Calcium in PDB 1y17: Crystal Structure of Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus

The structure of Crystal Structure of Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus, PDB code: 1y17 was solved by Z.Zhu, S.Liu, X.Mo, X.Yu, Z.Liang, J.Zang, W.Zhao, M.Teng, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.08 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.944, 53.894, 68.087, 90.00, 98.39, 90.00
R / Rfree (%)	18 / 23.6

The binding sites of Calcium atom in the Crystal Structure of Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus (pdb code 1y17). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus, PDB code: 1y17:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus


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 Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:39.3 occ:1.00 OE2 A:GLU128 2.4 22.0 1.0 OE2 A:GLU47 2.7 20.9 1.0 OG A:SER41 2.7 19.3 1.0 O A:SER41 2.7 18.8 1.0 OE1 A:GLU128 2.8 21.5 1.0 CD A:GLU128 3.0 19.0 1.0 OE2 A:GLU43 3.2 29.0 1.0 OE1 A:GLU47 3.3 18.7 1.0 CD A:GLU47 3.3 21.8 1.0 O A:HOH1029 3.5 33.7 1.0 C A:SER41 3.7 16.8 1.0 CB A:SER41 3.9 16.7 1.0 CD A:GLU43 4.1 29.1 1.0 CA A:SER41 4.2 16.5 1.0 N A:SER41 4.2 13.1 1.0 OH A:TYR14 4.3 16.7 1.0 O A:HOH1021 4.4 34.5 1.0 CG A:GLU43 4.4 25.4 1.0 CG A:GLU128 4.5 17.4 1.0 ND2 B:ASN81 4.5 23.2 1.0 N A:ILE42 4.7 17.9 1.0 CD2 A:HIS12 4.7 38.0 1.0 CG A:GLU47 4.8 21.2 1.0 N A:GLU43 4.8 19.5 1.0 NE2 A:HIS12 4.9 39.0 1.0 CB A:GLU43 5.0 21.4 1.0 CE2 A:TYR14 5.0 16.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus


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 Aa-X-Bp-II, A Snake Venom Protein with the Activity of Binding to Coagulation Factor X From Agkistrodon Acutus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:32.7 occ:1.00 O B:SER41 2.4 22.9 1.0 OE2 B:GLU120 2.5 23.1 1.0 OE2 B:GLU47 2.6 31.0 1.0 OG B:SER41 2.7 17.8 1.0 OE1 B:GLU120 3.0 22.8 1.0 OE1 B:GLN43 3.1 34.2 1.0 CD B:GLU120 3.1 22.3 1.0 C B:SER41 3.3 21.4 1.0 CD B:GLU47 3.4 29.4 1.0 OE1 B:GLU47 3.4 32.6 1.0 CB B:SER41 3.8 17.5 1.0 CA B:SER41 4.0 20.3 1.0 N B:SER41 4.1 19.3 1.0 CD2 B:HIS12 4.2 27.2 1.0 OH B:TYR14 4.3 17.5 1.0 CD B:GLN43 4.3 35.9 1.0 N B:PHE42 4.3 22.4 1.0 NE2 B:HIS12 4.5 26.6 1.0 CG B:GLU120 4.6 23.2 1.0 CA B:PHE42 4.6 24.1 1.0 N B:GLN43 4.7 26.6 1.0 CG B:GLU47 4.8 29.5 1.0 OD2 A:ASP85 4.8 24.4 1.0 CE2 B:TYR14 4.8 13.1 1.0

Z.Zhu, S.Liu, X.Mo, X.Yu, Z.Liang, J.Zang, W.Zhao, M.Teng, L.Niu. Characterizations and Crystal Structures of Two Snake Venom Proteins with the Activity of Binding Coagulation Factor X From Agkistrodon Acutus To Be Published.