Calcium in PDB 5bqt: Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding.

The structure of Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding., PDB code: 5bqt was solved by M.U.Ahmad, K.Diederichs, W.Welte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.84 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.298, 235.143, 63.511, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.9

The binding sites of Calcium atom in the Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding. (pdb code 5bqt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding., PDB code: 5bqt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:0.0 occ:1.01 OD1 B:ASN79 2.4 0.2 1.0 O D:LEU137 2.5 85.2 1.0 OE2 D:GLU141 2.5 0.2 1.0 HG3 D:GLU141 2.5 0.5 1.0 CD D:GLU141 2.9 0.4 1.0 CG D:GLU141 3.1 0.5 1.0 H B:HIS76 3.3 99.8 1.0 HG2 D:GLU141 3.3 0.5 1.0 CG B:ASN79 3.4 0.9 1.0 HB3 B:HIS76 3.5 0.6 1.0 HG13 B:VAL75 3.5 90.2 1.0 HB2 B:ASN79 3.5 0.8 1.0 C D:LEU137 3.6 90.7 1.0 HB2 B:HIS76 3.6 0.6 1.0 HH12 B:ARG73 3.7 0.3 1.0 CB B:ASN79 3.9 0.3 1.0 HB3 B:ASN79 3.9 0.8 1.0 HA D:LYS138 3.9 0.5 1.0 HH22 B:ARG73 3.9 0.2 1.0 OE1 D:GLU141 4.0 84.9 1.0 CB B:HIS76 4.0 0.7 1.0 N B:HIS76 4.1 83.2 1.0 HA D:LEU137 4.1 0.8 1.0 HG12 B:VAL75 4.3 90.2 1.0 CG1 B:VAL75 4.3 75.2 1.0 HE1 B:MET63 4.3 0.1 1.0 HB3 D:LEU137 4.4 0.6 1.0 CA D:LEU137 4.4 0.0 1.0 CB D:GLU141 4.5 81.0 1.0 H D:GLU141 4.5 0.0 1.0 NH1 B:ARG73 4.5 0.6 1.0 HE3 B:MET63 4.5 0.1 1.0 ND2 B:ASN79 4.5 0.6 1.0 HB3 D:LYS140 4.5 0.3 1.0 HA B:VAL75 4.6 0.1 1.0 HB2 D:GLU141 4.6 97.1 1.0 N D:LYS138 4.6 0.6 1.0 CA D:LYS138 4.7 0.0 1.0 CA B:HIS76 4.7 77.6 1.0 HD21 B:ASN79 4.7 0.1 1.0 NH2 B:ARG73 4.7 0.9 1.0 HG11 B:VAL75 4.8 90.2 1.0 CE B:MET63 4.9 0.2 1.0 HD2 D:LYS138 4.9 0.1 1.0 CB D:LEU137 5.0 0.3 1.0 N D:GLU141 5.0 94.2 1.0

Calcium binding site 2 out of 2 in the Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of TRMBL2, An Archaeal Chromatin Protein, Shows A Novel Mode of Dna Binding. within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:0.8 occ:1.00 OE1 D:GLU144 2.7 0.0 1.0 OE2 D:GLU144 2.9 1.0 1.0 CD D:GLU144 3.2 0.9 1.0 HD21 B:ASN79 3.4 0.1 1.0 HE3 D:LYS140 3.8 0.8 1.0 HG2 D:GLU141 3.8 0.5 1.0 OD1 B:ASN79 3.9 0.2 1.0 ND2 B:ASN79 4.1 0.6 1.0 CG B:ASN79 4.4 0.9 1.0 HG2 D:LYS140 4.5 0.2 1.0 HA D:GLU141 4.5 0.5 1.0 CG D:GLU144 4.7 0.1 1.0 CE D:LYS140 4.7 0.5 1.0 CG D:GLU141 4.7 0.5 1.0 HG3 D:GLU141 4.8 0.5 1.0 HD22 B:ASN79 4.8 0.1 1.0 HB3 B:HIS76 4.8 0.6 1.0 HD3 D:LYS140 4.9 0.0 1.0 HE2 D:LYS140 4.9 0.8 1.0 HG3 D:GLU144 5.0 0.8 1.0 CG B:HIS76 5.0 88.2 1.0

M.U.Ahmad, I.Waege, W.Hausner, M.Thomm, W.Boos, K.Diederichs, W.Welte. Structural Insights Into Nonspecific Binding of Dna By TRMBL2, An Archaeal Chromatin Protein. J.Mol.Biol. V. 427 3216 2015.
ISSN: ESSN 1089-8638
PubMed: 26299937
DOI: 10.1016/J.JMB.2015.08.012