Calcium in PDB 4pmy: Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose

The structure of Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose, PDB code: 4pmy was solved by C.R.Santos, V.P.M.Martins, L.M.Zanphorlin, R.Ruller, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.97 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.866, 48.201, 77.798, 90.00, 90.12, 90.00
R / Rfree (%)	18.6 / 22.7

The binding sites of Calcium atom in the Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose (pdb code 4pmy). 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 GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose, PDB code: 4pmy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose


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 GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:27.0 occ:1.00 OE1 A:GLN118 2.4 16.6 1.0 O A:HOH532 2.4 17.2 1.0 OD1 A:ASP68 2.4 20.5 1.0 OE2 A:GLU64 2.5 13.9 1.0 O A:HOH538 2.5 22.7 1.0 OE1 A:GLU115 2.6 12.4 1.0 CD A:GLU64 3.3 14.1 1.0 CD A:GLN118 3.5 18.7 1.0 OE1 A:GLU64 3.5 14.3 1.0 CD A:GLU115 3.6 12.3 1.0 CG A:ASP68 3.7 20.7 1.0 OE2 A:GLU115 4.0 11.7 1.0 CG A:GLN118 4.1 16.4 1.0 CA A:ASP68 4.2 20.0 1.0 N A:ASP68 4.2 17.3 1.0 CB A:ASP68 4.5 20.4 1.0 NE2 A:GLN118 4.5 20.3 1.0 CB A:GLN118 4.5 15.3 1.0 OD2 A:ASP68 4.6 20.6 1.0 CH2 A:TRP103 4.7 10.9 1.0 CG A:GLU64 4.8 13.1 1.0 CG A:GLU115 5.0 12.1 1.0 CZ2 A:TRP103 5.0 10.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose


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 GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:26.3 occ:1.00 OE1 B:GLN118 2.4 21.9 1.0 OD1 B:ASP68 2.4 20.6 1.0 OE2 B:GLU64 2.5 13.9 1.0 OE1 B:GLU115 2.5 11.5 1.0 O B:HOH540 2.6 20.5 1.0 O B:HOH539 2.7 24.6 1.0 CD B:GLU64 3.4 12.2 1.0 CD B:GLN118 3.5 19.4 1.0 OE1 B:GLU64 3.5 13.3 1.0 CD B:GLU115 3.6 11.9 1.0 CG B:ASP68 3.6 20.1 1.0 OE2 B:GLU115 3.9 12.9 1.0 CG B:GLN118 4.2 17.1 1.0 N B:ASP68 4.2 15.7 1.0 CA B:ASP68 4.2 18.4 1.0 NE2 B:GLN118 4.5 18.3 1.0 OD2 B:ASP68 4.5 21.7 1.0 CB B:ASP68 4.5 18.6 1.0 CH2 B:TRP103 4.5 10.9 1.0 CB B:GLN118 4.6 15.5 1.0 CG B:GLU64 4.8 12.2 1.0 CG B:GLU115 4.9 11.6 1.0 CZ2 B:TRP103 4.9 11.0 1.0 CG B:ARG67 4.9 11.6 1.0

C.R.Santos, Z.B.Hoffmam, V.P.Martins, L.M.Zanphorlin, L.H.Assis, R.V.Honorato, P.S.Oliveira, R.Ruller, M.T.Murakami. Molecular Mechanisms Associated with Xylan Degradation By Xanthomonas Plant Pathogens. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25266726
DOI: 10.1074/JBC.M114.605105