Calcium in PDB 1x2t: Crystal Structure of Habu IX-Bp at pH 6.5

The structure of Crystal Structure of Habu IX-Bp at pH 6.5, PDB code: 1x2t was solved by N.Suzuki, Z.Fujimoto, T.Morita, A.Fukamizu, H.Mizuno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.26 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.710, 63.509, 66.902, 90.00, 117.00, 90.00
R / Rfree (%)	19.1 / 22.2

The binding sites of Calcium atom in the Crystal Structure of Habu IX-Bp at pH 6.5 (pdb code 1x2t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Habu IX-Bp at pH 6.5, PDB code: 1x2t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Habu IX-Bp at pH 6.5


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 Habu IX-Bp at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:19.8 occ:1.00 OG A:SER41 2.3 12.5 1.0 OE2 A:GLU128 2.3 14.8 1.0 OE2 A:GLU47 2.5 11.1 1.0 OE2 A:GLU43 2.5 15.5 0.3 O A:SER41 2.5 10.4 1.0 OE1 A:GLU128 2.6 14.6 1.0 O A:HOH627 2.7 48.2 1.0 CD A:GLU128 2.8 14.6 1.0 CD A:GLU47 3.2 12.1 1.0 OE1 A:GLU47 3.2 10.6 1.0 C A:SER41 3.4 9.3 1.0 CB A:SER41 3.5 9.6 1.0 OE2 A:GLU43 3.6 16.7 0.6 CD A:GLU43 3.7 16.4 0.3 CA A:SER41 3.8 8.8 1.0 N A:SER41 3.9 7.8 1.0 OH A:TYR14 4.1 13.5 1.0 ND1 A:HIS12 4.3 25.2 1.0 CG A:GLU128 4.4 10.2 1.0 CD A:GLU43 4.4 17.9 0.6 CG A:GLU43 4.4 15.8 1.0 O A:HOH640 4.4 23.4 1.0 N A:ILE42 4.5 10.7 1.0 CG A:GLU47 4.6 9.8 1.0 OE1 A:GLU43 4.7 18.4 0.3 CE2 A:TYR14 4.7 13.3 1.0 CE1 A:HIS12 4.7 26.8 1.0 ND2 B:ASN81 4.7 19.7 1.0 CZ A:TYR14 4.9 12.4 1.0 N A:GLU43 4.9 10.7 1.0 O A:HOH708 4.9 26.5 1.0 O A:HOH719 4.9 28.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Habu IX-Bp at pH 6.5


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 Habu IX-Bp at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:14.2 occ:1.00 O B:SER41 2.3 14.4 1.0 O B:HOH626 2.4 14.0 1.0 OE1 B:GLN43 2.4 16.2 1.0 OE2 B:GLU47 2.4 15.4 1.0 OG B:SER41 2.6 12.9 1.0 OE2 B:GLU120 2.6 14.7 1.0 OE1 B:GLU120 2.7 15.3 1.0 O B:HOH633 2.7 20.9 1.0 CD B:GLU120 3.0 14.4 1.0 CD B:GLU47 3.2 15.0 1.0 OE1 B:GLU47 3.3 16.5 1.0 C B:SER41 3.3 14.6 1.0 CD B:GLN43 3.5 16.2 1.0 CB B:SER41 3.7 15.2 1.0 CA B:SER41 3.9 13.4 1.0 N B:SER41 4.0 13.1 1.0 NE2 B:GLN43 4.1 18.8 1.0 ND1 B:HIS12 4.3 15.0 1.0 N B:PHE42 4.4 14.6 1.0 OH B:TYR14 4.4 14.7 1.0 O B:HOH619 4.4 17.8 1.0 CG B:GLU120 4.5 12.7 1.0 N B:GLN43 4.6 16.5 1.0 CE1 B:HIS12 4.6 17.9 1.0 O B:HOH689 4.6 20.0 1.0 O B:HOH675 4.6 22.7 1.0 CG B:GLU47 4.6 14.4 1.0 O B:HOH627 4.7 21.0 1.0 CA B:PHE42 4.7 14.6 1.0 CG B:GLN43 4.7 17.3 1.0 OD2 A:ASP85 4.7 27.9 1.0 CE2 B:TYR14 4.8 12.0 1.0 CB B:GLN43 4.9 15.3 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Habu IX-Bp at pH 6.5


