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Manganese in PDB 4yzg: Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii

Enzymatic activity of Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii

All present enzymatic activity of Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii:
3.1.3.16;

Protein crystallography data

The structure of Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii, PDB code: 4yzg 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) 26.73 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.399, 73.879, 81.998, 90.00, 109.15, 90.00
R / Rfree (%) 18 / 20.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii (pdb code 4yzg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii, PDB code: 4yzg:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4yzg

Go back to Manganese Binding Sites List in 4yzg
Manganese binding site 1 out of 4 in the Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii


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, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:16.1
occ:1.00
 OD1 A:ASP93 2.1 14.1 1.0
O A:HOH589 2.1 16.4 1.0
O A:HOH596 2.1 12.8 1.0
O A:GLY94 2.2 14.7 1.0
O A:HOH507 2.3 19.3 1.0
O A:HOH518 2.3 15.5 1.0
CG A:ASP93 3.3 13.6 1.0
C A:GLY94 3.4 15.8 1.0
OD2 A:ASP93 3.8 14.9 1.0
MN A:MN402 3.9 13.5 1.0
N A:GLY94 4.0 12.3 1.0
C A:ASP93 4.1 11.5 1.0
O A:HOH546 4.1 17.0 1.0
O4 A:SO4403 4.2 29.9 1.0
O3 A:SO4403 4.2 40.6 1.0
OD1 A:ASP74 4.2 12.3 1.0
CB A:GLU73 4.3 14.7 1.0
CA A:GLY94 4.3 13.7 1.0
OE1 A:GLU73 4.3 22.0 1.0
O A:HOH625 4.4 14.0 1.0
N A:HIS95 4.4 15.3 1.0
O A:HOH636 4.4 22.6 1.0
O A:HOH531 4.4 17.7 1.0
O A:ASP93 4.4 12.5 1.0
OD1 A:ASP339 4.4 16.3 1.0
OD1 A:ASN340 4.5 14.4 1.0
CB A:ASP93 4.5 12.4 1.0
CA A:HIS95 4.5 16.4 1.0
CA A:ASP93 4.6 11.2 1.0
NH1 A:ARG69 4.6 26.6 1.0
S A:SO4403 4.8 35.5 1.0
CB A:HIS95 4.8 18.9 1.0
O A:GLU73 4.8 13.3 1.0
C A:GLU73 4.8 12.3 1.0

Manganese binding site 2 out of 4 in 4yzg

Go back to Manganese Binding Sites List in 4yzg
Manganese binding site 2 out of 4 in the Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii


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, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:13.5
occ:1.00
 OD1 A:ASP296 2.1 14.2 1.0
OD2 A:ASP339 2.1 15.0 1.0
OD2 A:ASP93 2.2 14.9 1.0
O A:HOH531 2.2 17.7 1.0
O A:HOH625 2.2 14.0 1.0
O A:HOH518 2.4 15.5 1.0
CG A:ASP339 3.1 18.0 1.0
CG A:ASP93 3.1 13.6 1.0
CG A:ASP296 3.1 14.9 1.0
OD1 A:ASP93 3.4 14.1 1.0
OD1 A:ASP339 3.4 16.3 1.0
OD2 A:ASP296 3.5 18.3 1.0
MN A:MN401 3.9 16.1 1.0
O4 A:SO4403 4.0 29.9 1.0
O A:HOH507 4.1 19.3 1.0
O A:HOH627 4.2 12.8 1.0
N A:GLY297 4.3 12.2 1.0
CB A:ASP339 4.4 18.3 1.0
O A:HOH596 4.4 12.8 1.0
OD1 A:ASP74 4.4 12.3 1.0
CB A:ASP93 4.5 12.4 1.0
CB A:ASP296 4.5 13.3 1.0
O A:ASN340 4.5 13.4 1.0
N A:ASP296 4.6 12.0 1.0
C A:ASP296 4.7 14.2 1.0
CA A:ASP296 4.8 12.2 1.0
CB A:SER295 4.8 14.1 1.0
OG A:SER295 5.0 12.1 1.0

