Calcium in PDB 9das: Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila

The structure of Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila, PDB code: 9das was solved by T.D.R.Vance, Q.Ye, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.97 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.235, 156.288, 57.496, 90, 99.23, 90
R / Rfree (%)	19.1 / 20.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila (pdb code 9das). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila, PDB code: 9das:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4801 b:12.0 occ:1.00 O A:ASP4580 2.3 13.7 1.0 OD2 A:ASP4552 2.3 13.5 1.0 O A:GLY4586 2.4 13.0 1.0 O A:HOH4986 2.4 15.0 1.0 OG A:SER4509 2.4 12.0 1.0 O A:SER4509 2.4 11.2 1.0 O A:HOH4934 2.5 13.6 1.0 CG A:ASP4552 3.2 13.9 1.0 CB A:SER4509 3.3 11.6 1.0 C A:SER4509 3.3 11.1 1.0 C A:GLY4586 3.4 13.8 1.0 C A:ASP4580 3.4 15.1 1.0 CA A:GLY4586 3.7 15.3 1.0 CB A:ASP4552 3.7 11.9 1.0 CA A:SER4509 3.9 12.3 1.0 N A:ASP4580 4.1 16.6 1.0 OD1 A:ASP4552 4.1 14.2 1.0 CA A:ASP4580 4.2 16.7 1.0 O A:HOH4943 4.3 26.6 1.0 N A:SER4510 4.4 11.8 1.0 CB A:ASP4580 4.4 15.7 1.0 ND2 A:ASN4556 4.4 16.1 1.0 O A:HOH5045 4.4 29.4 1.0 N A:GLY4581 4.4 13.1 1.0 OD2 A:ASP4550 4.5 16.5 1.0 O A:SER4585 4.5 18.2 1.0 OD1 A:ASP4550 4.6 16.7 1.0 N A:GLY4587 4.6 14.4 1.0 CA A:GLY4581 4.6 14.5 1.0 CA A:SER4510 4.7 12.1 1.0 O A:PHE4551 4.9 13.4 1.0 N A:SER4509 4.9 10.9 1.0 N A:GLY4586 4.9 16.4 1.0 CG A:ASP4580 5.0 19.7 1.0 CG A:ASP4550 5.0 15.1 1.0

Calcium binding site 2 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4802 b:13.7 occ:1.00 O A:HOH4903 2.3 16.0 1.0 OG A:SER4512 2.4 14.4 1.0 OG1 A:THR4589 2.4 12.4 1.0 OG A:SER4510 2.4 13.7 1.0 CB A:SER4510 3.4 11.4 1.0 CB A:SER4512 3.4 15.6 1.0 CB A:THR4589 3.6 10.9 1.0 CG2 A:THR4589 3.8 13.1 1.0 OD1 A:ASP4622 4.0 18.0 1.0 N A:SER4512 4.2 14.7 1.0 CA A:SER4512 4.4 14.2 1.0 OD2 A:ASP4508 4.4 18.8 1.0 O A:GLN4624 4.5 14.4 1.0 OD1 A:ASP4508 4.5 14.1 1.0 CA A:SER4510 4.7 12.1 1.0 CA A:GLY4623 4.7 14.0 1.0 CA A:THR4589 4.8 11.6 1.0 C A:SER4510 4.9 14.3 1.0 CG A:ASP4508 4.9 14.8 1.0 C A:GLY4623 5.0 13.1 1.0

Calcium binding site 3 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4803 b:18.5 occ:1.00 O A:HOH5035 2.3 20.8 1.0 O A:SER4512 2.3 15.6 1.0 OD2 A:ASP4622 2.3 19.2 1.0 O A:HOH4961 2.4 19.9 1.0 O A:HOH5007 2.5 22.2 1.0 O A:HOH5034 2.5 28.9 1.0 O A:HOH5046 2.6 26.6 1.0 C A:SER4512 3.4 13.2 1.0 CG A:ASP4622 3.5 18.4 1.0 CB A:SER4512 4.0 15.6 1.0 CA A:SER4512 4.2 14.2 1.0 ND2 A:ASN4739 4.2 26.5 1.0 OD1 A:ASP4622 4.2 18.0 1.0 N A:ILE4513 4.3 14.5 1.0 CA A:ILE4513 4.4 14.7 1.0 CB A:ASP4622 4.4 12.6 1.0 O A:ILE4513 4.4 15.0 1.0 O A:HOH4910 4.5 13.8 1.0 OG A:SER4512 4.6 14.4 1.0 C A:ILE4513 4.7 15.0 1.0 O A:ASP4622 4.8 16.0 1.0

