Atomistry » Magnesium » PDB 5e7c-5egc » 5edk
Atomistry »
  Magnesium »
    PDB 5e7c-5egc »
      5edk »

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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 5edk

Go back to Magnesium Binding Sites List in 5edk
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 5edk

Go back to Magnesium Binding Sites List in 5edk
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 5edk

Go back to Magnesium Binding Sites List in 5edk
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 5edk

Go back to Magnesium Binding Sites List in 5edk
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

Reference:

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
Page generated: Sun Sep 29 03:38:12 2024

Last articles

Cl in 3ZO9
Cl in 3ZNX
Cl in 3ZNV
Cl in 3ZN5
Cl in 3ZNO
Cl in 3ZN6
Cl in 3ZMJ
Cl in 3ZMD
Cl in 3ZN4
Cl in 3ZMH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy