Atomistry » Magnesium » PDB 6bcr-6bqz » 6bjr
Atomistry »
  Magnesium »
    PDB 6bcr-6bqz »
      6bjr »

Magnesium in PDB 6bjr: Crystal Structure of Prothrombin Mutant S101C/A470C

Enzymatic activity of Crystal Structure of Prothrombin Mutant S101C/A470C

All present enzymatic activity of Crystal Structure of Prothrombin Mutant S101C/A470C:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Prothrombin Mutant S101C/A470C, PDB code: 6bjr was solved by M.Chinnaraj, Z.Chen, L.Pelc, Z.Grese, D.Bystranowska, E.Di Cera, N.Pozzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 6.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 114.126, 124.175, 157.093, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 29.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Prothrombin Mutant S101C/A470C (pdb code 6bjr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Prothrombin Mutant S101C/A470C, PDB code: 6bjr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6bjr

Go back to Magnesium Binding Sites List in 6bjr
Magnesium binding site 1 out of 6 in the Crystal Structure of Prothrombin Mutant S101C/A470C


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 Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.1
occ:1.00
 O A:ALA30 2.2 0.0 1.0
OE11 A:CGU32 2.3 0.0 1.0
OE21 A:CGU32 2.7 0.0 1.0
CG A:CGU32 2.8 0.0 1.0
CD1 A:CGU32 2.9 0.0 1.0
CD2 A:CGU32 3.2 0.0 1.0
C A:ALA30 3.2 0.0 1.0
CA A:ALA30 3.9 0.0 1.0
CD A:ARG9 3.9 0.9 1.0
O A:LEU31 4.0 0.0 1.0
NE A:ARG9 4.0 0.0 1.0
CG A:ARG9 4.1 0.2 1.0
OE12 A:CGU32 4.1 0.0 1.0
C A:LEU31 4.2 0.0 1.0
CB A:CGU32 4.2 0.0 1.0
N A:LEU31 4.3 0.0 1.0
CB A:ALA30 4.5 0.0 1.0
OE22 A:CGU32 4.5 0.0 1.0
N A:CGU32 4.6 0.0 1.0
CA A:LEU31 4.7 0.0 1.0
CB A:ARG9 5.0 0.2 1.0
ND2 A:ASN12 5.0 0.4 1.0

Magnesium binding site 2 out of 6 in 6bjr

Go back to Magnesium Binding Sites List in 6bjr
Magnesium binding site 2 out of 6 in the Crystal Structure of Prothrombin Mutant S101C/A470C


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 Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:0.5
occ:1.00
 OE12 A:CGU25 2.4 0.0 1.0
OE22 A:CGU25 2.5 0.0 1.0
OE11 A:CGU29 2.6 1.0 1.0
CD1 A:CGU25 3.0 0.0 1.0
CD2 A:CGU25 3.1 0.0 1.0
CG A:CGU25 3.1 0.0 1.0
CD1 A:CGU29 3.5 0.1 1.0
MG A:MG603 3.6 0.3 1.0
OE12 A:CGU29 3.6 0.9 1.0
OE11 A:CGU25 4.1 0.0 1.0
OE21 A:CGU25 4.2 0.0 1.0
O A:CGU25 4.4 1.0 1.0
CB A:CGU25 4.6 0.0 1.0
O A:PHE28 4.7 0.0 1.0
CG A:CGU29 4.8 0.7 1.0
OE21 A:CGU29 4.9 0.0 1.0

Magnesium binding site 3 out of 6 in 6bjr

Go back to Magnesium Binding Sites List in 6bjr
Magnesium binding site 3 out of 6 in the Crystal Structure of Prothrombin Mutant S101C/A470C


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 Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:0.3
occ:1.00
 OE21 A:CGU29 2.2 0.0 1.0
OE11 A:CGU29 2.4 1.0 1.0
O A:CGU25 2.9 1.0 1.0
OE12 A:CGU26 3.1 0.5 1.0
CD2 A:CGU29 3.2 0.8 1.0
CD1 A:CGU29 3.3 0.1 1.0
C A:CGU25 3.5 0.9 1.0
CA A:CGU26 3.5 0.4 1.0
MG A:MG602 3.6 0.5 1.0
CG A:CGU29 3.6 0.7 1.0
N A:CGU26 3.7 0.4 1.0
CD1 A:CGU26 3.8 0.7 1.0
CG A:CGU25 3.8 0.0 1.0
CB A:CGU29 3.9 0.0 1.0
OE11 A:CGU26 4.1 0.5 1.0
OE12 A:CGU25 4.2 0.0 1.0
OE22 A:CGU25 4.2 0.0 1.0
OE22 A:CGU29 4.3 0.2 1.0
MG A:MG604 4.3 0.0 1.0
CB A:CGU26 4.4 0.5 1.0
CB A:CGU25 4.4 0.0 1.0
OE12 A:CGU29 4.5 0.9 1.0
CD1 A:CGU25 4.5 0.0 1.0
C A:CGU26 4.5 0.8 1.0
CD2 A:CGU25 4.5 0.0 1.0
O A:CGU26 4.5 0.8 1.0
CA A:CGU25 4.5 0.2 1.0
O A:PHE28 4.6 0.0 1.0
CG A:CGU26 4.7 0.7 1.0