Calcium binding site 4 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4804 b:12.4 occ:1.00 ND2 A:ASN4716 2.3 11.9 1.0 O A:LEU4629 2.3 12.7 1.0 OE2 A:GLU4632 2.4 17.1 1.0 O A:HOH5031 2.4 21.7 1.0 OE2 A:GLU4592 2.4 17.2 1.0 O A:HOH4915 2.4 16.5 1.0 OE1 A:GLU4592 2.7 12.9 1.0 CD A:GLU4592 2.9 14.3 1.0 CD A:GLU4632 3.4 17.1 1.0 C A:LEU4629 3.4 13.7 1.0 CG A:ASN4716 3.5 13.1 1.0 OE1 A:GLU4632 3.7 17.1 1.0 CB A:ASN4716 4.0 11.7 1.0 CA A:LEU4629 4.3 12.3 1.0 N A:LEU4629 4.3 11.8 1.0 NZ A:LYS4596 4.3 15.6 1.0 CG A:GLU4592 4.3 12.7 1.0 N A:GLU4630 4.4 13.4 1.0 CB A:LEU4629 4.4 15.1 1.0 CA A:GLU4630 4.4 14.3 1.0 O A:HOH5044 4.5 30.0 1.0 OD1 A:ASN4716 4.6 16.9 1.0 CA A:ASN4716 4.7 13.3 1.0 CG A:GLU4632 4.7 16.8 1.0 CD2 A:TYR4628 4.7 14.9 1.0 O A:HOH5050 4.8 23.8 1.0 O A:HOH5000 4.8 31.8 1.0 O A:ASN4716 4.8 14.1 1.0

Calcium binding site 5 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4805 b:17.3 occ:1.00 O A:GLY4643 2.2 18.3 1.0 OD1 A:ASP4640 2.3 20.7 1.0 O A:ARG4641 2.4 18.7 1.0 O A:HOH5036 2.4 23.6 1.0 O A:HOH5025 2.4 25.1 1.0 OD2 A:ASP4647 2.6 15.9 1.0 OD1 A:ASP4647 2.6 14.8 1.0 CG A:ASP4647 2.9 14.5 1.0 C A:GLY4643 3.5 16.4 1.0 CG A:ASP4640 3.5 23.7 1.0 C A:ARG4641 3.5 16.0 1.0 N A:ARG4641 3.8 16.1 1.0 OD2 A:ASP4640 4.2 27.8 1.0 O A:HOH4930 4.2 15.9 1.0 N A:GLY4643 4.2 19.1 1.0 CA A:ARG4641 4.3 18.9 1.0 CA A:THR4644 4.3 15.6 1.0 C A:SER4642 4.3 17.6 1.0 N A:THR4644 4.4 14.9 1.0 C A:ASP4640 4.4 18.6 1.0 CB A:ASP4647 4.4 15.2 1.0 CA A:GLY4643 4.5 18.2 1.0 CA A:ASP4640 4.5 17.8 1.0 N A:SER4642 4.6 19.7 1.0 CB A:ASP4640 4.6 19.5 1.0 CA A:SER4642 4.7 23.1 1.0 O A:SER4642 4.7 20.2 1.0 CE A:MET4637 4.7 19.6 1.0 O A:HOH5019 4.7 30.7 1.0 O A:HOH4912 4.8 20.7 1.0 CG2 A:THR4644 4.9 17.6 1.0

