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Magnesium in PDB 5gwp: Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba

Enzymatic activity of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba

All present enzymatic activity of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba, PDB code: 5gwp was solved by S.Han, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.14 / 2.58
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 74.981, 133.684, 191.279, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba (pdb code 5gwp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba, PDB code: 5gwp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5gwp

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Magnesium binding site 1 out of 6 in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:29.2
occ:1.00
 OD2 A:ASP368 2.3 38.2 1.0
OD1 A:ASP306 2.3 42.9 1.0
OD2 A:ASP118 2.3 53.8 1.0
O A:HOH505 2.4 41.9 1.0
O A:HOH520 2.6 38.4 1.0
O A:HOH509 2.7 29.7 1.0
CG A:ASP118 3.2 52.0 1.0
CG A:ASP306 3.2 46.2 1.0
CG A:ASP368 3.2 38.3 1.0
OD1 A:ASP118 3.3 66.4 1.0
OD2 A:ASP306 3.4 46.9 1.0
OD1 A:ASP368 3.4 39.0 1.0
MG A:MG403 3.7 28.2 1.0
O A:HOH530 3.8 40.6 1.0
O A:HOH527 3.9 50.4 1.0
O A:HOH513 4.4 31.1 1.0
O A:HOH508 4.4 28.9 1.0
N A:GLY307 4.5 35.3 1.0
O A:HOH502 4.5 35.7 1.0
CB A:ASP118 4.6 45.5 1.0
CB A:ASP368 4.6 37.4 1.0
CB A:ASP306 4.6 30.1 1.0
N A:ASP306 4.8 38.5 1.0
OD1 A:ASP75 4.8 43.0 1.0
O A:ASN369 4.9 32.7 1.0
C A:ASP306 4.9 41.2 1.0

Magnesium binding site 2 out of 6 in 5gwp

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Magnesium binding site 2 out of 6 in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:49.4
occ:1.00
 O A:HOH516 2.1 61.7 1.0
OD2 A:ASP310 2.6 47.2 1.0
OD1 A:ASP310 2.7 50.1 1.0
OD2 A:ASP306 3.0 46.9 1.0
CG A:ASP310 3.0 46.1 1.0
CB A:ASP306 3.8 30.1 1.0
CG A:ASP306 3.8 46.2 1.0
CB A:ASP310 4.5 42.2 1.0
NZ A:LYS239 4.5 80.4 1.0
OD2 A:ASP220 4.6 70.3 1.0
O A:HOH513 4.8 31.1 1.0
CE A:LYS239 4.9 74.8 1.0
O A:HOH505 4.9 41.9 1.0
OD1 A:ASP306 5.0 42.9 1.0

Magnesium binding site 3 out of 6 in 5gwp

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Magnesium binding site 3 out of 6 in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:28.2
occ:1.00
 O A:HOH520 2.0 38.4 1.0
O A:GLY119 2.2 38.3 1.0
OD1 A:ASP118 2.3 66.4 1.0
O A:HOH503 2.4 34.4 1.0
O A:HOH530 2.4 40.6 1.0
O A:HOH502 2.5 35.7 1.0
C A:GLY119 3.3 35.7 1.0
CG A:ASP118 3.4 52.0 1.0
MG A:MG401 3.7 29.2 1.0
OD2 A:ASP118 3.9 53.8 1.0
OE1 A:GLU74 4.0 60.2 1.0
N A:GLY119 4.0 33.4 1.0
O A:HOH507 4.1 39.3 1.0
OD1 A:ASP75 4.1 43.0 1.0
C A:ASP118 4.2 33.6 1.0
N A:HIS120 4.2 33.5 1.0
CA A:GLY119 4.3 34.4 1.0
CA A:HIS120 4.3 36.8 1.0
CB A:GLU74 4.4 49.2 1.0
O A:ASP118 4.5 33.6 1.0
O A:HOH505 4.5 41.9 1.0
CB A:HIS120 4.5 34.5 1.0
CB A:ASP118 4.5 45.5 1.0
O A:HOH509 4.5 29.7 1.0
O A:HOH527 4.6 50.4 1.0
CA A:ASP118 4.6 40.8 1.0
OG C:SER100 4.7 48.7 1.0
OD1 A:ASP368 4.7 39.0 1.0
O A:GLU74 4.9 38.8 1.0
OD1 A:ASN369 4.9 38.9 1.0

