Calcium in PDB 4pmx: Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri in the Native Form

The structure of Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri in the Native Form, PDB code: 4pmx 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)	41.95 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.463, 71.834, 83.839, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 17.4

The binding sites of Calcium atom in the Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri in the Native Form (pdb code 4pmx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of GH10 Endo-B-1,4-Xylanase (Xynb) From Xanthomonas Axonopodis Pv Citri in the Native Form, PDB code: 4pmx:

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


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 in the Native Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.7 occ:1.00 OE1 A:GLN118 2.3 14.2 1.0 OD1 A:ASP68 2.3 15.1 1.0 OE1 A:GLU115 2.3 9.1 1.0 O A:HOH654 2.4 14.6 1.0 OE2 A:GLU64 2.4 12.5 1.0 O A:HOH646 2.4 13.1 1.0 CD A:GLU64 3.4 11.9 1.0 CD A:GLN118 3.4 12.8 1.0 CD A:GLU115 3.5 7.1 1.0 OE1 A:GLU64 3.6 12.0 1.0 CG A:ASP68 3.6 14.0 1.0 OE2 A:GLU115 3.9 9.8 1.0 CG A:GLN118 3.9 12.9 1.0 N A:ASP68 4.1 10.9 1.0 CA A:ASP68 4.1 15.7 1.0 NE2 A:GLN118 4.4 17.4 1.0 CB A:GLN118 4.5 10.4 1.0 CB A:ASP68 4.5 18.9 1.0 OD2 A:ASP68 4.5 13.6 1.0 O A:HOH605 4.7 23.4 1.0 CG A:GLU115 4.7 10.8 1.0 CG A:GLU64 4.8 10.7 1.0 CH2 A:TRP103 4.8 10.9 1.0 CA A:GLU115 4.9 8.8 1.0 CB A:GLU115 4.9 8.8 1.0 CG A:ARG67 5.0 10.6 1.0 O A:GLU115 5.0 9.0 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