Calcium in PDB 5doo: The Structure of PKMT2 From Rickettsia Typhi

The structure of The Structure of PKMT2 From Rickettsia Typhi, PDB code: 5doo was solved by N.Noinaj, A.Abeykoon, Y.He, D.C.Yang, S.K.Buchanan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 3.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.719, 90.528, 106.201, 90.00, 114.17, 90.00
R / Rfree (%)	23.3 / 28

The binding sites of Calcium atom in the The Structure of PKMT2 From Rickettsia Typhi (pdb code 5doo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The Structure of PKMT2 From Rickettsia Typhi, PDB code: 5doo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The Structure of PKMT2 From Rickettsia Typhi


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of PKMT2 From Rickettsia Typhi within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:55.6 occ:1.00 OE1 A:GLU513 2.3 83.8 1.0 CD A:GLU513 3.1 82.2 1.0 OE2 A:GLU513 3.4 83.8 1.0 OD2 A:ASP516 3.5 73.1 1.0 CB A:ASP516 4.1 73.5 1.0 CG A:ASP516 4.2 74.5 1.0 CG A:GLU513 4.5 72.2 1.0 NZ A:LYS512 4.5 50.4 1.0 CE A:LYS512 4.9 51.8 1.0

Calcium binding site 2 out of 2 in the The Structure of PKMT2 From Rickettsia Typhi


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of PKMT2 From Rickettsia Typhi within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:87.6 occ:1.00 OD2 A:ASP481 2.4 87.0 1.0 CG A:ASP481 3.4 84.7 1.0 OD1 A:ASP481 3.6 87.3 1.0 OD1 A:ASN478 4.0 80.6 1.0 CG A:ASN478 4.5 79.5 1.0 ND2 A:ASN478 4.6 83.8 1.0 CB A:ASP481 4.7 74.7 1.0 O A:THR476 4.7 71.1 1.0 N A:ASN478 4.9 59.1 1.0 CA A:HIS477 5.0 65.6 1.0

A.H.Abeykoon, N.Noinaj, B.E.Choi, L.Wise, Y.He, C.C.Chao, G.Wang, M.Gucek, W.M.Ching, P.B.Chock, S.K.Buchanan, D.C.Yang. Structural Insights Into Substrate Recognition and Catalysis in Outer Membrane Protein B (Ompb) By Protein-Lysine Methyltransferases From Rickettsia. J.Biol.Chem. V. 291 19962 2016.
ISSN: ESSN 1083-351X
PubMed: 27474738
DOI: 10.1074/JBC.M116.723460