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Zinc in PDB 7drj: Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate

Enzymatic activity of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate

All present enzymatic activity of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate:
2.7.8.5;

Protein crystallography data

The structure of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate, PDB code: 7drj was solved by B.W.Yang, Z.F.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.46 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.54, 59.376, 72.985, 90, 106.18, 90
R / Rfree (%) 21.2 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate (pdb code 7drj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate, PDB code: 7drj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7drj

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Zinc binding site 1 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn212

b:48.2
occ:1.00
 OD2 A:ASP78 2.0 74.6 1.0
OD1 A:ASP60 2.0 58.1 1.0
OD1 A:ASP57 2.1 65.8 1.0
O A:HOH319 2.1 49.2 1.0
C A:ASP57 2.7 43.9 1.0
CG A:ASP60 2.9 40.3 1.0
CG A:ASP78 3.0 49.9 1.0
CG A:ASP57 3.1 43.6 1.0
OD2 A:ASP60 3.1 41.2 1.0
CA A:ASP57 3.1 44.0 1.0
OD1 A:ASP78 3.4 47.3 1.0
CB A:ASP57 3.7 42.0 1.0
ZN A:ZN213 3.7 53.5 1.0
N A:GLY61 3.8 45.9 1.0
O44 A:PO9201 3.8 46.4 1.0
O A:HOH334 3.9 50.9 1.0
N A:PHE58 4.0 37.7 1.0
NH2 A:ARG11 4.0 48.2 1.0
OD2 A:ASP57 4.0 38.0 1.0
CB A:ASP60 4.3 51.3 1.0
O A:SER56 4.3 48.6 1.0
CB A:ASP78 4.4 48.2 1.0
N A:ASP57 4.4 41.8 1.0
CA A:GLY61 4.4 51.5 1.0
CA A:PHE58 4.5 44.4 1.0
CZ A:ARG11 4.6 48.2 1.0
C A:ASP60 4.6 54.3 1.0
NH1 A:ARG11 4.7 47.2 1.0
N A:ASP60 4.7 44.1 1.0
C A:PHE58 4.7 46.6 1.0
CA A:ASP60 4.8 49.2 1.0
O A:PHE58 4.8 53.0 1.0
C A:SER56 4.8 45.2 1.0
OD1 A:ASP82 5.0 45.2 1.0

Zinc binding site 2 out of 4 in 7drj

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Zinc binding site 2 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn213

b:53.5
occ:1.00
 OD1 A:ASP57 2.0 65.8 1.0
OD2 A:ASP82 2.0 54.4 1.0
OD1 A:ASP78 2.0 47.3 1.0
OD2 A:ASP57 2.0 38.0 1.0
OD1 A:ASP82 2.1 45.2 1.0
CG A:ASP57 2.2 43.6 1.0
O44 A:PO9201 2.3 46.4 1.0
CG A:ASP82 2.3 47.1 1.0
CG A:ASP78 3.0 49.9 1.0
OD2 A:ASP78 3.5 74.6 1.0
P43 A:PO9201 3.5 49.1 1.0
O A:ASP78 3.6 35.4 1.0
ZN A:ZN212 3.7 48.2 1.0
CB A:ASP57 3.7 42.0 1.0
O46 A:PO9201 3.7 44.8 1.0
CB A:ASP82 3.8 43.6 1.0
NH2 A:ARG11 3.8 48.2 1.0
C A:ASP78 4.0 40.4 1.0
CB A:ASP78 4.3 48.2 1.0
O A:HOH319 4.3 49.2 1.0
C41 A:PO9201 4.5 43.5 1.0
O55 A:PO9201 4.5 47.1 1.0
O42 A:PO9201 4.5 44.4 1.0
CZ A:ARG11 4.5 48.2 1.0
C48 A:PO9201 4.5 45.9 1.0
O45 A:PO9201 4.5 48.4 1.0
CA A:ASP57 4.5 44.0 1.0
CA A:ASP78 4.6 44.7 1.0
CG2 A:THR138 4.6 43.5 1.0
N A:PRO79 4.6 42.7 1.0
C47 A:PO9201 4.6 47.7 1.0
NE A:ARG11 4.7 41.1 1.0
CA A:ASP82 4.7 37.6 1.0
CA A:PRO79 4.8 41.0 1.0
N A:ASP82 4.8 35.2 1.0
C A:ASP57 5.0 43.9 1.0

