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

The structure of Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri Complexed with Xylobiose, PDB code: 4pmz 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)	42.35 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.056, 49.238, 83.035, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.5

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 Xylobiose (pdb code 4pmz). 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 Xylobiose, PDB code: 4pmz:
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 Xylobiose


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 Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:22.2 occ:1.00 OE1 A:GLN118 2.3 20.5 1.0 OD1 A:ASP68 2.4 21.2 1.0 O A:HOH718 2.4 20.9 1.0 OE1 A:GLU115 2.4 13.6 1.0 O A:HOH655 2.4 18.4 1.0 OE2 A:GLU64 2.5 15.5 1.0 CD A:GLN118 3.4 18.1 1.0 CD A:GLU64 3.4 14.3 1.0 CD A:GLU115 3.5 13.8 1.0 OE1 A:GLU64 3.5 14.6 1.0 CG A:ASP68 3.6 21.0 1.0 OE2 A:GLU115 3.9 12.4 1.0 CG A:GLN118 4.0 16.3 1.0 CA A:ASP68 4.2 19.6 1.0 N A:ASP68 4.2 16.9 1.0 NE2 A:GLN118 4.4 19.1 1.0 OD2 A:ASP68 4.5 23.1 1.0 CB A:ASP68 4.5 21.3 1.0 CB A:GLN118 4.5 15.5 1.0 CH2 A:TRP103 4.7 13.2 1.0 O A:HOH582 4.7 26.2 1.0 CG A:GLU64 4.8 13.1 1.0 CG A:GLU115 4.8 13.0 1.0 O A:GLU115 4.9 11.9 1.0 CB A:GLU115 5.0 12.4 1.0 CA A:GLU115 5.0 12.2 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 Xylobiose


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 Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:22.7 occ:1.00 OE1 B:GLN118 2.4 19.8 1.0 OE1 B:GLU115 2.4 12.9 1.0 OD1 B:ASP68 2.4 21.5 1.0 O B:HOH665 2.4 18.8 1.0 O B:HOH727 2.5 21.5 1.0 OE2 B:GLU64 2.5 14.9 1.0 CD B:GLU64 3.4 13.8 1.0 CD B:GLN118 3.4 18.1 1.0 CD B:GLU115 3.5 13.1 1.0 OE1 B:GLU64 3.6 13.8 1.0 CG B:ASP68 3.6 20.2 1.0 OE2 B:GLU115 3.9 12.7 1.0 CG B:GLN118 4.0 16.9 1.0 CA B:ASP68 4.2 18.5 1.0 N B:ASP68 4.2 15.6 1.0 NE2 B:GLN118 4.4 19.8 1.0 OD2 B:ASP68 4.5 22.4 1.0 CB B:GLN118 4.5 15.2 1.0 CB B:ASP68 4.5 20.1 1.0 CH2 B:TRP103 4.7 12.7 1.0 CG B:GLU64 4.8 14.4 1.0 CG B:GLU115 4.8 13.4 1.0 CB B:GLU115 4.9 12.8 1.0 O B:GLU115 5.0 12.3 1.0 CA B:GLU115 5.0 13.4 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