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Calcium in PDB 1j35: Crystal Structure of Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein

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

All present enzymatic activity of Crystal Structure of 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 Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein, PDB code: 1j35 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) 19.54 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.959, 39.074, 63.949, 90.00, 99.56, 90.00
R / Rfree (%) 22.7 / 27

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein (pdb code 1j35). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein, PDB code: 1j35:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1j35

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Calcium binding site 1 out of 10 in the Crystal Structure of 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 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:25.3
occ:1.00
 O A:HOH603 2.3 18.8 1.0
OE1 A:GLU43 2.4 27.6 1.0
OE2 A:GLU47 2.4 19.5 1.0
O A:SER41 2.5 21.3 1.0
OE1 A:GLU128 2.5 27.6 1.0
O A:HOH823 2.6 39.9 1.0
OG A:SER41 2.6 22.8 1.0
OE2 A:GLU128 2.6 24.7 1.0
CD A:GLU128 2.9 23.9 1.0
CD A:GLU47 3.2 19.1 1.0
OE1 A:GLU47 3.3 17.1 1.0
C A:SER41 3.5 21.1 1.0
CD A:GLU43 3.6 25.5 1.0
CB A:SER41 3.7 20.7 1.0
CA A:SER41 4.0 21.9 1.0
ND1 A:HIS12 4.1 34.0 1.0
N A:SER41 4.1 22.7 1.0
OH A:TYR14 4.3 20.5 1.0
CG A:GLU43 4.4 25.9 1.0
CG A:GLU128 4.4 23.1 1.0
O A:HOH683 4.5 31.2 1.0
CE1 A:HIS12 4.5 35.7 1.0
OE2 A:GLU43 4.5 26.3 1.0
O A:HOH746 4.6 40.5 1.0
N A:ILE42 4.7 21.9 1.0
CG A:GLU47 4.7 17.6 1.0
O A:HOH651 4.7 30.9 1.0
O A:HOH604 4.8 21.5 1.0
N A:GLU43 4.8 21.3 1.0
CB A:GLU43 4.8 22.0 1.0
CE2 A:TYR14 4.9 21.4 1.0
ND2 B:ASN281 4.9 32.9 1.0

Calcium binding site 2 out of 10 in 1j35

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Calcium binding site 2 out of 10 in the Crystal Structure of 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 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:32.7
occ:1.00
 OE1 B:GLU247 2.2 24.0 1.0
O B:HOH829 2.3 28.0 1.0
OE1 B:GLU320 2.4 28.6 1.0
OE1 B:GLN243 2.4 28.8 1.0
O B:SER241 2.4 29.4 1.0
O B:HOH822 2.5 34.0 1.0
OG B:SER241 2.5 29.0 1.0
OE2 B:GLU320 2.8 29.9 1.0
CD B:GLU320 2.9 29.3 1.0
CD B:GLU247 3.0 28.1 1.0
OE2 B:GLU247 3.1 25.7 1.0
C B:SER241 3.4 29.9 1.0
CD B:GLN243 3.5 29.2 1.0
CB B:SER241 3.6 30.9 1.0
CA B:SER241 3.9 28.9 1.0
N B:SER241 4.0 28.4 1.0
NE2 B:GLN243 4.0 29.7 1.0
OH B:TYR214 4.3 29.5 1.0
ND1 B:HIS212 4.4 34.9 1.0
CG B:GLU247 4.4 27.9 1.0
CG B:GLU320 4.5 26.7 1.0
N B:PHE242 4.5 28.9 1.0
N B:GLN243 4.6 29.9 1.0
CE1 B:HIS212 4.6 37.6 1.0
O B:HOH787 4.6 28.5 1.0
CG B:GLN243 4.7 30.1 1.0
CE1 B:TYR214 4.8 29.3 1.0
CA B:PHE242 4.9 28.9 1.0
OD1 A:ASP85 4.9 40.7 1.0
CB B:GLN243 5.0 29.3 1.0

Calcium binding site 3 out of 10 in 1j35

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Calcium binding site 3 out of 10 in the Crystal Structure of 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 Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:21.0
occ:1.00
 OE2 A:GLU98 2.2 24.1 1.0
OE21 C:CGU426 2.2 20.5 1.0
OE12 C:CGU426 2.4 22.4 1.0
OE12 C:CGU430 2.4 22.8 1.0
OE22 C:CGU430 2.5 22.5 1.0
O B:HOH617 2.5 26.8 1.0
CD2 C:CGU426 3.0 18.7 1.0
CD A:GLU98 3.2 23.0 1.0
CD1 C:CGU430 3.2 23.1 1.0
CD1 C:CGU426 3.2 20.6 1.0
CD2 C:CGU430 3.3 22.8 1.0
CG C:CGU430 3.3 22.8 1.0
CG C:CGU426 3.3 19.9 1.0
OE1 A:GLU98 3.5 22.6 1.0
OH B:TYR298 3.9 21.3 1.0
NH2 C:ARG429 4.0 22.9 1.0
OE22 C:CGU426 4.1 23.5 1.0
O C:HOH655 4.2 32.6 1.0
OE11 C:CGU430 4.3 24.1 1.0
O B:HOH643 4.4 34.2 1.0
OE11 C:CGU426 4.4 19.5 1.0
OE21 C:CGU430 4.5 22.5 1.0
CG A:GLU98 4.5 20.7 1.0
CA C:CA502 4.5 26.9 1.0
NZ A:LYS100 4.5 21.0 1.0
O C:CGU426 4.7 23.1 1.0
NH1 B:ARG307 4.8 21.4 1.0
CB C:CGU430 4.8 22.4 1.0
CB C:CGU426 4.9 20.0 1.0
O B:HOH611 5.0 20.3 1.0

Calcium binding site 4 out of 10 in 1j35

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Calcium binding site 4 out of 10 in the Crystal Structure of 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 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:26.9
occ:1.00
 OE22 C:CGU408 2.2 28.4 1.0
OE12 C:CGU408 2.3 24.2 1.0
O C:HOH655 2.4 32.6 1.0
OE22 C:CGU430 2.4 22.5 1.0
O B:HOH643 2.5 34.2 1.0
OE11 C:CGU427 2.5 27.1 1.0
OE21 C:CGU430 2.6 22.5 1.0
CD2 C:CGU430 2.8 22.8 1.0
CD1 C:CGU408 3.2 29.0 1.0
CD2 C:CGU408 3.3 30.2 1.0
CD1 C:CGU427 3.3 24.0 1.0
OE12 C:CGU427 3.4 25.2 1.0
CG C:CGU408 3.7 29.5 1.0
CA C:CA503 3.8 26.6 1.0
OE11 C:CGU408 4.1 27.6 1.0
O C:HOH723 4.3 29.6 1.0
CG C:CGU430 4.3 22.8 1.0
ND2 C:ASN402 4.4 32.3 1.0
OE21 C:CGU408 4.4 32.9 1.0
O C:HOH722 4.4 30.2 1.0
CB C:CGU408 4.5 30.5 1.0
OD1 C:ASN402 4.5 31.8 1.0
CA C:CA501 4.5 21.0 1.0
O C:HOH661 4.7 25.4 1.0
O B:HOH617 4.7 26.8 1.0
OE12 C:CGU426 4.7 22.4 1.0
CG C:CGU427 4.8 26.5 1.0
CG C:ASN402 4.8 34.2 1.0
O C:HOH762 4.8 38.0 1.0
CD1 C:CGU430 4.9 23.1 1.0
CD1 C:CGU426 4.9 20.6 1.0
CG C:CGU426 5.0 19.9 1.0
O C:HOH849 5.0 50.3 1.0

Calcium binding site 5 out of 10 in 1j35

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Calcium binding site 5 out of 10 in the Crystal Structure of 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 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:26.6
occ:1.00
 O C:HOH636 2.3 21.6 1.0
O C:HOH625 2.3 31.8 1.0
OE12 C:CGU408 2.4 24.2 1.0
O C:HOH661 2.5 25.4 1.0
OE21 C:CGU430 2.5 22.5 1.0
OE12 C:CGU427 2.6 25.2 1.0
OE22 C:CGU417 2.7 33.6 1.0
OE11 C:CGU408 2.8 27.6 1.0
CD1 C:CGU408 3.0 29.0 1.0
CD2 C:CGU417 3.6 35.8 1.0
CD1 C:CGU427 3.7 24.0 1.0
CD2 C:CGU430 3.7 22.8 1.0
CA C:CA504 3.8 32.5 1.0
OE21 C:CGU417 3.8 34.9 1.0
CA C:CA502 3.8 26.9 1.0
CB C:CGU430 4.2 22.4 1.0
OE11 C:CGU427 4.2 27.1 1.0
O C:HOH723 4.3 29.6 1.0
CA C:GLY412 4.4 35.5 1.0
CG C:CGU408 4.5 29.5 1.0
CG C:CGU430 4.5 22.8 1.0
O C:CGU427 4.6 24.6 1.0
OE22 C:CGU430 4.6 22.5 1.0
O C:HOH664 4.6 31.2 1.0
CA C:CGU427 4.7 23.9 1.0
CB C:CGU427 4.8 24.1 1.0
CG C:CGU427 4.8 26.5 1.0
N C:GLY412 4.9 36.3 1.0
O C:VAL410 4.9 37.3 1.0
OD1 C:ASN402 4.9 31.8 1.0
CA C:CGU408 5.0 32.3 1.0
OE22 C:CGU408 5.0 28.4 1.0
O C:HOH768 5.0 36.0 1.0

