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Magnesium in PDB 6c2w: Crystal Structure of Human Prothrombin Mutant S101C/A470C

Enzymatic activity of Crystal Structure of Human Prothrombin Mutant S101C/A470C

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

Protein crystallography data

The structure of Crystal Structure of Human Prothrombin Mutant S101C/A470C, PDB code: 6c2w 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) 30.32 / 4.12
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 85.030, 85.074, 153.801, 105.35, 90.00, 90.05
R / Rfree (%) 27.8 / 33.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Prothrombin Mutant S101C/A470C (pdb code 6c2w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of Human Prothrombin Mutant S101C/A470C, PDB code: 6c2w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 6c2w

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Magnesium binding site 1 out of 12 in the Crystal Structure of Human 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 Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.9
occ:1.00
 O A:CGU29 2.0 0.1 1.0
OE22 A:CGU32 2.6 0.3 1.0
C A:CGU29 3.1 0.3 1.0
CD2 A:CGU32 3.4 0.9 1.0
OE21 A:CGU32 3.5 0.7 1.0
CA A:CGU29 3.8 0.8 1.0
N A:ALA30 4.1 0.4 1.0
CA A:ALA30 4.4 0.8 1.0
N A:CGU29 4.6 0.8 1.0
CG A:CGU32 4.8 0.3 1.0

Magnesium binding site 2 out of 12 in 6c2w

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Magnesium binding site 2 out of 12 in the Crystal Structure of Human 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 Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:84.2
occ:1.00
 OE12 A:CGU29 2.3 0.8 1.0
OE11 A:CGU25 3.1 0.4 1.0
CD1 A:CGU29 3.3 0.3 1.0
O A:CGU25 3.3 0.3 1.0
MG A:MG603 3.5 92.6 1.0
OE11 A:CGU29 3.5 0.4 1.0
CG A:CGU25 3.6 0.7 1.0
CD1 A:CGU25 3.8 0.2 1.0
OE21 A:CGU25 4.0 0.4 1.0
O A:PHE28 4.1 0.8 1.0
CD2 A:CGU25 4.3 0.5 1.0
C A:CGU25 4.4 0.8 1.0
CG A:CGU29 4.7 0.7 1.0
OE22 A:CGU29 4.7 0.4 1.0
CB A:CGU25 4.7 0.9 1.0
CA A:CGU25 5.0 1.0 1.0

Magnesium binding site 3 out of 12 in 6c2w

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Magnesium binding site 3 out of 12 in the Crystal Structure of Human 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 Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:92.6
occ:1.00
 OE22 A:CGU29 2.3 0.4 1.0
OE12 A:CGU29 2.9 0.8 1.0
CD2 A:CGU29 3.4 0.2 1.0
OE11 A:CGU26 3.4 0.2 1.0
MG A:MG602 3.5 84.2 1.0
O A:CGU25 3.5 0.3 1.0
CA A:CGU26 3.6 0.4 1.0
CD1 A:CGU26 3.7 0.5 1.0
CD1 A:CGU29 3.7 0.3 1.0
OE12 A:CGU26 3.8 0.5 1.0
CG A:CGU29 4.1 0.7 1.0
N A:CGU26 4.1 0.2 1.0
C A:CGU25 4.1 0.8 1.0
CB A:CGU26 4.3 0.4 1.0
OE21 A:CGU29 4.4 0.9 1.0
CG A:CGU26 4.5 0.8 1.0
O A:CGU26 4.6 0.2 1.0
C A:CGU26 4.6 0.2 1.0
OE11 A:CGU29 4.7 0.4 1.0
CB A:CGU29 4.7 0.0 1.0

