Zinc in PDB 2fir: Crystal Structure of Dfpr-Viia/Stf

All present enzymatic activity of Crystal Structure of Dfpr-Viia/Stf:
3.4.21.21;

The structure of Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir was solved by S.P.Bajaj, A.E.Schmidt, K.Padmanabhan, M.S.Bajaj, 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 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.020, 80.980, 126.330, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 28.1

The structure of Crystal Structure of Dfpr-Viia/Stf also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Crystal Structure of Dfpr-Viia/Stf (pdb code 2fir). 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 Dfpr-Viia/Stf, PDB code: 2fir:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1011 b:49.6 occ:1.00 O H:HOH1132 2.5 73.6 1.0 O H:HOH1135 2.6 99.1 1.0 OE1 H:GLU80 3.0 26.8 1.0 O H:HOH1136 3.1 25.9 1.0 ND1 H:HIS76 3.2 26.7 1.0 CE1 H:HIS76 3.5 27.7 1.0 OG H:SER82 3.7 19.8 1.0 CB H:GLU80 3.8 16.1 1.0 O H:HOH1120 3.9 26.8 1.0 CG1 H:VAL67 4.0 9.7 1.0 CD H:GLU80 4.0 26.5 1.0 O H:HOH1137 4.1 36.8 1.0 CG H:GLU80 4.5 20.6 1.0 CG H:HIS76 4.5 26.6 1.0 OE1 H:GLU70 4.6 18.6 1.0 NE2 H:HIS76 4.7 31.6 1.0 CG2 H:VAL67 4.8 12.8 1.0 O H:HOH1166 4.9 53.4 1.0 O H:HOH1227 4.9 45.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Dfpr-Viia/Stf


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 Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn1012 b:42.5 occ:1.00 NZ H:LYS24 2.6 20.3 1.0 O H:HOH1052 2.8 18.7 1.0 O H:GLY69 2.9 13.3 1.0 O H:HOH1081 3.2 12.1 1.0 ND1 H:HIS117 3.3 10.9 1.0 CG H:LYS24 3.6 12.7 1.0 CB H:HIS117 3.7 11.8 1.0 CE H:LYS24 3.7 18.4 1.0 C H:GLY69 3.7 12.3 1.0 CB H:ASP79 3.7 15.1 1.0 OD1 H:ASP79 3.7 17.1 1.0 CG H:HIS117 3.7 6.2 1.0 CA H:GLY69 4.1 13.0 1.0 CD H:LYS24 4.2 15.6 1.0 CG H:ASP79 4.2 16.5 1.0 CE1 H:HIS117 4.3 10.2 1.0 O H:HOH1026 4.4 14.3 1.0 N H:GLY25 4.5 12.7 1.0 O H:GLU70 4.6 17.0 1.0 CB H:HIS71 4.6 13.1 1.0 O H:HIS117 4.7 12.9 1.0 N H:GLU70 4.7 12.7 1.0 C H:GLU70 4.8 14.9 1.0 OD1 H:ASP77 4.8 17.8 1.0 CA H:HIS117 4.8 12.0 1.0 CD2 H:HIS117 4.8 5.8 1.0 CA H:GLY25 4.9 14.6 1.0 CB H:LYS24 4.9 12.5 1.0

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