Chlorine 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
Zinc	(Zn)	2 atoms
Calcium	(Ca)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Crystal Structure of Dfpr-Viia/Stf (pdb code 2fir). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Dfpr-Viia/Stf, PDB code: 2fir:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1013 b:41.8 occ:1.00 O H:GLY216 3.0 22.6 1.0 NE H:0G7701 3.1 16.2 1.0 C H:GLY216 3.2 20.2 1.0 N H:GLY219 3.2 21.4 1.0 NH2 H:0G7701 3.4 15.8 1.0 O H:HOH461 3.5 43.0 1.0 CA H:GLY216 3.6 17.4 1.0 C H:GLY219 3.6 21.8 1.0 CA H:GLY219 3.7 20.0 1.0 N H:GLY216 3.7 12.8 1.0 CZ1 H:0G7701 3.7 16.5 1.0 O H:GLY219 3.8 24.9 1.0 CG2 H:0G7701 3.8 12.4 1.0 O H:0G7701 3.9 17.2 1.0 N H:GLN217 3.9 23.3 1.0 CD3 H:0G7701 4.1 17.4 1.0 N H:CYS220 4.1 20.0 1.0 C H:GLN217 4.2 22.8 1.0 SG H:CYS220 4.3 22.8 1.0 CA H:GLN217 4.5 22.8 1.0 C H:TRP215 4.7 13.2 1.0 N H:0G7701 4.7 26.5 1.0 CA H:CYS220 4.8 17.7 1.0 C H:0G7701 4.9 22.4 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1014 b:20.6 occ:1.00 N H:ARG84 3.2 20.3 1.0 CD2 H:HIS109 3.4 27.0 1.0 CB H:HIS109 3.7 20.2 1.0 CA H:ARG83 3.7 16.7 1.0 O H:HOH1074 3.7 33.2 1.0 O H:HOH1219 3.8 36.0 1.0 CD H:ARG83 3.8 11.6 1.0 CG H:HIS109 3.9 26.9 1.0 N H:GLN110 3.9 16.8 1.0 CG H:GLN110 3.9 21.2 1.0 C H:ARG83 4.0 17.6 1.0 CB H:GLN110 4.0 17.3 1.0 CG H:ARG84 4.0 29.6 1.0 CB H:ARG83 4.0 17.7 1.0 CB H:ARG84 4.1 23.9 1.0 CA H:ARG84 4.2 19.4 1.0 NE H:ARG84 4.3 46.2 1.0 O H:ARG84 4.5 13.5 1.0 C H:HIS109 4.5 16.6 1.0 CA H:HIS109 4.5 17.1 1.0 CG H:ARG83 4.5 16.2 1.0 CA H:GLN110 4.5 16.9 1.0 NE2 H:HIS109 4.6 29.5 1.0 CD H:ARG84 4.8 37.3 1.0 N H:HIS109 4.8 18.1 1.0 C H:ARG84 4.8 16.2 1.0 O H:SER82 4.9 16.4 1.0 NE H:ARG83 4.9 9.4 1.0 O H:GLN110 5.0 15.6 1.0 N H:ARG83 5.0 17.3 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Dfpr-Viia/Stf


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ T:Cl1015 b:21.5 occ:1.00 OH T:TYR153 3.2 13.6 1.0 ND2 T:ASN173 3.4 16.8 1.0 N T:GLU130 3.4 19.8 1.0 O T:HOH1128 3.5 36.0 1.0 N T:ARG144 3.5 18.7 1.0 CB T:ARG144 3.6 15.9 1.0 CB T:SER142 3.7 18.1 1.0 N T:LEU143 3.8 17.8 1.0 CA T:ASP129 3.9 21.2 1.0 CB T:LEU143 4.0 16.6 1.0 OG T:SER142 4.0 17.6 1.0 OD1 T:ASN173 4.1 19.1 1.0 O T:GLU130 4.1 22.3 1.0 CE2 T:TYR153 4.1 11.6 1.0 CZ T:TYR153 4.1 12.9 1.0 C T:ASP129 4.1 20.3 1.0 CG T:ASN173 4.1 17.9 1.0 CA T:ARG144 4.2 18.5 1.0 CA T:LEU143 4.3 16.8 1.0 C T:LEU143 4.4 17.5 1.0 CB T:GLU130 4.4 17.0 1.0 CA T:GLU130 4.4 20.8 1.0 CB T:ASP129 4.4 22.2 1.0 CD2 T:LEU151 4.5 13.5 1.0 OD1 T:ASP129 4.5 26.1 1.0 C T:SER142 4.5 18.6 1.0 CA T:SER142 4.6 18.6 1.0 C T:GLU130 4.7 21.5 1.0 O T:GLU128 4.9 16.0 1.0 CG T:ARG144 5.0 14.9 1.0 CG T:ASP129 5.0 27.4 1.0 CG T:GLU130 5.0 17.4 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