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Magnesium in PDB 6hh4: Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine

Protein crystallography data

The structure of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine, PDB code: 6hh4 was solved by A.Ariza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.39 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.145, 96.642, 105.908, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine (pdb code 6hh4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine, PDB code: 6hh4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6hh4

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Magnesium binding site 1 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:30.4
occ:1.00
 O A:HOH679 2.3 35.3 1.0
OD1 A:ASP63 2.3 29.1 1.0
O15 A:F2R403 2.3 32.6 1.0
OD2 A:ASP305 2.3 34.7 1.0
OD1 A:ASP64 2.3 24.0 1.0
OG1 A:THR62 2.4 24.6 1.0
CB A:THR62 3.2 24.7 1.0
C21 A:F2R403 3.3 31.7 1.0
CG A:ASP305 3.4 30.4 1.0
CG A:ASP63 3.4 26.9 1.0
CG A:ASP64 3.6 22.7 1.0
C7 A:F2R403 3.7 33.2 1.0
N4 A:F2R403 3.8 38.7 1.0
OD1 A:ASP305 3.9 31.1 1.0
OE2 A:GLU33 3.9 32.5 1.0
MG A:MG402 3.9 33.7 1.0
OD2 A:ASP63 4.0 28.4 1.0
CG2 A:THR62 4.0 24.9 1.0
N A:ASP63 4.0 23.0 1.0
N A:ASP64 4.1 21.8 1.0
O A:HOH577 4.2 41.8 1.0
O A:GLY101 4.2 30.6 1.0
OD1 A:ASP26 4.3 23.2 1.0
OE1 A:GLU33 4.3 34.8 1.0
OD2 A:ASP64 4.4 23.5 1.0
CD A:GLU33 4.4 34.9 1.0
CA A:THR62 4.5 23.0 1.0
CB A:ASP64 4.5 22.1 1.0
CB A:ASP305 4.5 26.6 1.0
C A:THR62 4.6 23.0 1.0
CB A:ASP63 4.6 25.4 1.0
O B:HOH704 4.7 53.3 1.0
C20 A:F2R403 4.7 30.4 1.0
CA A:ASP63 4.7 23.2 1.0
OG1 A:THR306 4.7 25.2 1.0
O A:ARG100 4.7 28.4 1.0
C1 A:F2R403 4.8 44.9 1.0
C A:GLY101 4.9 30.0 1.0
C A:ASP63 4.9 22.2 1.0
CA A:ASP64 4.9 21.9 1.0

Magnesium binding site 2 out of 4 in 6hh4

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Magnesium binding site 2 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.7
occ:1.00
 OE2 A:GLU33 2.0 32.5 1.0
OD1 A:ASP303 2.1 30.8 1.0
O14 A:F2R403 2.2 30.2 1.0
OD1 A:ASP305 2.2 31.1 1.0
O15 A:F2R403 2.2 32.6 1.0
OG1 A:THR306 2.2 25.2 1.0
C20 A:F2R403 3.0 30.4 1.0
CG A:ASP303 3.0 29.6 1.0
C21 A:F2R403 3.0 31.7 1.0
CD A:GLU33 3.1 34.9 1.0
CG A:ASP305 3.1 30.4 1.0
OD2 A:ASP303 3.3 28.4 1.0
CB A:THR306 3.3 23.6 1.0
OD2 A:ASP305 3.5 34.7 1.0
N4 A:F2R403 3.5 38.7 1.0
N A:THR306 3.6 23.6 1.0
CG A:GLU33 3.7 32.9 1.0
C7 A:F2R403 3.9 33.2 1.0
MG A:MG401 3.9 30.4 1.0
CA A:THR306 4.0 22.4 1.0
OD1 A:ASP64 4.1 24.0 1.0
OE1 A:GLU33 4.1 34.8 1.0
C8 A:F2R403 4.2 31.9 1.0
OD2 A:ASP64 4.3 23.5 1.0
CB A:ASP303 4.4 28.2 1.0
CB A:ASP305 4.4 26.6 1.0
C A:ASP305 4.4 23.2 1.0
CG2 A:THR306 4.5 23.1 1.0
O A:HOH720 4.5 53.5 1.0
N A:ASP305 4.5 25.1 1.0
CG A:ASP64 4.6 22.7 1.0
CA A:ASP303 4.6 27.5 1.0
C A:ASP303 4.7 26.8 1.0
CA A:ASP305 4.7 25.1 1.0
O3 A:F2R403 4.7 32.9 1.0
C1 A:F2R403 4.7 44.9 1.0
O A:ASP303 4.7 25.8 1.0
O A:HOH679 4.8 35.3 1.0
CB A:GLU33 4.9 33.3 1.0
N2 A:F2R403 5.0 49.4 1.0