Magnesium binding site 4 out of 12 in 6c2w

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Magnesium binding site 4 out of 12 in the Crystal Structure of Human 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 Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:0.5
occ:1.00
 OE12 A:CGU26 2.3 0.5 1.0
OE12 A:CGU16 2.4 0.7 1.0
OE21 A:CGU29 2.8 0.9 1.0
MG A:MG605 3.1 90.9 1.0
CD1 A:CGU16 3.2 0.5 1.0
CD1 A:CGU26 3.4 0.5 1.0
CD2 A:CGU29 3.4 0.2 1.0
OE22 A:CGU29 3.4 0.4 1.0
OE11 A:CGU16 3.4 0.2 1.0
CG A:CGU26 3.8 0.8 1.0
O A:CGU26 3.9 0.2 1.0
OE21 A:CGU16 4.4 0.8 1.0
OE11 A:CGU26 4.4 0.2 1.0
OE22 A:CGU26 4.5 0.9 1.0
CG A:CGU16 4.5 0.4 1.0
CB A:CGU29 4.6 0.0 1.0
CG A:CGU29 4.6 0.7 1.0
CD2 A:CGU26 4.6 0.6 1.0
C A:CGU26 4.7 0.2 1.0
CD2 A:CGU16 4.9 1.0 1.0
CB A:CGU26 5.0 0.4 1.0

Magnesium binding site 5 out of 12 in 6c2w

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Magnesium binding site 5 out of 12 in the Crystal Structure of Human 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 Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:90.9
occ:1.00
 OE21 A:CGU16 2.2 0.8 1.0
OE12 A:CGU16 2.9 0.7 1.0
OE12 A:CGU26 3.0 0.5 1.0
CD2 A:CGU16 3.1 1.0 1.0
OE22 A:CGU26 3.1 0.9 1.0
MG A:MG604 3.1 0.5 1.0
CD1 A:CGU16 3.3 0.5 1.0
CG A:CGU16 3.5 0.4 1.0
CD1 A:CGU26 3.5 0.5 1.0
CD2 A:CGU26 3.7 0.6 1.0
CB A:CGU16 3.8 0.9 1.0
CG A:CGU26 3.9 0.8 1.0
OE11 A:CGU16 4.1 0.2 1.0
OE11 A:CGU26 4.2 0.2 1.0
OE22 A:CGU16 4.2 0.2 1.0
OE21 A:CGU26 4.6 0.1 1.0
CA A:CGU16 4.9 0.3 1.0

Magnesium binding site 6 out of 12 in 6c2w

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Magnesium binding site 6 out of 12 in the Crystal Structure of Human 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 Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:57.7
occ:1.00
 OE22 A:CGU14 2.6 0.1 1.0
OE12 A:CGU19 2.7 0.5 1.0
CD1 A:CGU19 3.4 0.2 1.0
CD2 A:CGU14 3.5 0.6 1.0
CG A:CGU14 3.5 0.3 1.0
OE12 A:CGU14 3.6 0.7 1.0
NH1 A:ARG15 3.7 0.0 1.0
CD1 A:CGU14 3.8 0.3 1.0
CD2 A:CGU19 3.9 0.4 1.0
OE21 A:CGU19 4.0 96.3 1.0
CG A:CGU19 4.0 0.9 1.0
OE11 A:CGU19 4.1 0.3 1.0
NH1 A:ARG54 4.1 0.1 1.0
NH2 A:ARG54 4.4 0.7 1.0
OE22 A:CGU19 4.4 0.1 1.0
CZ A:ARG54 4.5 0.4 1.0
OE21 A:CGU14 4.7 0.7 1.0
OE11 A:CGU14 4.8 0.1 1.0
CZ A:ARG15 4.8 0.6 1.0
O A:CGU14 4.8 0.6 1.0
CB A:CGU14 5.0 0.3 1.0

