Calcium in PDB 1ixx: Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains

The structure of Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains, PDB code: 1ixx was solved by H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	172.200, 85.700, 65.200, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.1

The binding sites of Calcium atom in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains (pdb code 1ixx). 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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains, PDB code: 1ixx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca130 b:35.2 occ:1.00 O A:SER41 2.5 21.4 1.0 OE2 A:GLU128 2.6 23.9 1.0 OE1 A:GLU128 2.6 24.1 1.0 O A:HOH147 2.6 55.6 1.0 OE2 A:GLU47 2.6 32.8 1.0 OG A:SER41 2.7 27.2 1.0 OE2 A:GLU43 2.7 17.7 1.0 CD A:GLU128 2.9 19.6 1.0 CD A:GLU47 3.5 32.0 1.0 OE1 A:GLU47 3.6 37.6 1.0 C A:SER41 3.6 24.2 1.0 CD A:GLU43 3.8 21.7 1.0 CB A:SER41 3.9 12.6 1.0 OH A:TYR14 4.0 24.7 1.0 CA A:SER41 4.2 18.1 1.0 N A:SER41 4.3 10.2 1.0 CG A:GLU128 4.4 18.3 1.0 OE1 A:GLU43 4.5 25.4 1.0 CG A:GLU43 4.7 19.7 1.0 O A:HOH138 4.7 71.9 1.0 CD2 A:HIS12 4.7 20.7 1.0 N A:ILE42 4.7 20.1 1.0 O A:HOH146 4.8 35.7 1.0 CE2 A:TYR14 4.8 22.3 1.0 CZ A:TYR14 4.9 20.9 1.0 CG A:GLU47 4.9 30.4 1.0 N A:GLU43 4.9 22.1 1.0 CB A:GLU43 5.0 14.2 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca124 b:27.7 occ:1.00 O B:SER41 2.3 20.8 1.0 OE1 B:GLN43 2.4 35.0 1.0 OG B:SER41 2.4 31.7 1.0 OE2 B:GLU47 2.5 27.4 1.0 OE2 B:GLU120 2.7 31.1 1.0 OE1 B:GLU120 2.9 32.8 1.0 CD B:GLU120 3.1 27.1 1.0 C B:SER41 3.3 20.4 1.0 CD B:GLU47 3.3 19.4 1.0 OE1 B:GLU47 3.4 21.1 1.0 CB B:SER41 3.6 19.6 1.0 CD B:GLN43 3.6 32.8 1.0 CA B:SER41 3.9 21.7 1.0 N B:SER41 4.1 22.8 1.0 N B:PHE42 4.3 22.9 1.0 NE2 B:GLN43 4.4 30.9 1.0 OH B:TYR14 4.5 18.9 1.0 CG B:GLU120 4.6 20.7 1.0 CA B:PHE42 4.7 26.5 1.0 CG B:GLU47 4.7 19.3 1.0 OD2 A:ASP85 4.7 31.8 1.0 CG B:GLN43 4.7 39.6 1.0 N B:GLN43 4.7 30.8 1.0 O B:HOH137 4.8 28.6 1.0 CB B:GLN43 4.8 40.6 1.0 C B:PHE42 4.9 26.6 1.0 CE2 B:TYR14 4.9 19.1 1.0 CD2 B:HIS12 4.9 28.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca130 b:28.4 occ:1.00 O C:SER41 2.3 19.4 1.0 O C:HOH145 2.4 41.9 1.0 OG C:SER41 2.4 33.1 1.0 OE2 C:GLU47 2.5 22.9 1.0 OE2 C:GLU43 2.8 43.7 1.0 OE2 C:GLU128 2.8 55.3 1.0 OE1 C:GLU128 2.9 34.5 1.0 OE1 C:GLU47 3.2 28.9 1.0 CD C:GLU128 3.2 41.0 1.0 CD C:GLU47 3.2 15.9 1.0 C C:SER41 3.4 16.9 1.0 CB C:SER41 3.6 25.4 1.0 CD C:GLU43 3.6 34.3 1.0 CG C:GLU43 3.7 26.2 1.0 CA C:SER41 3.9 16.6 1.0 N C:SER41 4.1 16.0 1.0 OH C:TYR14 4.3 45.6 1.0 CB C:GLU43 4.5 20.9 1.0 N C:ILE42 4.5 18.2 1.0 N C:GLU43 4.5 22.2 1.0 CG C:GLU47 4.7 18.7 1.0 CG C:GLU128 4.7 39.1 1.0 OE1 C:GLU43 4.8 44.8 1.0 CE2 C:TYR14 4.9 38.3 1.0 CA C:ILE42 4.9 16.5 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca124 b:41.4 occ:1.00 OE1 D:GLN43 2.3 49.3 1.0 O D:SER41 2.3 42.8 1.0 OE2 D:GLU47 2.6 23.8 1.0 OE2 D:GLU120 2.6 36.5 1.0 OG D:SER41 2.7 56.9 1.0 OE1 D:GLU47 3.3 25.5 1.0 OE1 D:GLU120 3.3 38.2 1.0 CD D:GLU47 3.3 21.5 1.0 CD D:GLU120 3.4 32.5 1.0 C D:SER41 3.5 35.1 1.0 CD D:GLN43 3.5 42.7 1.0 CB D:SER41 3.9 45.5 1.0 CA D:SER41 4.1 37.1 1.0 NE2 D:GLN43 4.2 31.8 1.0 OH D:TYR14 4.3 31.3 1.0 N D:SER41 4.3 34.8 1.0 N D:PHE42 4.5 36.0 1.0 N D:GLN43 4.6 40.3 1.0 CB D:GLN43 4.6 40.1 1.0 CG D:GLN43 4.7 41.5 1.0 CA D:PHE42 4.7 38.1 1.0 CG D:GLU47 4.8 20.4 1.0 CG D:GLU120 4.8 26.0 1.0 C D:PHE42 4.9 39.8 1.0 CE2 D:TYR14 5.0 31.2 1.0 CD2 D:HIS12 5.0 36.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca130 b:25.9 occ:1.00 O E:SER41 2.4 25.0 1.0 OE1 E:GLU128 2.6 21.8 1.0 OG E:SER41 2.6 22.8 1.0 OE2 E:GLU47 2.6 11.1 1.0 OE2 E:GLU43 2.6 24.4 1.0 OE2 E:GLU128 2.8 24.3 1.0 CD E:GLU128 3.0 12.3 1.0 OE1 E:GLU47 3.1 7.1 1.0 CD E:GLU47 3.2 7.7 1.0 C E:SER41 3.5 18.1 1.0 CD E:GLU43 3.6 20.8 1.0 CB E:SER41 3.7 9.7 1.0 CG E:GLU43 3.8 18.6 1.0 O E:HOH154 4.0 37.7 1.0 CA E:SER41 4.0 17.2 1.0 N E:SER41 4.2 19.4 1.0 OH E:TYR14 4.3 21.7 1.0 CB E:GLU43 4.5 16.3 1.0 CG E:GLU128 4.5 12.7 1.0 N E:ILE42 4.6 14.5 1.0 O E:HOH139 4.6 27.4 1.0 N E:GLU43 4.6 16.3 1.0 CG E:GLU47 4.7 13.0 1.0 OE1 E:GLU43 4.8 26.5 1.0 O E:HOH136 4.9 26.7 1.0 CA E:ILE42 5.0 12.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains


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 Coagulation Factors IX/X-Binding Protein (IX/X- Bp) From Venom of Habu Snake with A Heterodimer of C-Type Lectin Domains within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca124 b:39.5 occ:1.00 OE1 F:GLN43 2.3 46.8 1.0 OG F:SER41 2.6 34.6 1.0 OE2 F:GLU47 2.7 15.2 1.0 O F:SER41 2.7 24.4 1.0 OE2 F:GLU120 2.7 42.4 1.0 OE1 F:GLU47 3.2 6.5 1.0 CD F:GLU47 3.3 9.1 1.0 OE1 F:GLU120 3.4 43.3 1.0 CD F:GLU120 3.4 39.4 1.0 CD F:GLN43 3.6 38.0 1.0 C F:SER41 3.6 25.6 1.0 CB F:SER41 3.8 22.4 1.0 CA F:SER41 4.2 22.8 1.0 OH F:TYR14 4.3 22.9 1.0 NE2 F:GLN43 4.3 39.3 1.0 N F:SER41 4.4 29.0 1.0 CG F:GLN43 4.6 41.0 1.0 N F:GLN43 4.7 26.9 1.0 OD2 E:ASP85 4.7 36.7 1.0 N F:PHE42 4.7 21.8 1.0 CB F:GLN43 4.7 35.1 1.0 CG F:GLU47 4.7 14.3 1.0 CD2 F:HIS12 4.8 25.2 1.0 CE2 F:TYR14 4.8 23.3 1.0 CG F:GLU120 4.8 38.0 1.0 NE2 F:HIS12 4.9 20.7 1.0 CA F:PHE42 5.0 14.2 1.0

H.Mizuno, Z.Fujimoto, M.Koizumi, H.Kano, H.Atoda, T.Morita. Structure of Coagulation Factors IX/X-Binding Protein, A Heterodimer of C-Type Lectin Domains. Nat.Struct.Biol. V. 4 438 1997.
ISSN: ISSN 1072-8368
PubMed: 9187649
DOI: 10.1038/NSB0697-438