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Calcium in PDB 8alk: Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1

Enzymatic activity of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1

All present enzymatic activity of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1:
3.6.5.2;

Protein crystallography data

The structure of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1, PDB code: 8alk was solved by M.S.Kaspers, C.Pett, C.Hedberg, A.Itzen, V.Pogenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.34 / 2.15
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 119.332, 119.332, 79.058, 90, 90, 120
R / Rfree (%) 18.1 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1 (pdb code 8alk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1, PDB code: 8alk:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8alk

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Calcium binding site 1 out of 4 in the Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:52.5
occ:1.00
 O B:HOH301 2.3 78.7 1.0
OD1 A:ASP254 2.3 52.2 1.0
OD2 A:ASP105 2.4 41.6 1.0
OD2 A:ASP394 2.4 51.8 1.0
O A:HOH601 2.4 78.8 1.0
O A:HOH613 2.5 48.8 1.0
OD1 A:ASP105 3.1 54.1 1.0
CG A:ASP105 3.1 43.8 1.0
CG A:ASP254 3.2 48.4 1.0
OD2 A:ASP254 3.3 70.2 1.0
CG A:ASP394 3.4 50.6 1.0
CA A:CA502 3.5 78.2 1.0
O3 B:OJU203 3.6 87.2 1.0
O A:HOH619 3.6 66.5 1.0
O A:HOH618 3.6 72.2 1.0
OD1 A:ASP394 3.8 45.5 1.0
O1 B:OJU203 4.1 75.8 1.0
CA A:CA503 4.2 81.4 1.0
O A:HOH616 4.4 44.0 1.0
O A:HOH628 4.4 37.6 1.0
O A:CYS395 4.5 41.5 1.0
P B:OJU203 4.5 76.5 1.0
N A:GLY255 4.5 35.2 1.0
CB A:ASP105 4.5 38.1 1.0
CB A:ASP254 4.6 44.3 1.0
CB A:ASP394 4.7 36.3 1.0
OD1 A:ASP82 4.7 41.2 1.0
N A:ASP254 4.7 38.1 1.0

Calcium binding site 2 out of 4 in 8alk

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Calcium binding site 2 out of 4 in the Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:78.2
occ:1.00
 O3 B:OJU203 2.0 87.2 1.0
O A:GLY106 2.2 48.7 1.0
OD1 A:ASP105 2.3 54.1 1.0
O A:HOH601 2.4 78.8 1.0
O A:HOH605 2.5 65.2 1.0
O A:HOH616 2.5 44.0 1.0
C A:GLY106 3.3 38.5 1.0
CG A:ASP105 3.5 43.8 1.0
CA A:CA501 3.5 52.5 1.0
P B:OJU203 3.6 76.5 1.0
OD2 A:ASP105 4.0 41.6 1.0
N A:GLY106 4.1 36.0 1.0
CA A:LEU107 4.1 50.7 1.0
N A:LEU107 4.1 50.8 1.0
O B:HOH301 4.2 78.7 1.0
O A:HOH613 4.2 48.8 1.0
C A:ASP105 4.3 40.2 1.0
O2 B:OJU203 4.3 83.9 1.0
CA A:GLY106 4.3 41.9 1.0
C06 B:OJU203 4.3 88.1 1.0
O1 B:OJU203 4.3 75.8 1.0
OD1 A:ASP394 4.4 45.5 1.0
OG1 B:THR76 4.4 89.0 1.0
O A:GLY108 4.5 67.7 1.0
N A:GLY108 4.5 54.9 1.0
OD1 A:ASP82 4.5 41.2 1.0
O A:ASP105 4.6 40.0 1.0
CB A:ASP105 4.7 38.1 1.0
CD2 A:LEU107 4.7 59.8 1.0
C A:LEU107 4.7 57.0 1.0
OD2 A:ASP394 4.7 51.8 1.0
CB A:LEU81 4.8 41.2 1.0
CA A:ASP105 4.8 38.9 1.0

Calcium binding site 3 out of 4 in 8alk

Go back to Calcium Binding Sites List in 8alk
Calcium binding site 3 out of 4 in the Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:81.4
occ:1.00
 O B:HOH301 2.3 78.7 1.0
OD2 A:ASP190 2.4 57.5 1.0
O A:HOH618 2.4 72.2 1.0
OD2 A:ASP254 2.4 70.2 1.0
O A:HOH621 2.5 73.3 1.0
O1 B:OJU203 3.3 75.8 1.0
CG A:ASP190 3.4 45.0 1.0
CG A:ASP254 3.4 48.4 1.0
O A:HOH619 3.5 66.5 1.0
OD1 A:ASP190 3.7 46.4 1.0
OD1 A:ASP254 4.0 52.2 1.0
CA A:CA501 4.2 52.5 1.0
CB A:ASP254 4.4 44.3 1.0
P B:OJU203 4.6 76.5 1.0
CG A:PRO220 4.6 56.4 1.0
CB A:ASP190 4.7 41.2 1.0
OD2 A:ASP105 4.8 41.6 1.0
O3 B:OJU203 5.0 87.2 1.0
OG1 B:THR76 5.0 89.0 1.0

Calcium binding site 4 out of 4 in 8alk

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Calcium binding site 4 out of 4 in the Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Legionella Phosphocholine Hydrolase LEM3 in Complex with Its Substrate RAB1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:57.5
occ:1.00
 OG B:SER22 2.3 56.4 1.0
OD2 B:ASP63 2.4 65.9 1.0
O B:HOH310 2.4 48.0 1.0
O B:HOH308 2.4 61.3 1.0
O1B B:GDP201 2.5 52.5 1.0
OD1 B:ASP44 2.5 83.2 1.0
O B:HOH303 2.5 62.1 1.0
CG B:ASP63 3.5 70.4 1.0
CB B:SER22 3.5 56.9 1.0
PB B:GDP201 3.6 54.4 1.0
CG B:ASP44 3.6 82.6 1.0
O2B B:GDP201 3.6 54.3 1.0
OD2 B:ASP44 4.0 92.3 1.0
N B:SER22 4.1 52.7 1.0
OD1 B:ASP63 4.1 68.0 1.0
CB B:ALA65 4.2 69.6 1.0
CA B:SER22 4.3 54.6 1.0
O3B B:GDP201 4.4 53.0 1.0
O2A B:GDP201 4.5 64.9 1.0
CB B:ASP63 4.5 61.5 1.0
CA B:ALA65 4.7 70.1 1.0
O3A B:GDP201 4.8 49.9 1.0
O B:HOH311 4.8 63.8 1.0
CB B:ASP44 4.9 79.2 1.0

Reference:

M.S.Kaspers, V.Pogenberg, S.Ernst, F.Ecker, C.Hedberg, M.Groll, A.Itzen. Dephosphocholination By Legionella Effector LEM3 Functions Through Remodelling of the Switch II Region of RAB1B Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-37621-7
Page generated: Fri Jul 19 06:57:49 2024

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