Magnesium binding site 4 out of 6 in 6bjr

Go back to Magnesium Binding Sites List in 6bjr
Magnesium binding site 4 out of 6 in the Crystal Structure of Prothrombin Mutant S101C/A470C


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 Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:0.0
occ:1.00
 CD2 A:CGU29 2.0 0.8 1.0
OE11 A:CGU26 2.2 0.5 1.0
OE22 A:CGU29 2.2 0.2 1.0
OE21 A:CGU29 2.3 0.0 1.0
CB A:CGU29 2.7 0.0 1.0
CG A:CGU29 2.8 0.7 1.0
CD1 A:CGU26 3.3 0.7 1.0
OE12 A:CGU26 3.6 0.5 1.0
O A:CGU26 3.9 0.8 1.0
CA A:CGU29 3.9 0.0 1.0
N A:ALA30 4.0 0.0 1.0
OE12 A:CGU16 4.0 0.0 1.0
C A:CGU29 4.1 0.0 1.0
CD1 A:CGU29 4.1 0.1 1.0
MG A:MG603 4.3 0.3 1.0
OE11 A:CGU29 4.5 1.0 1.0
CG A:CGU26 4.6 0.7 1.0
MG A:MG605 4.6 0.3 1.0
CB A:ALA30 4.7 0.0 1.0
O A:CGU29 4.9 0.0 1.0
C A:CGU26 4.9 0.8 1.0
N A:CGU29 4.9 0.0 1.0
CA A:ALA30 4.9 0.0 1.0
CA A:CGU26 5.0 0.4 1.0

Magnesium binding site 5 out of 6 in 6bjr

Go back to Magnesium Binding Sites List in 6bjr
Magnesium binding site 5 out of 6 in the Crystal Structure of Prothrombin Mutant S101C/A470C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:0.3
occ:1.00
 CD2 A:CGU26 2.1 0.8 1.0
CD1 A:CGU16 2.1 0.0 1.0
CD2 A:CGU16 2.2 0.0 1.0
CG A:CGU26 2.2 0.7 1.0
OE12 A:CGU16 2.2 0.0 1.0
OE21 A:CGU16 2.4 0.0 1.0
OE22 A:CGU16 2.5 0.0 1.0
OE21 A:CGU26 2.6 0.7 1.0
OE11 A:CGU16 2.6 0.0 1.0
OE22 A:CGU26 2.6 0.7 1.0
CD1 A:CGU26 2.6 0.7 1.0
OE11 A:CGU26 2.7 0.5 1.0
CG A:CGU16 2.7 0.0 1.0
OE12 A:CGU26 3.6 0.5 1.0
CB A:CGU26 3.7 0.5 1.0
CB A:CGU16 3.9 0.3 1.0
O A:CGU26 4.2 0.8 1.0
C A:CGU26 4.5 0.8 1.0
CA A:CGU26 4.5 0.4 1.0
MG A:MG604 4.6 0.0 1.0
CA A:CGU16 4.9 0.5 1.0

Magnesium binding site 6 out of 6 in 6bjr

Go back to Magnesium Binding Sites List in 6bjr
Magnesium binding site 6 out of 6 in the Crystal Structure of Prothrombin Mutant S101C/A470C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:0.4
occ:1.00
 OE11 A:CGU19 2.1 0.1 1.0
OE11 A:CGU14 2.4 0.3 1.0
OE21 A:CGU14 2.6 0.2 1.0
NH2 A:ARG54 2.7 0.3 1.0
OE22 A:CGU19 2.8 0.2 1.0
CD1 A:CGU19 2.9 0.1 1.0
CZ A:ARG54 3.1 0.2 1.0
CD1 A:CGU14 3.2 0.5 1.0
CG A:CGU14 3.2 0.6 1.0
CD2 A:CGU14 3.3 0.2 1.0
OE12 A:CGU19 3.5 0.9 1.0
NE A:ARG54 3.6 1.0 1.0
CD2 A:CGU19 3.8 0.3 1.0
NH1 A:ARG54 3.8 0.9 1.0
CD A:ARG15 3.9 0.8 1.0
CG A:CGU19 3.9 0.4 1.0
O A:CGU14 4.1 0.9 1.0
NE A:ARG15 4.3 0.6 1.0
OE12 A:CGU14 4.4 0.2 1.0
OE22 A:CGU14 4.5 0.3 1.0
CZ A:ARG15 4.7 0.4 1.0
CG A:ARG54 4.7 0.3 1.0
CD A:ARG54 4.7 0.4 1.0
CB A:CGU14 4.7 0.4 1.0
C A:CGU14 4.7 1.0 1.0
NH1 A:ARG15 4.8 0.7 1.0
OE21 A:CGU19 4.9 0.0 1.0

Reference:

M.Chinnaraj, Z.Chen, L.A.Pelc, Z.Grese, D.Bystranowska, E.Di Cera, N.Pozzi. Structure of Prothrombin in the Closed Form Reveals New Details on the Mechanism of Activation. Sci Rep V. 8 2945 2018.
ISSN: ESSN 2045-2322
PubMed: 29440720
DOI: 10.1038/S41598-018-21304-1
Page generated: Mon Sep 30 19:46:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy