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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

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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

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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

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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

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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

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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

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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: Wed Aug 13 02:38:55 2025

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