LYS24 5.0 11.6 1.0
CA H:HIS71 5.0 10.5 1.0
O H:HOH3028 5.0 11.5 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: Thu Oct 29 07:45:17 2020
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