Manganese in PDB 4yzh: Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate

All present enzymatic activity of Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate:
3.1.3.16;

The structure of Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate, PDB code: 4yzh was solved by X.P.Wei, J.T.Guo, M.Li, Z.F.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.51 / 2.00
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.291, 64.079, 100.079, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.7

The binding sites of Manganese atom in the Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate (pdb code 4yzh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate, PDB code: 4yzh:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:10.5 occ:1.00 OD2 A:ASP339 2.2 8.5 1.0 OD1 A:ASP296 2.2 9.0 1.0 OD2 A:ASP93 2.2 10.2 1.0 O A:HOH519 2.4 8.0 1.0 O B:HOH501 2.4 9.7 1.0 O A:HOH574 2.5 11.2 1.0 CG A:ASP339 3.1 8.3 1.0 CG A:ASP93 3.1 12.4 1.0 CG A:ASP296 3.2 10.6 1.0 OD1 A:ASP93 3.4 8.8 1.0 OD2 A:ASP296 3.4 10.7 1.0 OD1 A:ASP339 3.4 8.6 1.0 O2P B:TPO403 3.9 9.9 1.0 MN A:MN402 3.9 11.8 1.0 O A:HOH550 4.0 9.5 1.0 O B:HOH502 4.2 7.7 1.0 O A:HOH562 4.3 9.6 1.0 OD1 A:ASP74 4.4 8.5 1.0 CB A:ASP339 4.4 8.5 1.0 O1P B:TPO403 4.4 10.9 1.0 N A:GLY297 4.4 9.9 1.0 O A:HOH601 4.5 16.4 1.0 N A:ASP296 4.5 7.1 1.0 CB A:ASP296 4.5 8.8 1.0 CB A:ASP93 4.5 9.0 1.0 O B:HOH510 4.5 19.0 1.0 O A:ASN340 4.7 7.6 1.0 P B:TPO403 4.7 12.2 1.0 O A:HOH527 4.7 12.3 1.0 CB A:SER295 4.8 8.2 1.0 CA A:ASP296 4.9 9.0 1.0 C A:ASP296 4.9 9.9 1.0

Manganese binding site 2 out of 2 in the Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Arabidopsis TAP38/PPH1 in Complex with PLHCB1 Phosphopeptide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:11.8 occ:1.00 O1P B:TPO403 2.1 10.9 1.0 OD1 A:ASP93 2.2 8.8 1.0 O A:HOH518 2.4 10.5 1.0 O B:HOH501 2.4 9.7 1.0 O A:GLY94 2.4 9.5 1.0 O A:HOH527 2.5 12.3 1.0 P B:TPO403 3.1 12.2 1.0 CG A:ASP93 3.4 12.4 1.0 O2P B:TPO403 3.4 9.9 1.0 C A:GLY94 3.6 10.5 1.0 O B:HOH503 3.6 11.4 1.0 MN A:MN401 3.9 10.5 1.0 OD2 A:ASP93 3.9 10.2 1.0 O3P B:TPO403 4.0 14.6 1.0 N A:GLY94 4.1 10.9 1.0 C A:ASP93 4.2 11.9 1.0 OD1 A:ASP74 4.3 8.5 1.0 OE1 A:GLU73 4.3 17.3 1.0 OG1 B:TPO403 4.4 11.8 1.0 CB A:GLU73 4.4 13.9 1.0 CA A:GLY94 4.4 11.3 1.0 OD1 A:ASP339 4.5 8.6 1.0 O A:ASP93 4.5 8.1 1.0 OD1 A:ASN340 4.5 8.1 1.0 N A:HIS95 4.5 12.1 1.0 O A:HOH519 4.5 8.0 1.0 CB A:ASP93 4.5 9.0 1.0 CA A:HIS95 4.6 14.1 1.0 O A:HOH544 4.6 15.0 1.0 CA A:ASP93 4.6 10.9 1.0 O A:HOH574 4.6 11.2 1.0 CB A:HIS95 4.7 8.8 1.0 NH1 A:ARG69 4.8 26.3 1.0 C A:GLU73 5.0 12.3 1.0

X.Wei, J.Guo, M.Li, Z.Liu. Structural Mechanism Underlying the Specific Recognition Between the Arabidopsis State-Transition Phosphatase TAP38/PPH1 and Phosphorylated Light-Harvesting Complex Protein LHCB1 Plant Cell V. 27 1113 2015.
ISSN: ESSN 1532-298X
PubMed: 25888588
DOI: 10.1105/TPC.15.00102