Magnesium binding site 7 out of 12 in 6c2w

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Magnesium binding site 7 out of 12 in the Crystal Structure of Human Prothrombin Mutant S101C/A470C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.5
occ:1.00
 O B:CGU29 2.6 1.0 1.0
OE12 B:CGU29 2.6 0.2 1.0
CD1 B:CGU29 3.3 0.5 1.0
C B:CGU29 3.4 0.1 1.0
CG B:CGU29 3.5 0.6 1.0
CA B:CGU29 3.6 0.3 1.0
CB B:CGU29 4.1 0.5 1.0
OE11 B:CGU29 4.4 0.5 1.0
OE21 B:CGU32 4.5 0.7 1.0
N B:ALA30 4.5 0.4 1.0
CD2 B:CGU29 4.7 0.5 1.0
N B:CGU29 4.9 0.2 1.0

Magnesium binding site 8 out of 12 in 6c2w

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Magnesium binding site 8 out of 12 in the Crystal Structure of Human Prothrombin Mutant S101C/A470C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:92.5
occ:1.00
 OE11 B:CGU29 2.5 0.5 1.0
OE12 B:CGU25 3.6 0.4 1.0
CD1 B:CGU29 3.7 0.5 1.0
OE12 B:CGU29 4.1 0.2 1.0
O B:CGU25 4.1 0.2 1.0
CD1 B:CGU25 4.3 0.7 1.0
O B:PHE28 4.4 0.4 1.0
CG B:CGU25 4.5 0.1 1.0
OE22 B:CGU29 4.9 0.9 1.0
CG B:CGU29 4.9 0.6 1.0

Magnesium binding site 9 out of 12 in 6c2w

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Magnesium binding site 9 out of 12 in the Crystal Structure of Human Prothrombin Mutant S101C/A470C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:84.6
occ:1.00
 OE22 B:CGU29 2.1 0.9 1.0
OE12 B:CGU26 2.7 0.7 1.0
OE11 B:CGU26 2.9 0.1 1.0
CD1 B:CGU26 3.0 0.8 1.0
CD2 B:CGU29 3.1 0.5 1.0
OE21 B:CGU29 3.7 0.9 1.0
CA B:CGU26 3.8 0.6 1.0
OE11 B:CGU29 3.9 0.5 1.0
CG B:CGU29 4.1 0.6 1.0
CG B:CGU26 4.1 0.2 1.0
O B:CGU26 4.1 1.0 1.0
O B:CGU25 4.2 0.2 1.0
CB B:CGU26 4.3 1.0 1.0
CB B:CGU29 4.4 0.5 1.0
CD1 B:CGU29 4.4 0.5 1.0
C B:CGU26 4.5 0.8 1.0
MG B:MG604 4.6 83.5 1.0
N B:CGU26 4.7 0.8 1.0
C B:CGU25 4.8 0.7 1.0

Magnesium binding site 10 out of 12 in 6c2w

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Magnesium binding site 10 out of 12 in the Crystal Structure of Human Prothrombin Mutant S101C/A470C


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Human Prothrombin Mutant S101C/A470C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg604

b:83.5
occ:1.00
 OE12 B:CGU16 2.4 0.4 1.0
OE21 B:CGU29 2.4 0.9 1.0
OE11 B:CGU26 3.1 0.1 1.0
MG B:MG605 3.1 79.6 1.0
CD1 B:CGU16 3.4 0.3 1.0
CD2 B:CGU29 3.5 0.5 1.0
OE11 B:CGU16 3.7 0.1 1.0
OE22 B:CGU29 4.0 0.9 1.0
CD1 B:CGU26 4.3 0.8 1.0
O B:CGU26 4.5 1.0 1.0
MG B:MG603 4.6 84.6 1.0
CG B:CGU29 4.6 0.6 1.0
CB B:ALA30 4.7 0.4 1.0
CB B:CGU29 4.7 0.5 1.0
OE22 B:CGU16 4.7 0.6 1.0
CG B:CGU16 4.7 0.3 1.0
CG B:CGU26 4.9 0.2 1.0
ND2 B:ASN12 5.0 0.6 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 20:07:24 2024

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