Magnesium 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:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	6 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1001 b:37.4 occ:1.00 OE12 L:CGU25 1.9 37.2 1.0 OE21 L:CGU25 2.0 38.6 1.0 O L:HOH1054 2.2 39.3 1.0 OE21 L:CGU29 2.2 24.6 1.0 OE11 L:CGU29 2.2 25.5 1.0 CD2 L:CGU25 2.6 39.2 1.0 CD1 L:CGU25 2.6 38.3 1.0 CG L:CGU25 2.7 37.3 1.0 O L:HOH1150 2.8 31.5 1.0 CD1 L:CGU29 2.9 25.0 1.0 CD2 L:CGU29 3.0 23.9 1.0 CG L:CGU29 3.0 24.5 1.0 OE22 L:CGU25 3.7 41.5 1.0 OE11 L:CGU25 3.9 40.8 1.0 NH1 L:ARG28 4.0 53.4 1.0 O L:HOH1116 4.1 40.5 1.0 OE12 L:CGU29 4.1 26.1 1.0 OE22 L:CGU29 4.2 23.4 1.0 CB L:CGU25 4.2 33.6 1.0 O L:CGU25 4.3 28.9 1.0 O L:HOH1170 4.4 39.5 1.0 CZ L:ARG28 4.4 52.4 1.0 CB L:CGU29 4.5 25.8 1.0 NH2 L:ARG28 4.7 54.7 1.0 C L:CGU25 4.8 29.4 1.0 CA L:CGU25 5.0 31.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1004 b:36.9 occ:1.00 OE11 L:CGU16 1.9 30.6 1.0 OE11 L:CGU26 1.9 41.1 1.0 OE21 L:CGU16 2.0 33.6 1.0 OE22 L:CGU26 2.0 33.3 1.0 O L:HOH1028 2.1 24.4 1.0 O L:HOH1061 2.2 36.0 1.0 CD1 L:CGU16 2.8 31.5 1.0 CD1 L:CGU26 2.9 39.6 1.0 CD2 L:CGU16 2.9 34.4 1.0 CD2 L:CGU26 3.0 34.9 1.0 CG L:CGU16 3.3 32.4 1.0 CG L:CGU26 3.4 37.0 1.0 CB L:CGU16 3.8 32.7 1.0 O L:HOH1056 3.9 23.0 1.0 OE12 L:CGU26 3.9 43.7 1.0 OE22 L:CGU16 3.9 33.6 1.0 OE12 L:CGU16 3.9 32.3 1.0 CB L:CGU26 4.0 34.5 1.0 OE21 L:CGU26 4.1 36.0 1.0 O L:HOH1042 4.2 43.2 1.0 CA L:CA1005 4.2 61.3 1.0 OE12 L:CGU7 4.3 40.6 1.0 O L:HOH1036 4.5 50.9 1.0 O L:ALA1 4.5 69.8 1.0 O L:HOH1171 4.8 43.0 1.0 N L:ALA1 4.8 71.0 1.0 OE11 L:CGU7 4.9 43.0 1.0 CA L:CGU16 5.0 34.0 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Dfpr-Viia/Stf within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1007 b:46.9 occ:1.00 OE12 L:CGU19 1.8 49.5 1.0 OE22 L:CGU19 1.9 48.8 1.0 OE22 L:CGU14 2.0 51.7 1.0 OE11 L:CGU14 2.0 46.5 1.0 CD1 L:CGU19 2.6 49.9 1.0 CG L:CGU14 2.6 46.6 1.0 CD2 L:CGU19 2.7 48.5 1.0 CD1 L:CGU14 2.7 46.2 1.0 CD2 L:CGU14 2.7 48.6 1.0 CG L:CGU19 2.7 48.4 1.0 OE11 L:CGU19 3.8 51.2 1.0 OE12 L:CGU14 3.9 44.8 1.0 OE21 L:CGU19 3.9 47.8 1.0 OE21 L:CGU14 3.9 47.0 1.0 O L:CGU14 4.1 35.3 1.0 CB L:CGU14 4.1 42.3 1.0 CB L:CGU19 4.2 47.3 1.0 C L:CGU14 4.4 37.2 1.0 CA L:CGU14 4.8 38.6 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