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Calcium 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:

Magnesium (Mg) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 7 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1j34

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Calcium binding site 1 out of 7 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 Calcium with other atoms in the Ca 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
A:Ca511

b:17.8
occ:1.00
 OE2 A:GLU128 2.4 20.2 1.0
O A:SER41 2.4 18.1 1.0
OE2 A:GLU43 2.4 23.3 1.0
OE2 A:GLU47 2.4 16.6 1.0
O A:HOH809 2.4 21.6 1.0
OG A:SER41 2.5 18.0 1.0
O A:HOH837 2.5 26.6 1.0
OE1 A:GLU128 2.6 16.8 1.0
CD A:GLU128 2.8 16.7 1.0
CD A:GLU47 3.2 15.7 1.0
OE1 A:GLU47 3.3 16.2 1.0
C A:SER41 3.4 15.9 1.0
CD A:GLU43 3.5 22.8 1.0
CB A:SER41 3.6 16.6 1.0
CA A:SER41 3.9 15.8 1.0
N A:SER41 4.1 15.1 1.0
CG A:GLU43 4.1 21.1 1.0
OH A:TYR14 4.2 17.0 1.0
CG A:GLU128 4.3 14.6 1.0
O A:HOH720 4.5 29.6 1.0
OE1 A:GLU43 4.5 24.3 1.0
O A:HOH789 4.6 40.8 1.0
N A:ILE42 4.6 17.4 1.0
CG A:GLU47 4.7 15.3 1.0
CD2 A:HIS12 4.7 31.2 1.0
O A:HOH947 4.7 19.3 1.0
N A:GLU43 4.8 16.5 1.0
CB A:GLU43 4.8 18.9 1.0
O A:HOH880 4.9 31.7 1.0
CE2 A:TYR14 4.9 15.6 1.0
O A:HOH981 4.9 21.7 1.0
CZ A:TYR14 5.0 15.2 1.0

Calcium binding site 2 out of 7 in 1j34

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Calcium binding site 2 out of 7 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 Calcium with other atoms in the Ca 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
B:Ca512

b:20.7
occ:1.00
 OE1 B:GLN243 2.3 31.4 1.0
OE2 B:GLU247 2.4 22.1 1.0
O B:SER241 2.4 20.2 1.0
O B:HOH818 2.4 23.4 1.0
OE2 B:GLU320 2.4 17.5 1.0
O B:HOH820 2.5 27.4 1.0
OG B:SER241 2.6 19.9 1.0
OE1 B:GLU320 2.7 19.3 1.0
CD B:GLU320 2.9 18.6 1.0
CD B:GLU247 3.2 22.7 1.0
CD B:GLN243 3.3 31.8 1.0
C B:SER241 3.3 21.6 1.0
OE1 B:GLU247 3.4 22.3 1.0
CB B:SER241 3.7 19.7 1.0
NE2 B:GLN243 3.8 31.6 1.0
CA B:SER241 3.9 19.1 1.0
N B:SER241 4.0 19.0 1.0
ND1 B:HIS212 4.2 24.9 1.0
OH B:TYR214 4.2 18.7 1.0
N B:PHE242 4.4 22.5 1.0
CG B:GLU320 4.4 17.2 1.0
CG B:GLN243 4.5 30.9 1.0
CE1 B:HIS212 4.5 25.7 1.0
N B:GLN243 4.6 25.4 1.0
CG B:GLU247 4.6 19.6 1.0
OD2 A:ASP85 4.6 24.0 1.0
O B:HOH951 4.7 21.7 1.0
CA B:PHE242 4.7 24.2 1.0
O B:HOH903 4.8 29.5 1.0
CE2 B:TYR214 4.8 18.8 1.0
O A:HOH735 4.8 32.5 1.0
CZ B:TYR214 5.0 19.9 1.0

Calcium binding site 3 out of 7 in 1j34

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Calcium binding site 3 out of 7 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 Calcium with other atoms in the Ca 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:Ca502

