Calcium in PDB 3wa5: Crystal Structure of Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3

The structure of Crystal Structure of Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3, PDB code: 3wa5 was solved by J.Ding, T.Wang, W.Liu, D.C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.970, 109.970, 84.950, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.2

The binding sites of Calcium atom in the Crystal Structure of Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3 (pdb code 3wa5). 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 Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3, PDB code: 3wa5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3


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 Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:7.1 occ:1.00 OD1 A:ASN181 2.3 5.9 1.0 OE1 A:GLN254 2.4 4.5 1.0 OE1 A:GLU258 2.5 6.8 1.0 O A:ASP253 2.5 7.2 1.0 O A:HOH601 2.5 5.6 1.0 OE2 A:GLU258 2.5 8.5 1.0 O A:HOH602 2.5 8.8 1.0 CD A:GLU258 2.8 8.7 1.0 OE1 A:GLN280 3.3 6.5 1.0 CD A:GLN254 3.5 8.4 1.0 CG A:ASN181 3.6 9.1 1.0 C A:ASP253 3.7 6.4 1.0 CD A:GLN280 4.0 6.6 1.0 CA A:GLN254 4.1 5.4 1.0 NE2 A:GLN254 4.2 5.0 1.0 NH1 B:ARG60 4.2 6.7 1.0 O A:GLU250 4.3 6.8 1.0 CA A:CA505 4.3 7.5 1.0 CG A:GLU258 4.3 6.3 1.0 CB A:GLN254 4.3 6.2 1.0 CG A:GLN280 4.3 4.3 1.0 N A:GLN254 4.4 4.8 1.0 ND2 A:ASN181 4.4 8.5 1.0 O B:HOH301 4.5 9.6 1.0 CA A:ASN181 4.5 7.3 1.0 CG A:GLN254 4.5 5.4 1.0 CB A:ASN181 4.5 6.3 1.0 CB A:ASP253 4.6 4.9 1.0 OE2 B:GLU126 4.8 7.4 1.0 OE1 A:GLU250 4.8 5.0 1.0 CG A:ASP253 4.8 8.0 1.0 CA A:ASP253 4.8 5.5 1.0 N A:ASN181 4.8 8.0 1.0 NE2 A:GLN280 4.9 5.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3


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 Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:7.5 occ:1.00 OE1 A:GLN280 2.4 6.5 1.0 OE2 B:GLU126 2.4 7.4 1.0 O A:SER275 2.5 4.8 1.0 OE2 A:GLU258 2.5 8.5 1.0 OD1 A:ASP262 2.5 5.6 1.0 OD2 A:ASP262 2.6 5.6 1.0 OE1 B:GLU126 2.6 7.1 1.0 OG A:SER275 2.7 8.0 1.0 CG A:ASP262 2.8 8.1 1.0 CD B:GLU126 2.9 10.8 1.0 CD A:GLN280 3.4 6.6 1.0 C A:SER275 3.5 6.5 1.0 CD A:GLU258 3.6 8.7 1.0 O A:HOH602 3.8 8.8 1.0 CB A:SER275 3.8 7.8 1.0 NE2 A:GLN280 3.8 5.0 1.0 CA A:SER275 4.0 7.3 1.0 N A:SER275 4.0 10.2 1.0 CG A:GLU258 4.0 6.3 1.0 CB A:ASP262 4.2 6.1 1.0 NZ A:LYS261 4.3 9.8 1.0 CA A:CA504 4.3 7.1 1.0 CG B:GLU126 4.4 9.5 1.0 NE2 A:GLN254 4.4 5.0 1.0 O B:HOH301 4.5 9.6 1.0 OE1 A:GLN254 4.6 4.5 1.0 N A:ILE276 4.6 6.3 1.0 OE1 A:GLU258 4.7 6.8 1.0 CG A:GLN280 4.7 4.3 1.0 O A:HOH723 4.9 21.8 1.0 CD A:GLN254 5.0 8.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3


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 Type VI Peptidoglycan Muramidase Effector TSE3 in Complex with Its Cognate Immunity Protein TSI3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:8.2 occ:1.00 O A:ARG379 2.4 6.7 1.0 O A:ASN384 2.4 7.4 1.0 O A:HOH603 2.5 7.0 1.0 OD1 A:ASP382 2.5 8.1 1.0 OG A:SER378 2.5 5.5 1.0 OE1 A:GLU375 2.5 9.2 1.0 OE2 A:GLU375 2.6 6.5 1.0 CD A:GLU375 2.9 7.5 1.0 CG A:ASP382 3.4 8.7 1.0 C A:ARG379 3.5 8.1 1.0 C A:ASN384 3.6 11.0 1.0 CB A:SER378 3.6 6.1 1.0 OD2 A:ASP382 3.7 8.9 1.0 N A:ARG379 3.9 6.9 1.0 C A:SER378 4.1 7.8 1.0 CA A:ARG379 4.2 7.7 1.0 N A:ASN384 4.2 9.7 1.0 CA A:ASN384 4.3 7.8 1.0 CG A:GLU375 4.3 5.2 1.0 CB A:ASN384 4.4 8.7 1.0 O A:SER378 4.5 5.7 1.0 N A:ASP382 4.5 7.9 1.0 CA A:SER378 4.5 5.0 1.0 N A:TRP381 4.5 7.5 1.0 N A:PRO380 4.6 9.2 1.0 N A:LEU385 4.6 7.0 1.0 OG A:SER374 4.6 7.5 1.0 O A:SER374 4.6 4.6 1.0 CB A:ARG379 4.6 9.4 1.0 CA A:PRO380 4.6 7.3 1.0 CA A:GLU375 4.7 4.7 1.0 CA A:LEU385 4.7 7.7 1.0 CB A:ASP382 4.7 11.3 1.0 O A:HOH619 4.8 7.5 1.0 CB A:GLU375 4.9 6.3 1.0 C A:PRO380 4.9 7.6 1.0 O B:HOH463 4.9 24.8 1.0 CD2 A:LEU385 5.0 10.3 1.0

T.Wang, J.Ding, Y.Zhang, D.C.Wang, W.Liu. Complex Structure of Type VI Peptidoglycan Muramidase Effector and A Cognate Immunity Protein Acta Crystallogr.,Sect.D V. 69 1889 2013.
ISSN: ISSN 0907-4449
DOI: 10.1107/S090744491301576X