Calcium in PDB 1nl0: Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12

The structure of Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12, PDB code: 1nl0 was solved by M.Huang, B.C.Furie, B.Furie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.66 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	105.089, 71.614, 90.867, 90.00, 119.14, 90.00
R / Rfree (%)	23.3 / 27

The binding sites of Calcium atom in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 (pdb code 1nl0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12, PDB code: 1nl0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12


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 Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca901 b:47.2 occ:1.00 OE22 G:CGU26 2.1 47.5 1.0 OE22 G:CGU30 2.2 50.8 1.0 OE11 G:CGU26 2.4 52.6 1.0 OE11 G:CGU30 2.4 51.5 1.0 CD2 G:CGU26 3.1 48.7 1.0 CD2 G:CGU30 3.1 50.7 1.0 O G:HOH921 3.2 28.8 1.0 CD1 G:CGU26 3.3 50.7 1.0 CD1 G:CGU30 3.4 51.3 1.0 CG G:CGU26 3.5 49.4 1.0 CG G:CGU30 3.6 50.9 1.0 CA G:CA902 4.0 53.9 1.0 OE21 G:CGU30 4.2 50.5 1.0 NH2 G:ARG29 4.2 54.5 1.0 OE21 G:CGU26 4.2 48.9 1.0 OE12 G:CGU26 4.4 52.3 1.0 OE12 G:CGU30 4.6 52.0 1.0 O G:CGU26 4.7 47.4 1.0 CB G:CGU26 5.0 48.0 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12


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 Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca902 b:53.9 occ:1.00 OE21 G:CGU30 2.3 50.5 1.0 OE12 G:CGU8 2.6 46.1 1.0 OE22 G:CGU30 2.6 50.8 1.0 OE21 G:CGU8 2.7 44.1 1.0 CD2 G:CGU30 2.7 50.7 1.0 OE11 G:CGU27 2.8 46.1 1.0 O G:HOH921 2.9 28.8 1.0 CD2 G:CGU8 3.3 44.8 1.0 CD1 G:CGU8 3.5 46.2 1.0 CG G:CGU8 3.5 45.7 1.0 CD1 G:CGU27 3.7 47.6 1.0 OE12 G:CGU27 3.8 49.5 1.0 CA G:CA901 4.0 47.2 1.0 CA G:CA903 4.2 45.3 1.0 CG G:CGU30 4.2 50.9 1.0 OE22 G:CGU8 4.2 44.5 1.0 OE11 G:CGU26 4.5 52.6 1.0 CB G:CGU8 4.6 45.6 1.0 ND2 G:ASN2 4.6 42.2 1.0 OE11 G:CGU8 4.7 47.2 1.0 CD1 G:CGU26 4.8 50.7 1.0 OD1 G:ASN2 4.9 42.6 1.0 OE11 G:CGU30 4.9 51.5 1.0 CD1 G:CGU30 5.0 51.3 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12


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 Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca903 b:45.3 occ:1.00 OE12 G:CGU27 2.3 49.5 1.0 O G:HOH917 2.3 32.9 1.0 OE21 G:CGU8 2.3 44.1 1.0 OE11 G:CGU17 2.6 46.5 1.0 OE21 G:CGU30 2.7 50.5 1.0 CD2 G:CGU8 3.1 44.8 1.0 OE22 G:CGU8 3.1 44.5 1.0 CD1 G:CGU27 3.4 47.6 1.0 CD1 G:CGU17 3.5 46.1 1.0 CD2 G:CGU30 3.8 50.7 1.0 CA G:CA904 3.8 42.7 1.0 OE12 G:CGU17 3.9 44.5 1.0 OE11 G:CGU27 3.9 46.1 1.0 CB G:CGU30 4.0 50.1 1.0 CA G:CA902 4.2 53.9 1.0 CG G:CGU30 4.2 50.9 1.0 CA G:GLY12 4.3 43.9 1.0 O G:CGU27 4.5 47.5 1.0 CG G:CGU27 4.5 47.6 1.0 CG G:CGU8 4.6 45.7 1.0 O G:HOH908 4.7 31.6 1.0 N G:GLY12 4.8 43.7 1.0 CG G:CGU17 4.8 47.6 1.0 OE22 G:CGU30 4.8 50.8 1.0 CA G:CGU27 4.9 47.1 1.0 OD1 G:ASN2 4.9 42.6 1.0 O G:VAL10 4.9 43.2 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12


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 Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca904 b:42.7 occ:1.00 OE21 G:CGU17 2.3 47.3 1.0 OE22 G:CGU27 2.4 48.3 1.0 OE22 G:CGU8 2.4 44.5 1.0 OD1 G:ASN2 2.5 42.6 1.0 OE11 G:CGU7 2.5 45.6 1.0 OE12 G:CGU27 2.6 49.5 1.0 OE11 G:CGU17 2.7 46.5 1.0 CD2 G:CGU17 3.0 47.5 1.0 CD1 G:CGU27 3.2 47.6 1.0 CD2 G:CGU27 3.3 47.6 1.0 CG G:CGU17 3.4 47.6 1.0 CD1 G:CGU17 3.5 46.1 1.0 O G:TYR1 3.5 46.7 1.0 CG G:ASN2 3.5 43.5 1.0 CD1 G:CGU7 3.5 45.2 1.0 CD2 G:CGU8 3.6 44.8 1.0 CG G:CGU27 3.6 47.6 1.0 CA G:CA903 3.8 45.3 1.0 CA G:CA905 3.9 37.7 1.0 OE22 G:CGU17 3.9 46.0 1.0 C G:TYR1 4.0 45.7 1.0 O G:HOH908 4.1 31.6 1.0 OE12 G:CGU7 4.1 45.9 1.0 OE11 G:CGU27 4.1 46.1 1.0 OE21 G:CGU8 4.2 44.1 1.0 ND2 G:ASN2 4.3 42.2 1.0 CA G:ASN2 4.3 44.3 1.0 N G:ASN2 4.4 45.0 1.0 OE21 G:CGU27 4.4 48.1 1.0 N G:TYR1 4.5 46.0 1.0 CB G:ASN2 4.5 43.7 1.0 OE12 G:CGU17 4.6 44.5 1.0 CB G:CGU17 4.6 49.7 1.0 CG G:CGU7 4.7 45.7 1.0 CG G:CGU8 4.7 45.7 1.0 CA G:TYR1 4.9 45.8 1.0 CB G:CGU27 5.0 47.2 1.0 OE21 G:CGU21 5.0 53.7 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12


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 Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca905 b:37.7 occ:1.00 OE21 G:CGU21 2.0 53.7 1.0 OE12 G:CGU7 2.2 45.9 1.0 O G:TYR1 2.3 46.7 1.0 OE21 G:CGU17 2.4 47.3 1.0 O G:HOH912 2.5 48.6 1.0 OE22 G:CGU17 2.6 46.0 1.0 OE11 G:CGU7 2.8 45.6 1.0 CD1 G:CGU7 2.8 45.2 1.0 CD2 G:CGU17 2.8 47.5 1.0 CD2 G:CGU21 3.0 54.8 1.0 OE22 G:CGU21 3.3 55.1 1.0 C G:TYR1 3.6 45.7 1.0 CA G:CA904 3.9 42.7 1.0 N G:TYR1 4.2 46.0 1.0 CG G:CGU7 4.2 45.7 1.0 CG G:CGU17 4.3 47.6 1.0 CG G:CGU21 4.3 55.2 1.0 CA G:TYR1 4.4 45.8 1.0 N G:ASN2 4.5 45.0 1.0 OE22 G:CGU27 4.6 48.3 1.0 CA G:ASN2 4.6 44.3 1.0 O G:HOH908 4.6 31.6 1.0 CB G:TYR1 4.7 46.5 1.0 N G:SER3 4.8 44.3 1.0 CB G:CGU7 4.9 45.0 1.0 OG G:SER3 4.9 42.3 1.0 O G:ARG16 4.9 51.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12


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 Human Factor IX Gla Domain in Complex of An Inhibitory Antibody, 10C12 within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca907 b:57.0 occ:1.00 OE22 G:CGU15 2.4 57.9 1.0 OE12 G:CGU15 2.4 58.0 1.0 OE22 G:CGU20 2.5 61.9 1.0 CD2 G:CGU20 3.1 60.7 1.0 OE11 G:CGU20 3.1 61.8 1.0 CD1 G:CGU20 3.2 60.9 1.0 CD2 G:CGU15 3.3 57.1 1.0 CD1 G:CGU15 3.4 57.2 1.0 CG G:CGU20 3.5 60.4 1.0 CG G:CGU15 3.7 56.6 1.0 OE12 G:CGU20 3.7 61.6 1.0 OE21 G:CGU20 4.0 60.3 1.0 OE21 G:CGU15 4.4 57.5 1.0 OE11 G:CGU15 4.6 58.2 1.0 O G:CGU15 4.9 52.6 1.0

M.Huang, B.C.Furie, B.Furie. Crystal Structure of the Calcium-Stabilized Human Factor IX Gla Domain Bound to A Conformation-Specific Anti-Factor IX Antibody. J.Biol.Chem. V. 279 14338 2004.
ISSN: ISSN 0021-9258
PubMed: 14722079
DOI: 10.1074/JBC.M314011200