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Zinc in PDB 7drk: Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol

Enzymatic activity of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol

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

Protein crystallography data

The structure of Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol, PDB code: 7drk 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) 9.99 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.781, 59.432, 73.027, 90, 106.66, 90
R / Rfree (%) 25 / 29.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol (pdb code 7drk). 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 Cytidine Diphosphate-Diacylglycerol, PDB code: 7drk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7drk

Go back to Zinc Binding Sites List in 7drk
Zinc binding site 1 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol


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 Cytidine Diphosphate-Diacylglycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:56.8
occ:1.00
 OD1 A:ASP60 2.0 73.1 1.0
OD2 A:ASP60 2.0 69.2 1.0
OD1 A:ASP57 2.0 49.8 1.0
OD2 A:ASP78 2.1 49.1 1.0
O A:ASP57 2.1 46.4 1.0
OAT A:58A203 2.2 52.4 1.0
CG A:ASP60 2.3 55.4 1.0
C A:ASP57 3.0 54.0 1.0
CG A:ASP57 3.2 59.5 1.0
CG A:ASP78 3.2 58.9 1.0
CA A:ASP57 3.2 59.0 1.0
PAR A:58A203 3.6 54.0 1.0
ZN A:ZN202 3.6 61.5 1.0
N A:GLY61 3.7 63.9 1.0
OD1 A:ASP78 3.8 48.6 1.0
CB A:ASP57 3.8 53.5 1.0
CB A:ASP60 3.8 52.2 1.0
NH2 A:ARG11 3.8 60.7 1.0
OAU A:58A203 4.0 74.0 1.0
OAA A:58A203 4.1 68.9 1.0
OD2 A:ASP57 4.2 57.0 1.0
N A:PHE58 4.2 64.7 1.0
O A:SER56 4.4 66.8 1.0
CA A:GLY61 4.4 68.8 1.0
CB A:ASP78 4.4 45.9 1.0
C A:ASP60 4.5 60.9 1.0
CA A:ASP60 4.5 59.8 1.0
OAS A:58A203 4.5 60.6 1.0
N A:ASP57 4.5 57.2 1.0
OAX A:58A203 4.6 64.0 1.0
O5' A:58A203 4.6 52.0 1.0
CZ A:ARG11 4.6 60.0 1.0
N A:ASP60 4.6 53.1 1.0
NH1 A:ARG11 4.7 54.3 1.0
PAV A:58A203 4.8 64.7 1.0
CA A:PHE58 4.8 64.0 1.0
C A:SER56 4.9 53.2 1.0
C A:PHE58 4.9 68.7 1.0
OCL A:58A203 5.0 60.8 1.0

Zinc binding site 2 out of 4 in 7drk

Go back to Zinc Binding Sites List in 7drk
Zinc binding site 2 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol


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 Cytidine Diphosphate-Diacylglycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:61.5
occ:1.00
 OD2 A:ASP82 2.0 63.2 1.0
OD1 A:ASP57 2.0 49.8 1.0
OD2 A:ASP57 2.0 57.0 1.0
OD1 A:ASP78 2.0 48.6 1.0
OD1 A:ASP82 2.0 63.9 1.0
CG A:ASP57 2.2 59.5 1.0
CG A:ASP82 2.3 57.2 1.0
OAX A:58A203 2.6 64.0 1.0
CG A:ASP78 2.9 58.9 1.0
OD2 A:ASP78 3.2 49.1 1.0
ZN A:ZN201 3.6 56.8 1.0
O A:ASP78 3.6 39.2 1.0
CB A:ASP57 3.7 53.5 1.0
NH1 A:ARG11 3.8 54.3 1.0
CB A:ASP82 3.8 37.2 1.0
PAV A:58A203 3.9 64.7 1.0
OAU A:58A203 4.1 74.0 1.0
C A:ASP78 4.2 46.0 1.0
CB A:ASP78 4.3 45.9 1.0
CZ A:ARG11 4.4 60.0 1.0
CA A:ASP57 4.5 59.0 1.0
OAT A:58A203 4.6 52.4 1.0
OAY A:58A203 4.6 55.1 1.0
CA A:ASP78 4.6 50.9 1.0
CA A:ASP82 4.7 40.5 1.0
CG2 A:THR138 4.7 33.8 1.0
OD2 A:ASP60 4.7 69.2 1.0
NH2 A:ARG11 4.8 60.7 1.0
O A:ASP57 4.9 46.4 1.0
N A:ASP82 4.9 44.1 1.0
N A:PRO79 4.9 40.4 1.0
OBD A:58A203 5.0 60.7 1.0
OAW A:58A203 5.0 62.1 1.0