Calcium binding site 6 out of 10 in 1j35

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Calcium binding site 6 out of 10 in the Crystal Structure of 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 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:32.5
occ:1.00
 OD1 C:ASN402 2.3 31.8 1.0
OE22 C:CGU427 2.4 28.2 1.0
OE12 C:CGU427 2.5 25.2 1.0
OE11 C:CGU408 2.5 27.6 1.0
OE22 C:CGU417 2.5 33.6 1.0
OE12 C:CGU417 2.6 33.8 1.0
OE21 C:CGU407 2.8 40.6 1.0
CD1 C:CGU417 3.3 34.5 1.0
CD1 C:CGU427 3.3 24.0 1.0
O C:TYR401 3.4 37.8 1.0
CD2 C:CGU427 3.5 25.4 1.0
CD1 C:CGU408 3.5 29.0 1.0
CG C:ASN402 3.5 34.2 1.0
CD2 C:CGU417 3.6 35.8 1.0
CD2 C:CGU407 3.7 41.2 1.0
CA C:CA503 3.8 26.6 1.0
C C:TYR401 3.9 39.3 1.0
CG C:CGU427 3.9 26.5 1.0
CG C:CGU417 3.9 35.1 1.0
CA C:CA505 4.0 43.0 1.0
OE11 C:CGU417 4.0 32.8 1.0
O C:HOH664 4.0 31.2 1.0
OE12 C:CGU408 4.1 24.2 1.0
OE11 C:CGU427 4.2 27.1 1.0
N C:TYR401 4.2 40.8 1.0
N C:ASN402 4.2 38.1 1.0
CA C:ASN402 4.2 38.7 1.0
ND2 C:ASN402 4.3 32.3 1.0
OE22 C:CGU407 4.4 40.4 1.0
CB C:CGU417 4.4 35.1 1.0
CG C:CGU408 4.4 29.5 1.0
CB C:ASN402 4.5 36.1 1.0
CB C:CGU427 4.5 24.1 1.0
O C:HOH625 4.6 31.8 1.0
OE21 C:CGU427 4.6 27.5 1.0
CG C:CGU407 4.6 40.3 1.0
CA C:TYR401 4.7 41.3 1.0
OE21 C:CGU417 4.7 34.9 1.0
O C:HOH636 4.9 21.6 1.0

Calcium binding site 7 out of 10 in 1j35

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Calcium binding site 7 out of 10 in the Crystal Structure of 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 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:43.0
occ:1.00
 OE22 C:CGU421 2.3 44.1 1.0
O C:HOH692 2.3 40.6 1.0
O C:TYR401 2.3 37.8 1.0
OE12 C:CGU417 2.5 33.8 1.0
O C:HOH705 2.5 35.1 1.0
OE21 C:CGU407 2.5 40.6 1.0
OE11 C:CGU417 2.6 32.8 1.0
OE22 C:CGU407 2.7 40.4 1.0
OE21 C:CGU421 2.7 43.4 1.0
CD2 C:CGU421 2.8 42.8 1.0
CD1 C:CGU417 2.9 34.5 1.0
CD2 C:CGU407 2.9 41.2 1.0
C C:TYR401 3.5 39.3 1.0
CA C:CA504 4.0 32.5 1.0
CA C:TYR401 4.3 41.3 1.0
N C:TYR401 4.3 40.8 1.0
CG C:CGU421 4.3 43.5 1.0
CG C:CGU407 4.4 40.3 1.0
CG C:CGU417 4.4 35.1 1.0
CB C:TYR401 4.4 45.4 1.0
N C:ASN402 4.5 38.1 1.0
O C:HOH664 4.6 31.2 1.0
O C:HOH740 4.6 38.9 1.0
CD2 C:TYR401 4.6 52.1 1.0
CA C:ASN402 4.7 38.7 1.0
O C:HOH775 4.8 44.6 1.0
CB C:CGU407 4.8 39.2 1.0
OG C:SER403 4.8 47.3 1.0
CG C:TYR401 4.9 49.2 1.0
N C:SER403 4.9 43.5 1.0
CA C:CGU417 4.9 36.9 1.0
CB C:CGU421 4.9 42.6 1.0
OE22 C:CGU427 4.9 28.2 1.0
CB C:CGU417 5.0 35.1 1.0
O C:ARG416 5.0 41.7 1.0

