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Magnesium in PDB 5edm: Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )

Enzymatic activity of Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )

All present enzymatic activity of Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I ):
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I ), PDB code: 5edm 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) 92.07 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 109.884, 168.690, 144.315, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I ) (pdb code 5edm). 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 Deletion Mutant Residues 154-167 ( Form I ), PDB code: 5edm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5edm

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Magnesium binding site 1 out of 6 in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )


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 154-167 ( Form I ) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:54.5
occ:1.00
 O A:HOH804 2.1 57.6 1.0
O A:HOH775 2.1 52.3 1.0
O A:HOH712 2.2 70.0 1.0
OE12 A:CGU32 2.2 72.8 1.0
O A:CGU29 2.2 69.3 1.0
OE22 A:CGU32 2.2 74.0 1.0
CD1 A:CGU32 3.1 74.4 1.0
CD2 A:CGU32 3.2 74.4 1.0
C A:CGU29 3.3 61.9 1.0
CG A:CGU32 3.5 73.3 1.0
CA A:CGU29 4.0 63.5 1.0
O A:HOH790 4.2 58.9 1.0
OE11 A:CGU29 4.3 75.4 1.0
OE11 A:CGU32 4.3 75.2 1.0
OE21 A:CGU32 4.3 75.9 1.0
N A:ALA30 4.4 58.8 1.0
CB A:CGU29 4.4 65.1 1.0
CA A:ALA30 4.7 57.3 1.0
CG A:CGU29 4.7 72.0 1.0
O A:HOH753 4.8 61.3 1.0
O A:HOH1006 4.8 55.2 1.0
CD1 A:CGU29 5.0 74.0 1.0

Magnesium binding site 2 out of 6 in 5edm

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Magnesium binding site 2 out of 6 in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )


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 154-167 ( Form I ) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:59.5
occ:1.00
 O A:HOH719 2.1 63.0 1.0
OE21 A:CGU29 2.2 74.4 1.0
OE12 A:CGU29 2.2 78.8 1.0
OE21 A:CGU25 2.2 84.4 1.0
OE12 A:CGU25 2.2 81.4 1.0
CD1 A:CGU25 3.1 74.8 1.0
CD2 A:CGU29 3.1 73.0 1.0
CD2 A:CGU25 3.1 77.9 1.0
CD1 A:CGU29 3.2 74.0 1.0
CG A:CGU25 3.3 74.1 1.0
CG A:CGU29 3.7 72.0 1.0
O A:HOH851 3.9 83.3 1.0
OE22 A:CGU29 4.1 79.4 1.0
OE11 A:CGU25 4.2 72.1 1.0
OE22 A:CGU25 4.3 80.4 1.0
OE11 A:CGU29 4.3 75.4 1.0
O A:HOH798 4.6 66.4 1.0
O A:HOH958 4.9 74.2 1.0
CB A:CGU25 4.9 67.4 1.0
CB A:CGU29 4.9 65.1 1.0

Magnesium binding site 3 out of 6 in 5edm

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Magnesium binding site 3 out of 6 in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )


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 154-167 ( Form I ) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:76.0
occ:1.00
 O A:HOH1104 2.1 87.2 1.0
O A:HOH958 2.1 74.2 1.0
O A:HOH746 2.2 66.0 1.0
OE22 A:CGU29 2.2 79.4 1.0
OE11 A:CGU26 2.2 68.2 1.0
CD1 A:CGU26 2.9 56.0 1.0
OE12 A:CGU26 2.9 56.5 1.0
CD2 A:CGU29 3.3 73.0 1.0
O A:HOH798 3.5 66.4 1.0
OE21 A:CGU29 3.8 74.4 1.0
O A:HOH744 3.9 51.9 1.0
CG A:CGU26 4.3 54.4 1.0
O A:HOH764 4.3 60.2 1.0
CG A:CGU29 4.5 72.0 1.0
O A:HOH710 4.7 55.2 1.0
CA A:CGU26 4.7 53.3 1.0
CB A:CGU29 4.8 65.1 1.0
MG A:MG604 4.8 45.0 1.0
CB A:CGU26 4.9 52.6 1.0