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 Habu IX-Bp at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca605 b:17.0 occ:1.00 OG C:SER41 2.4 14.8 1.0 OE2 C:GLU47 2.4 14.8 1.0 O C:SER41 2.4 16.4 1.0 OE2 C:GLU128 2.4 16.5 1.0 O C:HOH656 2.5 34.5 1.0 OE1 C:GLU128 2.6 15.4 1.0 OE2 C:GLU43 2.6 20.1 0.3 CD C:GLU128 2.8 14.3 1.0 CD C:GLU47 3.2 16.9 1.0 OE1 C:GLU47 3.3 16.1 1.0 C C:SER41 3.3 15.2 1.0 CB C:SER41 3.5 13.0 1.0 OE2 C:GLU43 3.5 22.6 0.6 O D:HOH736 3.7 36.4 1.0 CD C:GLU43 3.8 19.9 0.3 CA C:SER41 3.8 13.8 1.0 N C:SER41 3.9 11.9 1.0 OH C:TYR14 4.0 13.0 1.0 ND1 C:HIS12 4.2 30.7 1.0 CD C:GLU43 4.3 21.1 0.6 CG C:GLU43 4.4 20.0 1.0 CG C:GLU128 4.4 13.7 1.0 N C:ILE42 4.5 16.1 1.0 CE2 C:TYR14 4.6 12.1 1.0 CG C:GLU47 4.6 15.8 1.0 O C:HOH702 4.6 17.1 1.0 CZ C:TYR14 4.7 12.9 1.0 CE1 C:HIS12 4.8 30.5 1.0 O C:HOH726 4.8 21.3 1.0 OE1 C:GLU43 4.8 19.7 0.3 ND2 D:ASN81 4.9 20.4 1.0 N C:GLU43 4.9 14.5 1.0 CA C:ILE42 4.9 16.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Habu IX-Bp at pH 6.5


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 Habu IX-Bp at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca606 b:10.4 occ:1.00 OE1 D:GLN43 2.3 13.6 1.0 O D:HOH628 2.4 12.7 1.0 OE2 D:GLU120 2.4 11.8 1.0 OE2 D:GLU47 2.4 11.2 1.0 O D:HOH637 2.5 14.3 1.0 O D:SER41 2.5 10.5 1.0 OG D:SER41 2.6 9.8 1.0 OE1 D:GLU120 2.8 11.8 1.0 CD D:GLU120 3.0 11.7 1.0 CD D:GLU47 3.2 11.1 1.0 OE1 D:GLU47 3.3 12.2 1.0 C D:SER41 3.4 10.7 1.0 CD D:GLN43 3.4 14.0 1.0 CB D:SER41 3.7 9.3 1.0 NE2 D:GLN43 3.9 14.7 1.0 CA D:SER41 3.9 10.4 1.0 N D:SER41 4.0 10.1 1.0 ND1 D:HIS12 4.3 15.4 1.0 OH D:TYR14 4.4 9.6 1.0 CG D:GLU120 4.5 11.8 1.0 N D:PHE42 4.5 11.4 1.0 O D:HOH704 4.5 31.0 1.0 O D:HOH623 4.6 16.3 1.0 OD2 C:ASP85 4.6 22.3 1.0 CE1 D:HIS12 4.6 14.8 1.0 N D:GLN43 4.6 13.3 1.0 CG D:GLU47 4.7 10.8 1.0 O D:HOH730 4.7 32.2 1.0 CG D:GLN43 4.7 15.7 1.0 CE2 D:TYR14 4.8 10.1 1.0 O D:HOH639 4.8 14.8 1.0 CA D:PHE42 4.9 12.2 1.0 CB D:GLN43 5.0 13.7 1.0

N.Suzuki, Z.Fujimoto, T.Morita, A.Fukamizu, H.Mizuno. pH-Dependent Structural Changes at Ca(2+)-Binding Sites of Coagulation Factor IX-Binding Protein J.Mol.Biol. V. 353 80 2005.
ISSN: ISSN 0022-2836
PubMed: 16165155
DOI: 10.1016/J.JMB.2005.08.018