Magnesium in PDB 7c7i: Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E)

Protein crystallography data

The structure of Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E), PDB code: 7c7i was solved by L.X.Xiao, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.502, 55.619, 189.884, 90, 90, 90
R / Rfree (%) 17.2 / 24.7

Other elements in 7c7i:

The structure of Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E) (pdb code 7c7i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E), PDB code: 7c7i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7c7i

Go back to Magnesium Binding Sites List in 7c7i
Magnesium binding site 1 out of 2 in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E)


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 SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:37.1
occ:1.00
O1G A:GTP201 2.0 27.8 1.0
O1A A:GTP201 2.4 24.0 1.0
O A:ASP33 2.6 25.6 1.0
PG A:GTP201 2.8 52.4 1.0
O3G A:GTP201 3.0 47.8 1.0
O3B A:GTP201 3.0 35.0 1.0
O A:HOH316 3.2 24.6 1.0
OG1 A:THR35 3.3 41.0 1.0
OG A:SER17 3.4 29.7 1.0
C A:ASP33 3.5 33.8 1.0
PA A:GTP201 3.6 26.2 1.0
CD1 A:TYR32 3.7 29.9 1.0
CE1 A:TYR32 3.8 32.0 1.0
O1B A:GTP201 3.8 31.9 1.0
PB A:GTP201 3.8 26.4 1.0
CB A:SER17 3.8 28.7 1.0
O3A A:GTP201 4.0 25.2 1.0
N A:ASP33 4.0 40.6 1.0
N A:THR35 4.0 29.1 1.0
CA A:PRO34 4.2 35.1 1.0
O2G A:GTP201 4.2 35.5 1.0
N A:PRO34 4.2 32.5 1.0
CA A:ASP33 4.3 46.7 1.0
CB A:THR35 4.3 26.8 1.0
O2A A:GTP201 4.3 25.0 1.0
C A:PRO34 4.4 32.1 1.0
CA A:THR35 4.8 28.0 1.0
C A:TYR32 4.8 35.6 1.0
O5' A:GTP201 4.9 26.4 1.0
CB A:ASP33 4.9 48.1 1.0
CG A:TYR32 5.0 30.7 1.0

Magnesium binding site 2 out of 2 in 7c7i

Go back to Magnesium Binding Sites List in 7c7i
Magnesium binding site 2 out of 2 in the Crystal Structure of SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E)


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 SHANK3 Spn Domain in Complex with Gtp-Bound RAP1B(E30D,K31E) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:38.3
occ:1.00
O3G B:GTP201 1.8 37.6 1.0
O2A B:GTP201 2.5 20.3 1.0
O B:ASP33 2.7 33.8 1.0
PG B:GTP201 2.8 53.7 1.0
O B:HOH317 3.0 33.5 1.0
O3B B:GTP201 3.1 28.3 1.0
O1G B:GTP201 3.2 45.1 1.0
OG B:SER17 3.3 26.4 1.0
OG1 B:THR35 3.4 42.6 1.0
C B:ASP33 3.5 30.4 1.0
CB B:SER17 3.6 22.0 1.0
O B:HOH305 3.6 30.5 1.0
PA B:GTP201 3.7 22.2 1.0
O B:HOH361 3.8 37.8 1.0
PB B:GTP201 3.9 25.0 1.0
CD1 B:TYR32 3.9 30.9 1.0
O2B B:GTP201 3.9 25.1 1.0
CE1 B:TYR32 3.9 24.8 1.0
N B:ASP33 4.0 27.3 1.0
O2G B:GTP201 4.1 33.8 1.0
N B:THR35 4.1 33.5 1.0
O3A B:GTP201 4.1 27.8 1.0
O1A B:GTP201 4.2 22.2 1.0
N B:PRO34 4.3 34.2 1.0
CA B:PRO34 4.3 34.1 1.0
CA B:ASP33 4.4 35.0 1.0
CB B:THR35 4.5 33.2 1.0
C B:PRO34 4.5 29.6 1.0
C B:TYR32 4.8 29.3 1.0
CA B:THR35 4.9 35.4 1.0
O5' B:GTP201 4.9 28.4 1.0
CA B:SER17 4.9 20.1 1.0
CA B:TYR32 5.0 29.0 1.0

Reference:

X.L.Xu, J.P.Liu, Y.L.Wang, Y.Wang, X.Gong, L.F.Pan. Mechanistic Insights Into the Interactions of Ras Subfamily Gtpases with the Spn Domain of Autism-Associated SHANK3. Chin.J.Chem. V. 38 1635 2020.
ISSN: ISSN 1001-604X
DOI: 10.1002/CJOC.202000278
Page generated: Sun Jul 11 16:06:09 2021

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