Calcium binding site 6 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4806 b:16.9 occ:1.00 O A:VAL4753 2.3 17.6 1.0 OE1 A:GLU4732 2.3 20.2 1.0 O A:HOH4968 2.4 18.5 1.0 O A:HOH4955 2.4 20.9 1.0 OD1 A:ASP4751 2.4 19.4 1.0 OD2 A:ASP4749 2.4 15.1 1.0 OD1 A:ASP4749 2.5 17.2 1.0 CG A:ASP4749 2.8 18.4 1.0 C A:VAL4753 3.4 18.4 1.0 CG A:ASP4751 3.4 21.2 1.0 CD A:GLU4732 3.6 21.0 1.0 OD2 A:ASP4751 3.8 24.8 1.0 N A:VAL4753 3.9 16.3 1.0 O A:HOH4917 4.0 26.8 1.0 CA A:VAL4753 4.1 18.4 1.0 CB A:VAL4753 4.2 22.3 1.0 OE2 A:GLU4732 4.2 23.3 1.0 CA A:GLU4732 4.3 12.9 1.0 CB A:ASP4749 4.3 15.9 1.0 N A:ASP4751 4.3 17.8 1.0 O A:HOH5039 4.4 30.5 1.0 O A:VAL4731 4.4 14.9 1.0 N A:ILE4754 4.5 17.5 1.0 N A:GLY4752 4.6 18.1 1.0 CB A:ASP4751 4.7 21.5 1.0 CB A:GLU4732 4.7 14.0 1.0 CG1 A:ILE4754 4.7 16.1 1.0 CG A:GLU4732 4.7 15.9 1.0 CA A:ILE4754 4.7 16.9 1.0 N A:ALA4733 4.8 12.3 1.0 CA A:ASP4751 4.8 20.8 1.0 N A:SER4750 4.9 18.8 1.0 C A:ASP4751 4.9 20.8 1.0 C A:GLY4752 4.9 19.6 1.0 O A:HOH4906 4.9 19.3 1.0

Calcium binding site 7 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4801 b:15.9 occ:1.00 O B:GLY4643 2.3 19.4 1.0 OD1 B:ASP4640 2.3 15.7 1.0 O B:ARG4641 2.4 16.3 1.0 O B:HOH4991 2.4 23.0 1.0 O B:HOH4984 2.5 18.2 1.0 OD2 B:ASP4647 2.5 16.0 1.0 OD1 B:ASP4647 2.5 14.8 1.0 CG B:ASP4647 2.9 14.6 1.0 C B:GLY4643 3.5 20.9 1.0 CG B:ASP4640 3.5 16.2 1.0 C B:ARG4641 3.6 15.7 1.0 N B:ARG4641 3.8 13.9 1.0 O B:HOH4941 4.1 16.9 1.0 OD2 B:ASP4640 4.2 18.3 1.0 N B:GLY4643 4.3 18.3 1.0 CA B:THR4644 4.3 21.6 1.0 O1 B:GOL4807 4.3 30.5 1.0 CA B:ARG4641 4.3 14.5 1.0 C B:SER4642 4.3 17.6 1.0 N B:THR4644 4.3 21.2 1.0 C B:ASP4640 4.4 12.7 1.0 CB B:ASP4647 4.4 15.9 1.0 CA B:ASP4640 4.4 13.7 1.0 CA B:GLY4643 4.5 19.4 1.0 O B:HOH4980 4.5 28.3 1.0 CB B:ASP4640 4.6 13.7 1.0 N B:SER4642 4.6 15.2 1.0 O B:SER4642 4.7 16.8 1.0 CA B:SER4642 4.7 17.3 1.0 CE B:MET4637 4.8 19.8 1.0 CG2 B:THR4644 4.9 21.9 1.0 O B:HOH4942 4.9 21.4 1.0

Calcium binding site 8 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4802 b:32.5 occ:1.00 OG B:SER4512 2.2 35.1 1.0 O B:HOH4917 2.4 31.4 1.0 OG B:SER4510 2.4 30.0 1.0 OD1 B:ASP4622 2.6 32.6 1.0 O B:HOH4994 2.7 32.8 1.0 CB B:SER4512 3.2 33.5 1.0 CB B:SER4510 3.5 30.4 1.0 CG B:ASP4622 3.6 36.0 1.0 OG1 B:THR4589 3.7 25.4 1.0 OD2 B:ASP4622 3.9 34.8 1.0 O B:HOH4926 4.1 32.1 1.0 N B:SER4512 4.2 35.7 1.0 CA B:SER4512 4.2 35.1 1.0 CA B:GLY4623 4.3 28.6 1.0 OD2 B:ASP4508 4.3 30.0 1.0 N B:GLY4623 4.4 29.5 1.0 C B:ASP4622 4.5 32.0 1.0 O B:HOH4985 4.5 31.9 1.0 O B:ASP4622 4.6 31.6 1.0 OD1 B:ASP4508 4.6 32.2 1.0 CA B:SER4510 4.7 28.0 1.0 C B:SER4510 4.8 33.7 1.0 C B:SER4512 4.9 37.7 1.0 CB B:ASP4622 4.9 31.1 1.0 CG B:ASP4508 4.9 30.6 1.0 N B:ILE4513 4.9 39.1 1.0