Zinc binding site 3 out of 4 in 7drk

Go back to Zinc Binding Sites List in 7drk
Zinc binding site 3 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol


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 Cytidine Diphosphate-Diacylglycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:61.1
occ:1.00
 OD1 B:ASP57 1.9 44.6 1.0
OD2 B:ASP60 2.0 68.0 1.0
OD1 B:ASP60 2.0 73.6 1.0
OD2 B:ASP78 2.1 44.6 1.0
O B:ASP57 2.1 56.7 1.0
CG B:ASP60 2.2 56.2 1.0
OAS B:58A203 2.5 59.3 1.0
C B:ASP57 2.9 58.9 1.0
CG B:ASP57 3.1 46.7 1.0
CA B:ASP57 3.2 58.1 1.0
CG B:ASP78 3.3 58.4 1.0
OAU B:58A203 3.5 61.9 1.0
PAR B:58A203 3.5 71.2 1.0
N B:GLY61 3.6 68.7 1.0
ZN B:ZN202 3.6 45.7 1.0
CB B:ASP60 3.7 51.4 1.0
CB B:ASP57 3.7 45.7 1.0
OAA B:58A203 3.9 75.3 1.0
OD1 B:ASP78 4.0 43.1 1.0
NH2 B:ARG11 4.1 45.6 1.0
OD2 B:ASP57 4.1 44.9 1.0
N B:PHE58 4.2 62.8 1.0
CA B:GLY61 4.3 67.3 1.0
C B:ASP60 4.3 71.2 1.0
O B:SER56 4.3 47.7 1.0
CA B:ASP60 4.3 65.0 1.0
CB B:ASP78 4.4 61.6 1.0
OAT B:58A203 4.5 77.0 1.0
N B:ASP60 4.5 59.8 1.0
N B:ASP57 4.5 49.7 1.0
C5' B:58A203 4.6 50.2 1.0
NH1 B:ARG11 4.7 44.0 1.0
CZ B:ARG11 4.7 43.0 1.0
O5' B:58A203 4.7 51.6 1.0
CA B:PHE58 4.8 63.1 1.0
C B:SER56 4.9 39.7 1.0
CAB B:58A203 4.9 69.1 1.0
PAV B:58A203 4.9 57.3 1.0
C B:PHE58 4.9 64.2 1.0

Zinc binding site 4 out of 4 in 7drk

Go back to Zinc Binding Sites List in 7drk
Zinc binding site 4 out of 4 in the Crystal Structure of Phosphatidylglycerol Phosphate Synthase in Complex with Cytidine Diphosphate-Diacylglycerol


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 Cytidine Diphosphate-Diacylglycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:45.7
occ:1.00
 OD2 B:ASP82 2.0 56.0 1.0
OD1 B:ASP78 2.0 43.1 1.0
OD2 B:ASP57 2.0 44.9 1.0
OAX B:58A203 2.1 62.0 1.0
OD1 B:ASP57 2.3 44.6 1.0
CG B:ASP57 2.4 46.7 1.0
CG B:ASP78 2.7 58.4 1.0
OD2 B:ASP78 2.7 44.6 1.0
OAU B:58A203 2.9 61.9 1.0
CG B:ASP82 2.9 57.2 1.0
PAV B:58A203 3.1 57.3 1.0
OD1 B:ASP82 3.2 55.9 1.0
ZN B:ZN201 3.6 61.1 1.0
CB B:ASP57 3.9 45.7 1.0
O B:ASP78 4.1 45.0 1.0
OAW B:58A203 4.1 59.1 1.0
CB B:ASP78 4.2 61.6 1.0
CAZ B:58A203 4.2 50.8 1.0
OAY B:58A203 4.2 53.2 1.0
CB B:ASP82 4.3 45.2 1.0
PAR B:58A203 4.3 71.2 1.0
NH2 B:ARG11 4.3 45.6 1.0
C B:ASP78 4.4 45.6 1.0
OAS B:58A203 4.4 59.3 1.0
CA B:ASP57 4.7 58.1 1.0
CA B:ASP78 4.7 45.7 1.0
OCK B:58A203 4.8 55.7 1.0
CG2 B:THR138 4.9 42.5 1.0
OD1 B:ASP60 4.9 73.6 1.0
N B:PRO79 4.9 48.1 1.0
O B:ASP57 5.0 56.7 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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