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Magnesium in PDB 1p0s: Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R

Enzymatic activity of Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R

All present enzymatic activity of Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R:
3.4.21.6;

Protein crystallography data

The structure of Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R, PDB code: 1p0s was solved by S.X.Wang, E.Hur, C.A.Sousa, L.Brinen, E.J.Slivka, R.J.Fletterick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 66.839, 108.050, 186.305, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.4

Other elements in 1p0s:

The structure of Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R (pdb code 1p0s). 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 Blood Coagulation Factor Xa in Complex with Ecotin M84R, PDB code: 1p0s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1p0s

Go back to Magnesium Binding Sites List in 1p0s
Magnesium binding site 1 out of 4 in the Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R


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 Blood Coagulation Factor Xa in Complex with Ecotin M84R within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg139

b:27.8
occ:1.00
 OE21 L:CGU26 2.3 35.6 1.0
OE22 L:CGU16 2.4 45.7 1.0
OE11 L:CGU26 2.5 38.4 1.0
OE11 L:CGU16 2.8 51.8 1.0
CG L:CGU16 3.1 28.5 1.0
CD1 L:CGU16 3.1 40.3 1.0
CD2 L:CGU16 3.2 36.6 1.0
CD2 L:CGU26 3.4 38.5 1.0
CD1 L:CGU26 3.6 32.6 1.0
CG L:CGU26 4.0 33.5 1.0
OE12 L:CGU16 4.1 58.3 1.0
OE21 L:CGU16 4.4 28.2 1.0
OE22 L:CGU26 4.5 36.0 1.0
CB L:CGU16 4.6 20.3 1.0
OE12 L:CGU26 4.7 32.1 1.0
CB L:CGU26 4.8 31.4 1.0

Magnesium binding site 2 out of 4 in 1p0s

Go back to Magnesium Binding Sites List in 1p0s
Magnesium binding site 2 out of 4 in the Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R


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 Blood Coagulation Factor Xa in Complex with Ecotin M84R within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg140

b:51.5
occ:1.00
 OE21 L:CGU19 2.3 43.4 1.0
OE11 L:CGU14 2.6 61.9 1.0
O L:HOH148 2.7 24.6 1.0
OE12 L:CGU19 3.1 45.4 1.0
O L:HOH147 3.3 24.6 1.0
OE22 L:CGU14 3.5 52.2 1.0
CD2 L:CGU19 3.5 46.0 1.0
CD1 L:CGU14 3.8 60.9 1.0
CD2 L:CGU14 4.1 48.6 1.0
CD1 L:CGU19 4.1 43.4 1.0
OE22 L:CGU19 4.3 41.7 1.0
CG L:CGU14 4.4 51.1 1.0
CG L:CGU19 4.4 38.9 1.0
OE12 L:CGU14 4.8 63.5 1.0
OE21 L:CGU14 4.9 43.0 1.0

Magnesium binding site 3 out of 4 in 1p0s

Go back to Magnesium Binding Sites List in 1p0s
Magnesium binding site 3 out of 4 in the Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R


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 Blood Coagulation Factor Xa in Complex with Ecotin M84R within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg141

b:33.2
occ:1.00
 OE21 L:CGU29 2.2 31.2 1.0
OE12 L:CGU25 2.5 43.6 1.0
OE21 L:CGU25 2.5 55.3 1.0
OE12 L:CGU29 2.7 49.4 1.0
O L:HOH144 3.0 29.9 1.0
CD2 L:CGU29 3.3 38.1 1.0
CD1 L:CGU25 3.5 43.9 1.0
CD2 L:CGU25 3.5 53.6 1.0
CD1 L:CGU29 3.6 49.7 1.0
CG L:CGU29 3.8 35.5 1.0
CG L:CGU25 3.9 45.5 1.0
NH1 L:ARG28 4.4 37.4 1.0
OE22 L:CGU29 4.4 39.0 1.0
OE11 L:CGU25 4.6 43.2 1.0
OE22 L:CGU25 4.7 51.9 1.0
OE11 L:CGU29 4.7 45.9 1.0
O L:HOH142 4.9 32.6 1.0

Magnesium binding site 4 out of 4 in 1p0s

Go back to Magnesium Binding Sites List in 1p0s
Magnesium binding site 4 out of 4 in the Crystal Structure of Blood Coagulation Factor Xa in Complex with Ecotin M84R


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 Blood Coagulation Factor Xa in Complex with Ecotin M84R within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg265

b:48.1
occ:1.00
 O H:ASN72 2.4 44.7 1.0
OE2 H:GLU80 2.4 49.5 1.0
O H:HOH273 2.6 41.2 1.0
O H:GLN75 2.6 65.8 1.0
OD1 H:ASP70 2.9 40.3 1.0
O H:HOH272 3.2 46.5 1.0
C H:GLN75 3.3 64.0 1.0
OD2 H:ASP70 3.4 45.4 1.0
CG H:ASP70 3.4 40.4 1.0
CD H:GLU80 3.5 42.1 1.0
C H:ASN72 3.5 42.1 1.0
O H:HOH289 3.6 24.6 1.0
CA H:GLU76 3.6 54.3 1.0
N H:GLU76 3.8 58.5 1.0
CG H:GLU80 3.8 46.2 1.0
CA H:THR73 4.0 43.3 1.0
C H:THR73 4.1 46.2 1.0
N H:THR73 4.2 39.6 1.0
O H:THR73 4.2 46.8 1.0
N H:GLN75 4.2 61.8 1.0
CA H:GLN75 4.4 63.4 1.0
N H:GLU77 4.5 49.0 1.0
C H:GLU76 4.5 51.2 1.0
N H:ASN72 4.6 39.7 1.0
OE1 H:GLU80 4.6 48.9 1.0
CA H:ASN72 4.6 40.5 1.0
N H:GLU74 4.7 54.0 1.0
CB H:GLU76 4.7 55.8 1.0
CB H:ASP70 4.8 29.7 1.0
CG H:GLU76 4.9 69.5 1.0
CB H:ASN72 4.9 49.3 1.0
C H:GLU74 5.0 57.4 1.0

Reference:

S.X.Wang, E.Hur, C.A.Sousa, L.Brinen, E.J.Slivka, R.J.Fletterick. The Extended Interactions and Gla Domain of Blood Coagulation Factor Xa Biochemistry V. 42 7959 2003.
ISSN: ISSN 0006-2960
PubMed: 12834348
DOI: 10.1021/BI027320A
Page generated: Tue Aug 13 10:46:13 2024

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