Magnesium binding site 4 out of 6 in 5gwp

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Magnesium binding site 4 out of 6 in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:36.9
occ:1.00
 OD1 B:ASP306 2.1 57.8 1.0
OD2 B:ASP368 2.2 51.0 1.0
OD2 B:ASP118 2.3 45.0 1.0
O B:HOH511 2.3 49.7 1.0
O B:HOH513 2.4 40.3 1.0
O B:HOH524 2.5 37.2 1.0
CG B:ASP306 3.0 54.7 1.0
CG B:ASP118 3.2 44.0 1.0
OD2 B:ASP306 3.2 60.9 1.0
CG B:ASP368 3.3 53.2 1.0
OD1 B:ASP118 3.3 49.5 1.0
OD1 B:ASP368 3.6 55.6 1.0
O B:HOH526 3.6 44.3 1.0
MG B:MG403 3.8 35.5 1.0
O B:HOH516 4.3 35.4 1.0
N B:GLY307 4.3 44.9 1.0
CB B:ASP306 4.4 50.4 1.0
O B:HOH504 4.5 37.5 1.0
O B:HOH501 4.5 39.7 1.0
CB B:ASP368 4.6 53.0 1.0
CB B:ASP118 4.6 41.3 1.0
N B:ASP306 4.6 52.4 1.0
C B:ASP306 4.8 46.5 1.0
O B:ASN369 4.8 39.1 1.0
CA B:ASP306 4.8 48.9 1.0
OD1 B:ASP75 4.9 48.8 1.0
CB B:SER305 5.0 45.9 1.0

Magnesium binding site 5 out of 6 in 5gwp

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Magnesium binding site 5 out of 6 in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:40.8
occ:1.00
 O B:HOH520 2.1 43.5 1.0
OD2 B:ASP310 2.3 47.2 1.0
O B:HOH509 2.5 44.0 1.0
OD1 B:ASP310 2.7 46.2 1.0
OD2 B:ASP306 2.8 60.9 1.0
CG B:ASP310 2.8 45.2 1.0
CB B:ASP306 3.4 50.4 1.0
CG B:ASP306 3.5 54.7 1.0
O B:HOH501 4.0 39.7 1.0
NZ B:LYS239 4.1 65.9 1.0
CB B:ASP310 4.3 42.3 1.0
OD2 B:ASP220 4.5 71.1 1.0
OD1 B:ASP306 4.7 57.8 1.0
CA B:ASP306 4.8 48.9 1.0
O B:ASP306 4.8 45.9 1.0

Magnesium binding site 6 out of 6 in 5gwp

Go back to Magnesium Binding Sites List in 5gwp
Magnesium binding site 6 out of 6 in the Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of RCAR3:PP2C Wild-Type with (+)-Aba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:35.5
occ:1.00
 OD1 B:ASP118 2.1 49.5 1.0
O B:GLY119 2.1 36.6 1.0
O B:HOH526 2.1 44.3 1.0
O B:HOH514 2.2 41.9 1.0
O B:HOH513 2.3 40.3 1.0
O B:HOH504 2.5 37.5 1.0
CG B:ASP118 3.2 44.0 1.0
O B:HOH523 3.2 71.3 1.0
C B:GLY119 3.3 38.8 1.0
OD2 B:ASP118 3.7 45.0 1.0
MG B:MG401 3.8 36.9 1.0
N B:GLY119 3.8 33.7 1.0
C B:ASP118 3.9 40.7 1.0
OD1 B:ASP75 4.0 48.8 1.0
CA B:GLY119 4.2 38.7 1.0
N B:HIS120 4.2 33.3 1.0
O B:HOH511 4.2 49.7 1.0
O B:ASP118 4.3 43.0 1.0
O B:HOH524 4.3 37.2 1.0
CB B:ASP118 4.3 41.3 1.0
OE1 B:GLU74 4.3 60.0 1.0
CA B:HIS120 4.4 49.6 1.0
CA B:ASP118 4.4 43.7 1.0
CB B:HIS120 4.7 41.8 1.0
CB B:GLU74 4.7 44.3 1.0
OD1 B:ASP368 4.8 55.6 1.0
O B:GLU74 4.9 47.7 1.0

Reference:

S.Han, M.K.Min, S.Y.Lee, C.W.Lim, N.Bhatnagar, Y.Lee, D.Shin, K.Y.Chung, S.C.Lee, B.G.Kim, S.Lee. Modulation of Aba Signaling By Altering Vxg Phi L Motif of PP2CS in Oryza Sativa. Mol Plant V. 10 1190 2017.
ISSN: ESSN 1752-9867
PubMed: 28827170
DOI: 10.1016/J.MOLP.2017.08.003
Page generated: Sun Sep 29 15:28:38 2024

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