Zinc binding site 3 out of 4 in 7drj

Go back to Zinc Binding Sites List in 7drj
Zinc binding site 3 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn711

b:51.6
occ:1.00
 OD2 B:ASP82 2.0 60.7 1.0
OD1 B:ASP78 2.0 45.8 1.0
OD2 B:ASP57 2.0 41.3 1.0
OD1 B:ASP82 2.1 55.0 1.0
OD1 B:ASP57 2.1 52.1 1.0
O44 B:PO9702 2.2 58.5 1.0
CG B:ASP82 2.3 54.8 1.0
CG B:ASP57 2.3 45.9 1.0
CG B:ASP78 3.0 54.2 1.0
OD2 B:ASP78 3.4 53.8 1.0
P43 B:PO9702 3.4 50.4 1.0
ZN B:ZN712 3.6 51.7 1.0
O46 B:PO9702 3.6 53.3 1.0
O B:ASP78 3.7 39.0 1.0
CB B:ASP57 3.8 44.2 1.0
CB B:ASP82 3.8 46.1 1.0
NH2 B:ARG11 4.0 52.2 1.0
O55 B:PO9702 4.1 42.8 1.0
C B:ASP78 4.1 46.0 1.0
O B:HOH804 4.2 45.3 1.0
CB B:ASP78 4.3 56.6 1.0
C47 B:PO9702 4.3 61.9 1.0
O45 B:PO9702 4.4 56.3 1.0
C41 B:PO9702 4.4 53.0 1.0
O42 B:PO9702 4.5 56.2 1.0
O B:ASP57 4.6 52.4 1.0
CZ B:ARG11 4.6 50.8 1.0
CG2 B:THR138 4.6 49.3 1.0
CA B:ASP57 4.6 48.9 1.0
CA B:ASP78 4.7 48.8 1.0
C48 B:PO9702 4.7 54.5 1.0
CA B:ASP82 4.7 44.8 1.0
N B:PRO79 4.7 51.2 1.0
N B:ASP82 4.8 43.1 1.0
NE B:ARG11 4.8 43.4 1.0
CA B:PRO79 4.9 47.0 1.0
C B:ASP57 5.0 53.3 1.0

Zinc binding site 4 out of 4 in 7drj

Go back to Zinc Binding Sites List in 7drj
Zinc binding site 4 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Phosphatidylglycerol Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn712

b:51.7
occ:1.00
 OD1 B:ASP57 2.0 52.1 1.0
O B:ASP57 2.0 52.4 1.0
OD2 B:ASP78 2.0 53.8 1.0
OD1 B:ASP60 2.0 62.5 1.0
O B:HOH804 2.1 45.3 1.0
CG B:ASP60 2.9 57.5 1.0
C B:ASP57 2.9 53.3 1.0
CG B:ASP78 3.0 54.2 1.0
CG B:ASP57 3.1 45.9 1.0
OD2 B:ASP60 3.1 52.5 1.0
CA B:ASP57 3.2 48.9 1.0
OD1 B:ASP78 3.4 45.8 1.0
ZN B:ZN711 3.6 51.6 1.0
CB B:ASP57 3.7 44.2 1.0
O44 B:PO9702 3.7 58.5 1.0
N B:GLY61 3.7 54.2 1.0
O B:HOH826 3.9 55.5 1.0
OD2 B:ASP57 4.0 41.3 1.0
NH2 B:ARG11 4.1 52.2 1.0
N B:PHE58 4.1 44.6 1.0
CA B:GLY61 4.2 56.7 1.0
CB B:ASP60 4.3 53.6 1.0
O B:SER56 4.3 54.2 1.0
CB B:ASP78 4.4 56.6 1.0
C B:ASP60 4.5 63.9 1.0
N B:ASP57 4.5 49.4 1.0
NH1 B:ARG11 4.6 51.7 1.0
CZ B:ARG11 4.6 50.8 1.0
CA B:PHE58 4.7 50.0 1.0
CA B:ASP60 4.7 52.5 1.0
N B:ASP60 4.8 50.5 1.0
C B:PHE58 4.9 53.4 1.0
C B:SER56 4.9 49.3 1.0
OD1 B:ASP82 4.9 55.0 1.0

Reference:

B.Yang, H.Yao, D.Li, Z.Liu. The Phosphatidylglycerol Phosphate Synthase Pgsa Utilizes A Trifurcated Amphipathic Cavity For Catalysis at the Membrane-Cytosol Interface Curr Res Struct Biol 2021.
ISSN: ESSN 2665-928X
DOI: 10.1016/J.CRSTBI.2021.11.005
Page generated: Tue Oct 29 19:14:39 2024

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