Chlorine in PDB 1nl2: Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine

All present enzymatic activity of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine:
3.4.21.5;

The structure of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine, PDB code: 1nl2 was solved by M.Huang, G.Huang, B.Furie, B.Seaton, B.C.Furie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.98 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.894, 53.217, 128.959, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 27.4

The structure of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Chlorine atom in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine (pdb code 1nl2). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine, PDB code: 1nl2:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl250 b:48.6 occ:1.00 O A:HOH560 2.7 52.4 1.0 NE A:ARG136 3.0 39.2 1.0 O A:HOH513 3.1 36.5 1.0 NH2 A:ARG136 3.4 36.9 1.0 CB A:TRP126 3.6 29.4 1.0 CZ A:ARG136 3.7 48.8 1.0 CG A:TRP126 3.8 31.4 1.0 N A:GLU138 3.9 42.3 1.0 CG A:ARG136 4.0 36.9 1.0 C A:GLU137 4.0 37.8 1.0 CA A:GLU137 4.1 35.0 1.0 CD A:ARG136 4.1 35.3 1.0 N A:GLU137 4.1 37.1 1.0 OG A:SER121 4.2 53.9 1.0 OG1 A:THR123 4.3 29.6 1.0 CD2 A:TRP126 4.3 37.8 1.0 C A:ARG136 4.4 36.3 1.0 CD1 A:TRP126 4.4 36.5 1.0 CB A:ARG136 4.4 38.2 1.0 O A:ARG136 4.5 47.5 1.0 OE1 A:GLU138 4.5 47.0 1.0 CA A:GLU138 4.6 32.6 1.0 O A:GLU137 4.6 40.8 1.0 CE3 A:TRP126 4.7 31.8 1.0 CB A:GLU138 4.8 37.4 1.0 CB A:SER121 4.9 46.4 1.0 NH1 A:ARG136 5.0 45.5 1.0

Chlorine binding site 2 out of 3 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl251 b:49.0 occ:1.00 N A:LYS97 3.2 37.8 1.0 NH1 A:ARG135 3.6 46.9 1.0 CE A:LYS97 3.8 75.0 1.0 CB A:LYS97 3.8 46.7 1.0 CA A:HIS96 4.0 44.8 1.0 CA A:LYS97 4.1 47.8 1.0 C A:HIS96 4.1 44.5 1.0 CG A:LYS97 4.3 67.1 1.0 O A:PRO95 4.5 42.9 1.0 O A:LYS97 4.5 43.2 1.0 CB A:HIS96 4.6 41.1 1.0 O A:HOH546 4.6 47.7 1.0 CD A:LYS97 4.6 71.2 1.0 C A:LYS97 4.7 42.8 1.0 CZ A:ARG135 4.8 32.1 1.0 ND1 A:HIS96 4.9 35.9 1.0 NZ A:LYS97 4.9 56.6 1.0

Chlorine binding site 3 out of 3 in the Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Bovine Prothrombin Fragment 1 in Complex with Calcium and Lysophosphotidylserine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl252 b:42.7 occ:1.00 N A:GLU112 3.2 35.2 1.0 O A:HOH552 3.4 43.8 1.0 NH1 A:ARG91 3.4 54.4 1.0 CA A:ARG111 3.9 41.8 1.0 CA A:GLU112 4.0 30.6 1.0 C A:ARG111 4.1 37.6 1.0 CB A:ARG111 4.4 47.1 1.0 CZ A:ARG91 4.5 64.8 1.0 CD A:ARG91 4.6 46.1 1.0 CG A:GLU112 4.6 58.6 1.0 CG A:ARG111 4.6 68.6 1.0 O A:LEU110 4.7 44.3 1.0 CG A:ARG91 4.9 37.2 1.0 CB A:GLU112 4.9 42.4 1.0 NE A:ARG91 5.0 53.3 1.0

M.Huang, A.C.Rigby, X.Morelli, M.A.Grant, G.Huang, B.Furie, B.Seaton, B.C.Furie. Structural Basis of Membrane Binding By Gla Domains of Vitamin K-Dependent Proteins. Nat.Struct.Biol. V. 10 751 2003.
ISSN: ISSN 1072-8368
PubMed: 12923575
DOI: 10.1038/NSB971