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

Protein crystallography data

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

Calcium Binding Sites:

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 5bqt

Go back to Calcium Binding Sites List in 5bqt
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 5bqt

Go back to Calcium Binding Sites List in 5bqt
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

Reference:

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
Page generated: Wed Jul 9 04:26:39 2025

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