Calcium in PDB 4ggb: Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops

The structure of Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops, PDB code: 4ggb was solved by M.W.Vetting, J.T.Bouvier, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.70 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.178, 132.178, 95.472, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.4

The structure of Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Calcium atom in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops (pdb code 4ggb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops, PDB code: 4ggb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops


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 A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:49.5 occ:1.00 OE2 A:GLU220 2.2 19.6 1.0 O A:HOH678 2.4 17.0 1.0 OE2 A:GLU246 2.5 33.2 1.0 OD2 A:ASP194 2.6 25.7 1.0 O A:HOH567 2.6 26.6 1.0 CD A:GLU220 3.4 17.4 1.0 CG A:ASP194 3.6 22.2 1.0 CD A:GLU246 3.7 34.3 1.0 OD1 A:ASP194 3.9 20.6 1.0 OE1 A:GLU221 4.0 41.2 1.0 CG A:GLU220 4.2 18.4 1.0 NZ A:LYS164 4.2 21.6 1.0 NE2 A:HIS296 4.3 25.6 1.0 OE1 A:GLU220 4.3 13.9 1.0 OE1 A:GLU246 4.3 35.9 1.0 CD2 A:HIS296 4.5 23.0 1.0 CG A:GLU246 4.8 28.1 1.0 CB A:ASP194 4.8 15.9 1.0 CE A:LYS164 4.9 22.6 1.0 CD A:GLU221 5.0 37.5 1.0 OD1 A:ASN196 5.0 26.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops


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 A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:28.7 occ:1.00 OE2 A:GLU154 2.2 39.7 1.0 O A:HOH533 2.4 24.1 1.0 OE2 A:GLU158 2.4 30.1 1.0 O A:HOH535 2.5 23.6 1.0 CD A:GLU154 3.3 44.2 1.0 CD A:GLU158 3.4 36.8 1.0 NH1 A:ARG155 3.7 38.4 1.0 CG A:GLU154 4.0 45.1 1.0 CG A:GLU158 4.1 29.4 1.0 OE1 A:GLU154 4.2 45.2 1.0 OE1 A:GLU158 4.3 27.1 1.0 CZ A:ARG155 4.9 36.2 1.0 NE A:ARG332 4.9 49.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops


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 A Proposed Galactarolactone Cycloisomerase From Agrobacterium Tumefaciens, Target Efi-500704, with Bound Ca, Disordered Loops within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:20.2 occ:1.00 O A:HOH668 2.3 17.9 1.0 O A:HOH669 2.3 19.1 1.0 O A:GLY237 2.3 16.4 1.0 O A:HOH676 2.3 24.1 1.0 O A:HOH675 2.4 33.3 1.0 OD2 A:ASP209 2.4 21.4 1.0 OD1 A:ASP209 2.6 22.2 1.0 CG A:ASP209 2.8 24.3 1.0 C A:GLY237 3.5 17.9 1.0 CG2 A:ILE205 4.3 13.0 1.0 CA A:GLN238 4.3 11.4 1.0 N A:GLN238 4.3 14.6 1.0 CB A:ASP209 4.3 21.7 1.0 CA A:GLY237 4.5 17.2 1.0 O A:HOH586 4.5 29.4 1.0 O A:HOH646 4.6 27.8 1.0 CB A:GLN238 4.8 10.9 1.0

M.W.Vetting, J.T.Bouvier, J.A.Gerlt, S.C.Almo. Purification, Crystallization and Structural Elucidation of D-Galactaro-1,4-Lactone Cycloisomerase From Agrobacterium Tumefaciens Involved in Pectin Degradation. Acta Crystallogr.,Sect.F V. 72 36 2016.
PubMed: 26750482
DOI: 10.1107/S2053230X15023286