Magnesium binding site 3 out of 4 in 6hh4

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Magnesium binding site 3 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:27.9
occ:1.00
 O B:HOH670 2.3 33.2 1.0
O15 B:F2R403 2.3 29.9 1.0
OD1 B:ASP64 2.3 23.2 1.0
OD1 B:ASP63 2.3 25.3 1.0
OD2 B:ASP305 2.3 30.2 1.0
OG1 B:THR62 2.3 23.9 1.0
CB B:THR62 3.2 22.6 1.0
C21 B:F2R403 3.3 28.4 1.0
CG B:ASP305 3.4 28.3 1.0
CG B:ASP63 3.4 24.9 1.0
CG B:ASP64 3.5 21.3 1.0
C7 B:F2R403 3.7 30.4 1.0
N4 B:F2R403 3.8 33.6 1.0
MG B:MG402 3.8 32.6 1.0
OD1 B:ASP305 4.0 29.1 1.0
CG2 B:THR62 4.0 23.3 1.0
OD2 B:ASP63 4.0 25.4 1.0
OE2 B:GLU33 4.0 34.2 1.0
N B:ASP63 4.0 22.5 1.0
N B:ASP64 4.1 20.5 1.0
OD1 B:ASP26 4.2 22.2 1.0
O B:HOH625 4.3 40.8 1.0
OE1 B:GLU33 4.3 35.2 1.0
O B:GLY101 4.3 25.9 1.0
OD2 B:ASP64 4.4 21.2 1.0
CD B:GLU33 4.5 35.7 1.0
CA B:THR62 4.5 22.5 1.0
CB B:ASP64 4.5 21.6 1.0
CB B:ASP305 4.5 26.1 1.0
C B:THR62 4.6 22.6 1.0
C20 B:F2R403 4.6 27.7 1.0
CB B:ASP63 4.6 23.7 1.0
OG1 B:THR306 4.7 22.3 1.0
CA B:ASP63 4.7 22.4 1.0
C1 B:F2R403 4.8 39.5 1.0
O B:ARG100 4.8 24.1 1.0
O14 B:F2R403 4.9 26.6 1.0
C B:ASP63 4.9 20.8 1.0
CA B:ASP64 4.9 20.4 1.0
C B:GLY101 4.9 25.7 1.0

Magnesium binding site 4 out of 4 in 6hh4

Go back to Magnesium Binding Sites List in 6hh4
Magnesium binding site 4 out of 4 in the Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Adp-Ribosylserine Hydrolase ARH3 of Latimeria Chalumnae in Complex with Adp-Ribosyl-L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:32.6
occ:1.00
 OE2 B:GLU33 2.1 34.2 1.0
OD1 B:ASP303 2.1 25.2 1.0
OD1 B:ASP305 2.1 29.1 1.0
O14 B:F2R403 2.2 26.6 1.0
O15 B:F2R403 2.2 29.9 1.0
OG1 B:THR306 2.3 22.3 1.0
C20 B:F2R403 3.0 27.7 1.0
CG B:ASP305 3.0 28.3 1.0
CG B:ASP303 3.1 24.1 1.0
C21 B:F2R403 3.1 28.4 1.0
CD B:GLU33 3.1 35.7 1.0
OD2 B:ASP303 3.3 22.8 1.0
CB B:THR306 3.4 21.1 1.0
OD2 B:ASP305 3.4 30.2 1.0
N4 B:F2R403 3.5 33.6 1.0
N B:THR306 3.5 21.4 1.0
CG B:GLU33 3.8 33.8 1.0
MG B:MG401 3.8 27.9 1.0
C7 B:F2R403 3.9 30.4 1.0
OD1 B:ASP64 4.0 23.2 1.0
CA B:THR306 4.0 20.2 1.0
OE1 B:GLU33 4.0 35.2 1.0
O B:HOH638 4.2 51.8 1.0
OD2 B:ASP64 4.3 21.2 1.0
C8 B:F2R403 4.3 29.7 1.0
CB B:ASP305 4.3 26.1 1.0
C B:ASP305 4.4 21.2 1.0
CB B:ASP303 4.4 23.4 1.0
N B:ASP305 4.5 23.6 1.0
CG B:ASP64 4.5 21.3 1.0
CG2 B:THR306 4.6 20.6 1.0
CA B:ASP305 4.6 22.4 1.0
O B:HOH670 4.6 33.2 1.0
O3 B:F2R403 4.7 32.2 1.0
C1 B:F2R403 4.7 39.5 1.0
CA B:ASP303 4.7 22.8 1.0
O B:ASP303 4.7 22.1 1.0
C B:ASP303 4.7 22.3 1.0
CB B:GLU33 5.0 35.0 1.0

Reference:

J.G.M.Rack, A.Ariza, B.S.Drown, C.Henfrey, E.Bartlett, T.Shirai, P.J.Hergenrother, I.Ahel. (Adp-Ribosyl)Hydrolases: Structural Basis For Differential Substrate Recognition and Inhibition. Cell Chem Biol V. 25 1533 2018.
ISSN: ESSN 2451-9448
PubMed: 30472116
DOI: 10.1016/J.CHEMBIOL.2018.11.001
Page generated: Tue Oct 1 01:45:47 2024

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