b:14.9
occ:1.00
 OE22 C:CGU408 2.3 16.7 1.0
O C:HOH807 2.3 19.5 1.0
OE22 C:CGU430 2.4 14.5 1.0
OE11 C:CGU408 2.4 14.9 1.0
OE12 C:CGU427 2.4 15.6 1.0
O B:HOH804 2.4 17.1 1.0
OE21 C:CGU430 2.6 14.0 1.0
CD2 C:CGU430 2.8 14.4 1.0
CD1 C:CGU408 3.2 18.1 1.0
CD2 C:CGU408 3.4 17.2 1.0
CD1 C:CGU427 3.4 16.7 1.0
OE11 C:CGU427 3.7 14.8 1.0
CG C:CGU408 3.8 17.3 1.0
CA C:CA503 3.9 15.5 1.0
O B:HOH711 4.1 27.3 1.0
OE12 C:CGU408 4.2 17.3 1.0
O C:HOH1006 4.2 12.3 1.0
CG C:CGU430 4.3 14.5 1.0
O C:HOH936 4.3 18.8 1.0
O C:HOH828 4.3 23.6 1.0
ND2 C:ASN402 4.3 17.5 1.0
MG C:MG501 4.3 11.6 1.0
OE12 C:CGU426 4.4 13.4 1.0
CB C:CGU408 4.4 17.2 1.0
OE21 C:CGU408 4.5 16.9 1.0
O C:HOH970 4.5 25.6 1.0
O C:HOH805 4.5 16.8 1.0
OD1 C:ASN402 4.6 16.6 1.0
CD1 C:CGU426 4.7 12.8 1.0
CG C:CGU427 4.7 15.0 1.0
CD1 C:CGU430 4.8 16.3 1.0
CG C:ASN402 4.8 18.6 1.0
CG C:CGU426 4.9 12.2 1.0
OE11 C:CGU430 4.9 14.1 1.0
OH B:TYR298 5.0 14.5 1.0

Calcium binding site 4 out of 7 in 1j34

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Calcium binding site 4 out of 7 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 Calcium with other atoms in the Ca binding site number 4 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:Ca503

b:15.5
occ:1.00
 O C:HOH803 2.3 14.1 1.0
OE11 C:CGU408 2.4 14.9 1.0
O C:HOH805 2.4 16.8 1.0
OE11 C:CGU427 2.5 14.8 1.0
O C:HOH810 2.5 16.8 1.0
OE21 C:CGU430 2.5 14.0 1.0
OE22 C:CGU417 2.7 17.7 1.0
OE12 C:CGU408 2.8 17.3 1.0
CD1 C:CGU408 2.9 18.1 1.0
CD1 C:CGU427 3.5 16.7 1.0
CD2 C:CGU417 3.6 18.3 1.0
CA C:CA504 3.7 15.5 1.0
OE21 C:CGU417 3.7 17.9 1.0
CD2 C:CGU430 3.7 14.4 1.0
CA C:CA502 3.9 14.9 1.0
OE12 C:CGU427 3.9 15.6 1.0
CB C:CGU430 4.1 14.3 1.0
O C:HOH936 4.3 18.8 1.0
CG C:CGU408 4.4 17.3 1.0
CA C:GLY412 4.5 17.9 1.0
CG C:CGU430 4.5 14.5 1.0
O C:CGU427 4.6 12.2 1.0
OE22 C:CGU430 4.6 14.5 1.0
O C:HOH953 4.6 20.0 1.0
O B:HOH682 4.7 26.8 1.0
CA C:CGU427 4.7 13.1 1.0
CG C:CGU427 4.7 15.0 1.0
CB C:CGU427 4.8 15.5 1.0
O B:HOH804 4.9 17.1 1.0
OD1 C:ASN402 4.9 16.6 1.0
CB C:CGU408 4.9 17.2 1.0
CA C:CGU408 5.0 17.5 1.0
OE22 C:CGU408 5.0 16.7 1.0

Calcium binding site 5 out of 7 in 1j34

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Calcium binding site 5 out of 7 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 Calcium with other atoms in the Ca binding site number 5 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:Ca504

