Magnesium in PDB 5edk: Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ).

All present enzymatic activity of Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ).:
3.4.21.5;

The structure of Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II )., PDB code: 5edk was solved by N.Pozzi, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	86.61 / 3.21
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.192, 84.192, 346.427, 90.00, 90.00, 90.00
R / Rfree (%)	29.1 / 32.3

The binding sites of Magnesium atom in the Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ). (pdb code 5edk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II )., PDB code: 5edk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ).


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 Prothrombin Deletion Mutant Residues 146-167 ( Form II ). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:35.1 occ:1.00 OE11 A:CGU19 2.1 50.0 1.0 OE21 A:CGU19 2.3 53.5 1.0 OE11 A:CGU14 3.0 62.0 1.0 CD1 A:CGU19 3.2 53.8 1.0 CD2 A:CGU19 3.2 53.4 1.0 CG A:CGU19 3.7 54.4 1.0 OE22 A:CGU14 4.2 79.0 1.0 CD1 A:CGU14 4.2 66.2 1.0 OE22 A:CGU19 4.3 51.9 1.0 OE12 A:CGU19 4.3 55.8 1.0 NE A:ARG54 4.6 66.5 1.0 NH2 A:ARG54 4.7 65.5 1.0 CD2 A:CGU14 4.8 74.4 1.0 CZ A:ARG54 4.8 66.6 1.0 CG A:CGU14 4.9 69.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ).


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 Prothrombin Deletion Mutant Residues 146-167 ( Form II ). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:77.6 occ:1.00 OE22 A:CGU26 2.3 83.5 1.0 OE11 A:CGU16 2.5 72.0 1.0 CD1 A:CGU16 3.1 77.2 1.0 CD2 A:CGU26 3.1 86.9 1.0 CG A:CGU26 3.2 92.4 1.0 CD2 A:CGU16 3.5 82.4 1.0 OE21 A:CGU16 3.5 87.2 1.0 MG A:MG608 3.6 51.6 1.0 OE12 A:CGU16 3.7 79.6 1.0 OE22 A:CGU16 3.8 83.7 1.0 CD1 A:CGU26 3.9 95.7 1.0 CG A:CGU16 3.9 80.1 1.0 OE11 A:CGU26 4.0 98.3 1.0 OE21 A:CGU26 4.3 83.4 1.0 CB A:CGU26 4.5 96.0 1.0 OE21 A:CGU29 4.6 0.7 1.0 OE12 A:CGU26 4.8 95.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ).


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 Prothrombin Deletion Mutant Residues 146-167 ( Form II ). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg607 b:74.1 occ:1.00 OE22 A:CGU29 2.1 0.6 1.0 OE22 A:CGU25 2.5 98.8 1.0 MG A:MG608 2.9 51.6 1.0 CD2 A:CGU25 3.0 0.5 1.0 OE11 A:CGU29 3.0 0.1 1.0 OE21 A:CGU25 3.1 0.3 1.0 OE12 A:CGU26 3.1 95.3 1.0 CD2 A:CGU29 3.2 0.0 1.0 CG A:CGU29 3.8 0.8 1.0 CD1 A:CGU29 3.9 0.7 1.0 CD1 A:CGU26 4.0 95.7 1.0 CG A:CGU25 4.2 0.5 1.0 OE21 A:CGU29 4.2 0.7 1.0 OE11 A:CGU26 4.3 98.3 1.0 N A:CGU26 4.9 0.6 1.0 CB A:CGU25 5.0 0.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ).


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Prothrombin Deletion Mutant Residues 146-167 ( Form II ). within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg608 b:51.6 occ:1.00 OE11 A:CGU26 2.6 98.3 1.0 CD1 A:CGU26 2.8 95.7 1.0 MG A:MG607 2.9 74.1 1.0 OE12 A:CGU26 3.0 95.3 1.0 OE22 A:CGU29 3.3 0.6 1.0 MG A:MG606 3.6 77.6 1.0 CG A:CGU26 3.6 92.4 1.0 CD2 A:CGU29 3.9 0.0 1.0 OE22 A:CGU26 4.2 83.5 1.0 OE21 A:CGU29 4.2 0.7 1.0 CD2 A:CGU26 4.4 86.9 1.0 CG A:CGU29 4.7 0.8 1.0 CB A:CGU26 4.9 96.0 1.0

N.Pozzi, Z.Chen, E.Di Cera. How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin. J.Biol.Chem. V. 291 6071 2016.
ISSN: ESSN 1083-351X
PubMed: 26763231
DOI: 10.1074/JBC.M115.700401