Manganese binding site 3 out of 4 in 4yzg

Go back to Manganese Binding Sites List in 4yzg
Manganese binding site 3 out of 4 in the Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:14.8
occ:1.00
 OD2 B:ASP93 2.1 16.6 1.0
OD1 B:ASP296 2.1 14.8 1.0
O B:HOH611 2.1 14.5 1.0
OD2 B:ASP339 2.2 18.1 1.0
O B:HOH527 2.2 20.5 1.0
O B:HOH530 2.4 18.2 1.0
CG B:ASP93 3.1 15.3 1.0
CG B:ASP296 3.1 16.8 1.0
CG B:ASP339 3.2 19.6 1.0
OD1 B:ASP93 3.3 14.1 1.0
OD2 B:ASP296 3.4 18.6 1.0
OD1 B:ASP339 3.5 17.2 1.0
MN B:MN402 3.9 17.7 1.0
O B:HOH596 4.0 17.5 1.0
O B:HOH509 4.2 21.2 1.0
N B:GLY297 4.3 15.0 1.0
O1 B:SO4403 4.3 38.5 1.0
OD1 B:ASP74 4.4 14.7 1.0
O B:HOH573 4.4 16.3 1.0
CB B:ASP93 4.4 14.3 1.0
O B:HOH513 4.4 28.1 1.0
CB B:ASP296 4.5 17.8 1.0
CB B:ASP339 4.5 23.4 1.0
N B:ASP296 4.5 14.0 1.0
O B:ASN340 4.6 14.6 1.0
C B:ASP296 4.7 17.4 1.0
CA B:ASP296 4.8 15.0 1.0
CB B:SER295 4.8 13.6 1.0

Manganese binding site 4 out of 4 in 4yzg

Go back to Manganese Binding Sites List in 4yzg
Manganese binding site 4 out of 4 in the Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of the Arabidopsis TAP38/PPH1, A State-Transition Phosphatase Responsible For Dephosphorylation of Lhcii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:17.7
occ:1.00
 OD1 B:ASP93 2.1 14.1 1.0
O B:HOH557 2.1 19.2 1.0
O B:HOH573 2.2 16.3 1.0
O B:HOH509 2.2 21.2 1.0
O B:GLY94 2.2 15.7 1.0
O B:HOH530 2.3 18.2 1.0
CG B:ASP93 3.2 15.3 1.0
C B:GLY94 3.4 16.3 1.0
OD2 B:ASP93 3.8 16.6 1.0
MN B:MN401 3.9 14.8 1.0
N B:GLY94 3.9 14.0 1.0
O B:HOH554 4.0 20.2 1.0
C B:ASP93 4.1 13.3 1.0
O2 B:SO4403 4.1 46.8 1.0
OD1 B:ASP74 4.2 14.7 1.0
O1 B:SO4403 4.2 38.5 1.0
CB B:GLU73 4.2 18.3 1.0
OE1 B:GLU73 4.2 21.6 1.0
CA B:GLY94 4.3 12.8 1.0
N B:HIS95 4.3 16.5 1.0
O B:HOH611 4.3 14.5 1.0
O B:HOH527 4.4 20.5 1.0
O B:ASP93 4.4 14.4 1.0
CB B:ASP93 4.4 14.3 1.0
CA B:HIS95 4.5 17.7 1.0
OD1 B:ASN340 4.5 16.7 1.0
CA B:ASP93 4.5 14.0 1.0
O B:HOH636 4.5 28.5 1.0
OD1 B:ASP339 4.6 17.2 1.0
CB B:HIS95 4.6 19.3 1.0
S B:SO4403 4.7 56.0 1.0
O B:GLU73 4.8 16.4 1.0
C B:GLU73 4.8 15.7 1.0
NH1 B:ARG69 5.0 39.6 1.0

Reference:

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
Page generated: Sat Oct 5 23:05:26 2024

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