Zinc in PDB 5ic5: Bacteriophytochrome Response Regulator Rtbrr

The structure of Bacteriophytochrome Response Regulator Rtbrr, PDB code: 5ic5 was solved by A.W.Baker, K.A.Satyshur, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.30 / 1.90
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	47.714, 47.714, 193.488, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.3

The structure of Bacteriophytochrome Response Regulator Rtbrr also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Arsenic	(As)	1 atom

The binding sites of Zinc atom in the Bacteriophytochrome Response Regulator Rtbrr (pdb code 5ic5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Bacteriophytochrome Response Regulator Rtbrr, PDB code: 5ic5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Bacteriophytochrome Response Regulator Rtbrr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bacteriophytochrome Response Regulator Rtbrr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:33.5 occ:1.00 O1 A:CAC205 2.0 33.8 0.4 NE2 A:HIS162 2.0 44.7 1.0 NE2 A:HIS165 2.0 43.1 1.0 CD2 A:HIS162 2.4 41.4 1.0 CD2 A:HIS165 3.0 40.4 1.0 CE1 A:HIS165 3.0 55.2 1.0 CE1 A:HIS162 3.2 54.6 1.0 AS A:CAC205 3.4 40.2 0.4 CG A:HIS162 3.8 41.4 1.0 C2 A:CAC205 3.8 38.9 0.4 ND1 A:HIS162 4.1 39.5 1.0 ND1 A:HIS165 4.1 50.6 1.0 CG A:HIS165 4.1 39.1 1.0 C1 A:CAC205 4.5 37.7 0.4 O A:HOH383 4.7 49.2 1.0 O2 A:CAC205 4.7 47.9 0.4

Zinc binding site 2 out of 3 in the Bacteriophytochrome Response Regulator Rtbrr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Bacteriophytochrome Response Regulator Rtbrr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:33.4 occ:1.00 OE2 A:GLU23 2.0 72.0 1.0 OE1 A:GLU152 2.0 47.6 1.0 NE2 A:HIS164 2.0 42.0 1.0 NE2 A:HIS166 2.1 45.2 1.0 OE1 A:GLU23 2.1 47.9 1.0 OE2 A:GLU152 2.1 55.6 1.0 CD A:GLU23 2.4 51.0 1.0 CD A:GLU152 2.4 43.8 1.0 CE1 A:HIS166 2.5 49.4 1.0 CD2 A:HIS164 2.9 38.0 1.0 CE1 A:HIS164 3.1 50.5 1.0 CD2 A:HIS166 3.4 45.2 1.0 ND1 A:HIS166 3.8 55.2 1.0 CG A:GLU152 4.0 45.1 1.0 CG A:GLU23 4.0 50.3 1.0 CG A:HIS164 4.1 43.2 1.0 NH1 A:ARG149 4.1 58.0 1.0 ND1 A:HIS164 4.2 42.4 1.0 CG A:HIS166 4.2 49.1 1.0 O A:HOH374 4.2 42.5 1.0 O A:HOH345 4.3 58.1 1.0 CZ A:ARG149 4.7 65.1 1.0 CB A:GLU23 4.9 31.2 1.0 CB A:GLU152 4.9 34.0 1.0

Zinc binding site 3 out of 3 in the Bacteriophytochrome Response Regulator Rtbrr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Bacteriophytochrome Response Regulator Rtbrr within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:34.6 occ:1.00 NE2 A:HIS163 2.0 37.2 1.0 OE1 A:GLU16 2.0 64.5 1.0 NE2 A:HIS161 2.0 35.6 1.0 OE2 A:GLU16 2.0 63.3 1.0 CD A:GLU16 2.4 53.9 1.0 CE1 A:HIS163 2.9 51.1 1.0 CE1 A:HIS161 3.0 34.6 1.0 CD2 A:HIS161 3.0 37.1 1.0 CD2 A:HIS163 3.0 39.0 1.0 CG A:GLU16 4.0 51.4 1.0 ND1 A:HIS163 4.1 50.3 1.0 ND1 A:HIS161 4.1 35.1 1.0 CG A:HIS163 4.1 49.3 1.0 CG A:HIS161 4.2 33.0 1.0 O A:HOH362 4.3 40.5 1.0 CD1 A:LEU159 4.4 41.2 1.0 O A:HOH364 4.6 40.9 1.0 CB A:GLU16 4.8 34.8 1.0

A.W.Baker, K.A.Satyshur, N.Moreno Morales, K.T.Forest. Arm-in-Arm Response Regulator Dimers Promote Intermolecular Signal Transduction. J.Bacteriol. V. 198 1218 2016.
ISSN: ESSN 1098-5530
PubMed: 26833410
DOI: 10.1128/JB.00872-15