Magnesium binding site 4 out of 6 in 5edm

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Magnesium binding site 4 out of 6 in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )


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 154-167 ( Form I ) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:45.0
occ:1.00
 OE22 A:CGU16 2.1 55.4 1.0
OE12 A:CGU26 2.2 56.5 1.0
O A:HOH710 2.2 55.2 1.0
O A:HOH744 2.2 51.9 1.0
OE21 A:CGU26 2.2 54.5 1.0
OE12 A:CGU16 2.2 58.6 1.0
CD1 A:CGU16 2.8 56.9 1.0
CD2 A:CGU16 2.9 55.9 1.0
CD2 A:CGU26 3.1 53.1 1.0
CD1 A:CGU26 3.1 56.0 1.0
CG A:CGU16 3.2 56.0 1.0
CG A:CGU26 3.3 54.4 1.0
CB A:CGU16 3.7 53.3 1.0
OE11 A:CGU16 3.7 62.1 1.0
OE21 A:CGU16 4.0 56.8 1.0
O A:HOH764 4.0 60.2 1.0
OE11 A:CGU26 4.3 68.2 1.0
OE22 A:CGU26 4.3 51.7 1.0
O A:HOH746 4.4 66.0 1.0
CA A:CGU16 4.8 52.6 1.0
MG A:MG603 4.8 76.0 1.0
CB A:CGU26 4.8 52.6 1.0

Magnesium binding site 5 out of 6 in 5edm

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Magnesium binding site 5 out of 6 in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )


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 Deletion Mutant Residues 154-167 ( Form I ) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:61.5
occ:1.00
 O A:HOH1086 2.1 58.1 1.0
O A:HOH701 2.2 59.8 1.0
O A:HOH914 2.2 71.5 1.0
OE12 A:CGU20 2.2 66.3 1.0
O A:HOH754 2.2 63.9 1.0
OE22 A:CGU20 2.2 72.3 1.0
CD1 A:CGU20 3.0 59.9 1.0
CD2 A:CGU20 3.0 63.4 1.0
CG A:CGU20 3.1 59.7 1.0
OE11 A:CGU20 4.2 57.5 1.0
OE21 A:CGU20 4.3 63.5 1.0
O A:CGU19 4.3 57.3 1.0
CB A:CGU20 4.6 54.3 1.0
CB A:CGU19 4.6 57.1 1.0
O A:HOH897 4.7 61.4 1.0
OE12 A:CGU19 4.7 60.9 1.0
O A:ARG15 4.7 62.1 1.0
C A:CGU19 4.8 55.0 1.0

Magnesium binding site 6 out of 6 in 5edm

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Magnesium binding site 6 out of 6 in the Crystal Structure of Prothrombin Deletion Mutant Residues 154-167 ( Form I )


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 Deletion Mutant Residues 154-167 ( Form I ) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg606

b:50.1
occ:1.00
 O A:HOH982 2.1 61.6 1.0
O A:HOH770 2.2 64.4 1.0
OE12 A:CGU14 2.2 66.3 1.0
OE21 A:CGU19 2.2 69.0 1.0
OE11 A:CGU19 2.2 64.3 1.0
OE22 A:CGU14 2.2 71.6 1.0
CD1 A:CGU19 3.1 61.2 1.0
CD2 A:CGU14 3.1 66.6 1.0
CD1 A:CGU14 3.1 61.8 1.0
CD2 A:CGU19 3.1 62.6 1.0
CG A:CGU14 3.4 62.2 1.0
CG A:CGU19 3.4 59.7 1.0
NE A:ARG54 3.7 63.9 1.0
NH1 A:ARG15 4.1 90.4 1.0
CD A:ARG54 4.2 64.8 1.0
OE12 A:CGU19 4.2 60.9 1.0
OE21 A:CGU14 4.2 68.4 1.0
OE22 A:CGU19 4.3 65.5 1.0
OE11 A:CGU14 4.3 58.5 1.0
CZ A:ARG54 4.4 64.0 1.0
NH2 A:ARG54 4.6 61.6 1.0
CB A:CGU14 4.9 58.1 1.0
CB A:CGU19 4.9 57.1 1.0
CG A:ARG54 5.0 63.0 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 03:38:36 2024

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