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Magnesium in PDB 1j34: Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein

Enzymatic activity of Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein

All present enzymatic activity of Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein:
3.4.21.22;

Protein crystallography data

The structure of Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein, PDB code: 1j34 was solved by Y.Shikamoto, T.Morita, Z.Fujimoto, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.63 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.552, 37.204, 62.626, 90.00, 103.56, 90.00
R / Rfree (%) 18.3 / 21.2

Other elements in 1j34:

The structure of Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein (pdb code 1j34). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein, PDB code: 1j34:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1j34

Go back to Magnesium Binding Sites List in 1j34
Magnesium binding site 1 out of 3 in the Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein


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 Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:11.6
occ:1.00
 O C:HOH1006 2.0 12.3 1.0
OE2 A:GLU98 2.1 15.4 1.0
OE12 C:CGU426 2.1 13.4 1.0
OE11 C:CGU430 2.1 14.1 1.0
OE21 C:CGU426 2.1 12.8 1.0
OE22 C:CGU430 2.2 14.5 1.0
CD2 C:CGU426 2.9 12.7 1.0
CD1 C:CGU430 3.0 16.3 1.0
CD1 C:CGU426 3.0 12.8 1.0
CD A:GLU98 3.1 15.2 1.0
CD2 C:CGU430 3.1 14.4 1.0
CG C:CGU430 3.2 14.5 1.0
CG C:CGU426 3.2 12.2 1.0
OE1 A:GLU98 3.4 14.0 1.0
O C:HOH807 3.8 19.5 1.0
NH2 C:ARG429 3.8 13.9 1.0
OH B:TYR298 4.0 14.5 1.0
OE22 C:CGU426 4.0 14.4 1.0
OE12 C:CGU430 4.2 15.7 1.0
OE11 C:CGU426 4.2 15.3 1.0
O B:HOH804 4.3 17.1 1.0
OE21 C:CGU430 4.3 14.0 1.0
CA C:CA502 4.3 14.9 1.0
CG A:GLU98 4.4 14.6 1.0
NZ A:LYS100 4.5 15.2 1.0
CB C:CGU430 4.7 14.3 1.0
CB C:CGU426 4.7 12.8 1.0
O C:CGU426 4.7 14.2 1.0
NH1 B:ARG307 4.8 13.8 1.0
CZ C:ARG429 4.9 14.8 1.0
O B:HOH928 4.9 14.6 1.0
O B:SER308 4.9 13.8 1.0
CB B:ARG307 4.9 14.3 1.0

Magnesium binding site 2 out of 3 in 1j34

Go back to Magnesium Binding Sites List in 1j34
Magnesium binding site 2 out of 3 in the Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein


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 Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg507

b:23.5
occ:1.00
 OE12 C:CGU415 2.1 22.5 1.0
OE21 C:CGU415 2.1 21.6 1.0
O C:HOH821 2.1 22.6 1.0
O C:HOH826 2.1 28.4 1.0
OE21 C:CGU420 2.1 21.9 1.0
OE12 C:CGU420 2.2 21.9 1.0
CD2 C:CGU415 2.9 21.8 1.0
CD1 C:CGU415 2.9 20.2 1.0
CD2 C:CGU420 3.0 21.5 1.0
CD1 C:CGU420 3.0 22.7 1.0
CG C:CGU415 3.1 20.6 1.0
CG C:CGU420 3.2 21.4 1.0
OE22 C:CGU415 4.0 21.6 1.0
O C:HOH699 4.1 25.4 1.0
OE11 C:CGU415 4.1 20.5 1.0
OE22 C:CGU420 4.2 22.3 1.0
O C:HOH731 4.2 41.7 1.0
OE11 C:CGU420 4.2 22.1 1.0
O C:HOH925 4.3 45.3 1.0
O C:HOH748 4.4 41.9 1.0
O C:HOH698 4.4 21.2 1.0
O C:HOH614 4.5 37.4 1.0
CB C:CGU415 4.6 20.3 1.0
CB C:CGU420 4.7 21.4 1.0
O C:HOH616 4.7 47.3 1.0

Magnesium binding site 3 out of 3 in 1j34

Go back to Magnesium Binding Sites List in 1j34
Magnesium binding site 3 out of 3 in the Crystal Structure of Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein


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 Mg(II)-and Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg508

b:15.3
occ:1.00
 OE11 C:CGU440 2.1 16.1 1.0
OE21 C:CGU440 2.1 16.9 1.0
OE21 C:CGU436 2.1 15.0 1.0
O C:HOH802 2.1 15.1 1.0
O C:HOH806 2.2 23.5 1.0
OE11 C:CGU436 2.2 16.4 1.0
CD2 C:CGU436 2.9 14.0 1.0
CD2 C:CGU440 3.0 15.1 1.0
CD1 C:CGU440 3.0 17.2 1.0
CD1 C:CGU436 3.0 17.8 1.0
CG C:CGU436 3.1 13.8 1.0
CG C:CGU440 3.2 15.5 1.0
O C:HOH669 3.9 27.5 1.0
OE22 C:CGU436 4.1 13.7 1.0
O C:HOH738 4.1 38.1 1.0
O C:HOH605 4.1 34.8 1.0
OE22 C:CGU440 4.1 16.4 1.0
O C:HOH961 4.1 19.1 1.0
O C:HOH683 4.2 22.8 1.0
OE12 C:CGU440 4.2 17.3 1.0
OE12 C:CGU436 4.2 17.5 1.0
CB C:CGU436 4.6 14.7 1.0
O C:CGU436 4.6 13.8 1.0
CB C:CGU440 4.7 15.1 1.0

Reference:

Y.Shikamoto, T.Morita, Z.Fujimoto, H.Mizuno. Crystal Structure of MG2+- and CA2+-Bound Gla Domain of Factor IX Complexed with Binding Protein J.Biol.Chem. V. 278 24090 2003.
ISSN: ISSN 0021-9258
PubMed: 12695512
DOI: 10.1074/JBC.M300650200
Page generated: Sat Aug 9 22:49:39 2025

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