Calcium binding site 8 out of 10 in 1j35

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Calcium binding site 8 out of 10 in the Crystal Structure of 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 8 of Crystal Structure of 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:54.0
occ:1.00
 O C:HOH740 2.4 38.9 1.0
O C:HOH810 2.5 54.7 1.0
O C:HOH675 2.5 46.7 1.0
O C:HOH708 2.5 35.1 1.0
OE21 C:CGU421 2.6 43.4 1.0
OE12 C:CGU421 2.6 44.6 1.0
CD2 C:CGU421 3.5 42.8 1.0
CD1 C:CGU421 3.5 43.7 1.0
CG C:CGU421 3.6 43.5 1.0
O C:HOH705 4.2 35.1 1.0
O C:HOH692 4.6 40.6 1.0
O C:ARG416 4.6 41.7 1.0
OE22 C:CGU421 4.6 44.1 1.0
OE11 C:CGU421 4.7 44.2 1.0
CG C:ARG416 4.8 40.9 1.0
OE22 C:CGU420 4.8 46.1 1.0

Calcium binding site 9 out of 10 in 1j35

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Calcium binding site 9 out of 10 in the Crystal Structure of 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 9 of Crystal Structure of Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca507

b:46.0
occ:1.00
 OE22 C:CGU415 2.4 46.0 1.0
OE21 C:CGU420 2.4 45.4 1.0
OE11 C:CGU415 2.5 46.2 1.0
O C:HOH776 2.7 49.0 1.0
CD2 C:CGU420 3.2 46.1 1.0
CD2 C:CGU415 3.2 46.4 1.0
CD1 C:CGU415 3.3 46.2 1.0
CG C:CGU415 3.4 45.6 1.0
CG C:CGU420 3.4 46.4 1.0
OE11 C:CGU420 3.4 49.5 1.0
CD1 C:CGU420 3.5 47.5 1.0
OE22 C:CGU420 4.2 46.1 1.0
OE12 C:CGU420 4.3 47.1 1.0
OE21 C:CGU415 4.4 47.9 1.0
OE12 C:CGU415 4.5 45.4 1.0
CB C:CGU420 4.9 44.5 1.0
CB C:CGU415 4.9 44.8 1.0

Calcium binding site 10 out of 10 in 1j35

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Calcium binding site 10 out of 10 in the Crystal Structure of 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 10 of Crystal Structure of Ca(II)-Bound Gla Domain of Factor IX Complexed with Binding Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca508

b:27.9
occ:1.00
 OE12 C:CGU440 2.2 36.8 1.0
O C:HOH654 2.3 26.5 1.0
O C:HOH840 2.4 37.4 1.0
O C:HOH725 2.4 40.6 1.0
OE22 C:CGU440 2.4 31.1 1.0
OE21 C:CGU436 2.4 26.6 1.0
OE12 C:CGU436 2.4 27.3 1.0
CD2 C:CGU436 3.3 26.6 1.0
CD1 C:CGU436 3.4 25.7 1.0
CD1 C:CGU440 3.4 37.8 1.0
CD2 C:CGU440 3.5 35.4 1.0
CG C:CGU436 3.5 25.6 1.0
O C:HOH862 4.0 31.8 1.0
CG C:CGU440 4.0 37.8 1.0
OE11 C:CGU440 4.4 39.1 1.0
OE22 C:CGU436 4.5 22.5 1.0
OE11 C:CGU436 4.5 22.7 1.0
OE21 C:CGU440 4.6 33.8 1.0
CB C:CGU440 4.9 36.4 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: Thu Jul 11 10:36:07 2024

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