b:15.5
occ:1.00
 OE22 C:CGU427 2.3 18.4 1.0
OE12 C:CGU408 2.3 17.3 1.0
OD1 C:ASN402 2.3 16.6 1.0
OE11 C:CGU417 2.3 16.0 1.0
OE11 C:CGU427 2.4 14.8 1.0
OE22 C:CGU417 2.5 17.7 1.0
OE21 C:CGU407 2.5 20.1 1.0
CD1 C:CGU417 3.2 17.9 1.0
CD1 C:CGU427 3.2 16.7 1.0
O C:TYR401 3.3 17.9 1.0
CD1 C:CGU408 3.4 18.1 1.0
CD2 C:CGU427 3.4 14.9 1.0
CD2 C:CGU417 3.5 18.3 1.0
CG C:ASN402 3.5 18.6 1.0
CD2 C:CGU407 3.6 19.6 1.0
CA C:CA503 3.7 15.5 1.0
CG C:CGU417 3.8 17.1 1.0
CG C:CGU427 3.8 15.0 1.0
C C:TYR401 3.8 19.2 1.0
CA C:CA505 3.9 19.7 1.0
OE11 C:CGU408 4.0 14.9 1.0
OE12 C:CGU427 4.0 15.6 1.0
O C:HOH953 4.0 20.0 1.0
OE12 C:CGU417 4.1 17.9 1.0
CA C:ASN402 4.3 21.0 1.0
N C:ASN402 4.3 20.7 1.0
ND2 C:ASN402 4.3 17.5 1.0
OE22 C:CGU407 4.3 18.9 1.0
N C:TYR401 4.4 17.3 1.0
CG C:CGU407 4.4 21.0 1.0
CG C:CGU408 4.4 17.3 1.0
CB C:CGU417 4.4 16.9 1.0
O C:HOH810 4.4 16.8 1.0
CB C:ASN402 4.5 19.5 1.0
OE21 C:CGU427 4.5 16.6 1.0
CB C:CGU427 4.6 15.5 1.0
OE21 C:CGU417 4.6 17.9 1.0
CA C:TYR401 4.7 19.6 1.0
O C:HOH803 4.9 14.1 1.0

Calcium binding site 6 out of 7 in 1j34

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Calcium binding site 6 out of 7 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 Calcium with other atoms in the Ca binding site number 6 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:Ca505

b:19.7
occ:1.00
 O C:TYR401 2.3 17.9 1.0
O C:HOH816 2.4 21.4 1.0
O C:HOH808 2.4 18.5 1.0
OE11 C:CGU417 2.5 16.0 1.0
OE21 C:CGU407 2.5 20.1 1.0
OE22 C:CGU421 2.5 23.1 1.0
OE22 C:CGU407 2.5 18.9 1.0
OE12 C:CGU417 2.6 17.9 1.0
CD2 C:CGU407 2.8 19.6 1.0
CD1 C:CGU417 2.9 17.9 1.0
OE21 C:CGU421 2.9 23.4 1.0
CD2 C:CGU421 3.1 24.4 1.0
C C:TYR401 3.5 19.2 1.0
CA C:CA504 3.9 15.5 1.0
N C:TYR401 4.0 17.3 1.0
CA C:TYR401 4.3 19.6 1.0
CG C:CGU407 4.3 21.0 1.0
CG C:CGU417 4.4 17.1 1.0
O C:HOH813 4.5 24.6 1.0
O C:HOH847 4.5 28.5 1.0
N C:ASN402 4.5 20.7 1.0
CG C:CGU421 4.5 23.7 1.0
O C:HOH603 4.6 27.6 1.0
CB C:TYR401 4.6 20.5 1.0
O C:HOH762 4.6 22.7 1.0
O C:HOH953 4.6 20.0 1.0
CA C:ASN402 4.7 21.0 1.0
OG C:SER403 4.8 25.5 1.0
CB C:CGU407 4.8 21.8 1.0
N C:SER403 4.8 23.7 1.0
OE22 C:CGU427 4.8 18.4 1.0
CA C:CGU417 5.0 16.9 1.0
CB C:CGU417 5.0 16.9 1.0
CA C:CA506 5.0 28.7 1.0

Calcium binding site 7 out of 7 in 1j34

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Calcium binding site 7 out of 7 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 Calcium with other atoms in the Ca binding site number 7 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:Ca506

b:28.7
occ:1.00
 O C:HOH817 2.2 20.7 1.0
O C:HOH847 2.3 28.5 1.0
O C:HOH646 2.3 42.9 1.0
OE12 C:CGU421 2.4 25.9 1.0
OE21 C:CGU421 2.4 23.4 1.0
O C:HOH813 2.4 24.6 1.0
O C:HOH1011 3.1 53.5 1.0
CD1 C:CGU421 3.2 25.1 1.0
CD2 C:CGU421 3.2 24.4 1.0
CG C:CGU421 3.3 23.7 1.0
O C:HOH816 4.2 21.4 1.0
OE11 C:CGU421 4.4 25.8 1.0
OE22 C:CGU421 4.4 23.1 1.0
O C:ARG416 4.5 18.3 1.0
O C:HOH808 4.6 18.5 1.0
CG C:ARG416 4.7 19.2 1.0
CB C:CGU421 4.9 21.9 1.0
OE22 C:CGU420 5.0 22.3 1.0
CA C:CA505 5.0 19.7 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: Mon Jul 7 16:00:54 2025

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