Calcium binding site 9 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4803 b:26.9 occ:1.00 O B:ASP4580 2.3 29.2 1.0 OD2 B:ASP4552 2.3 25.1 1.0 O B:HOH4949 2.4 28.5 1.0 O B:HOH4913 2.4 29.6 1.0 OG B:SER4509 2.4 26.9 1.0 O B:SER4509 2.5 27.9 1.0 O B:GLY4586 2.5 26.5 1.0 CG B:ASP4552 3.2 27.5 1.0 CB B:SER4509 3.4 26.6 1.0 C B:SER4509 3.4 27.0 1.0 C B:ASP4580 3.4 32.2 1.0 C B:GLY4586 3.5 30.1 1.0 CB B:ASP4552 3.7 22.7 1.0 CA B:GLY4586 3.8 34.0 1.0 CA B:SER4509 4.0 25.1 1.0 OD1 B:ASP4552 4.1 26.0 1.0 N B:ASP4580 4.1 32.6 1.0 CA B:ASP4580 4.2 33.0 1.0 CB B:ASP4580 4.4 34.9 1.0 ND2 B:ASN4556 4.4 26.1 1.0 N B:SER4510 4.4 27.1 1.0 N B:GLY4581 4.4 33.5 1.0 O B:SER4585 4.5 37.2 1.0 OD1 B:ASP4550 4.5 28.8 1.0 OD2 B:ASP4550 4.5 29.8 1.0 CA B:GLY4581 4.6 34.4 1.0 N B:GLY4587 4.7 30.1 1.0 CA B:SER4510 4.8 28.0 1.0 N B:SER4509 4.9 24.2 1.0 O B:PHE4551 5.0 23.0 1.0 CG B:ASP4550 5.0 28.9 1.0 N B:GLY4586 5.0 35.4 1.0

Calcium binding site 10 out of 12 in the Crystal Structure of Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila


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 Vwfa Domain From Large Adhesion Protein of Aeromonas Hydrophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4804 b:17.3 occ:1.00 OE2 B:GLU4632 2.3 20.2 1.0 OD1 B:ASN4716 2.3 17.9 1.0 O B:LEU4629 2.4 18.3 1.0 OE2 B:GLU4592 2.4 20.3 1.0 O B:HOH4992 2.4 29.3 1.0 O B:HOH4936 2.4 20.4 1.0 OE1 B:GLU4592 2.7 16.1 1.0 CD B:GLU4592 2.9 16.5 1.0 CD B:GLU4632 3.3 21.2 1.0 CG B:ASN4716 3.4 18.1 1.0 C B:LEU4629 3.5 19.7 1.0 OE1 B:GLU4632 3.7 20.8 1.0 CB B:ASN4716 4.0 18.0 1.0 CA B:LEU4629 4.2 18.4 1.0 NZ B:LYS4596 4.3 22.2 1.0 N B:LEU4629 4.3 17.4 1.0 CB B:LEU4629 4.3 19.2 1.0 CG B:GLU4592 4.4 17.0 1.0 N B:GLU4630 4.4 18.6 1.0 CA B:GLU4630 4.5 19.2 1.0 ND2 B:ASN4716 4.5 20.5 1.0 CD2 B:TYR4628 4.6 20.3 1.0 CG B:GLU4632 4.6 20.2 1.0 CA B:ASN4716 4.8 19.1 1.0

Q.Ye, R.Eves, T.D.R.Vance, T.Hansen, A.P.Sage, A.Petkovic, B.Bradley, C.Escobedo, L.A.Graham, J.S.Allingham, P.L.Davies. Aeromonas Hydrophila Rtx Adhesin Has Three Ligand-Binding Domains That Give the Bacterium the Potential to Adhere to and Aggregate A Wide Variety of Cell Types. Mbio 15824 2025.
ISSN: ESSN 2150-7511
PubMed: 40243363
DOI: 10.1128/MBIO.03158-24