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Magnesium in PDB 3t1o: Mgla Bound to Gdp

Enzymatic activity of Mgla Bound to Gdp

All present enzymatic activity of Mgla Bound to Gdp:
3.6.5.2;

Protein crystallography data

The structure of Mgla Bound to Gdp, PDB code: 3t1o was solved by M.Miertzschke, I.R.Vetter, C.Koerner, A.Wittinghofer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.10 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.300, 47.850, 53.080, 108.37, 100.10, 92.92
R / Rfree (%) 19.3 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mgla Bound to Gdp (pdb code 3t1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Mgla Bound to Gdp, PDB code: 3t1o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3t1o

Go back to Magnesium Binding Sites List in 3t1o
Magnesium binding site 1 out of 6 in the Mgla Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mgla Bound to Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg197

b:25.4
occ:1.00
 O A:VAL79 2.5 19.1 1.0
O A:HOH213 2.7 22.4 1.0
O A:GLY81 2.7 19.6 1.0
NH2 A:ARG89 2.8 21.0 0.5
NZ A:LYS25 2.9 15.4 1.0
CE A:LYS25 3.4 11.1 1.0
N A:GLY81 3.5 20.3 1.0
CA A:GLY21 3.5 15.6 1.0
C A:PRO80 3.6 20.4 1.0
C A:VAL79 3.6 19.3 1.0
CG2 A:VAL83 3.7 32.1 1.0
C A:GLY81 3.8 24.0 1.0
CA A:PRO80 3.9 19.1 1.0
CZ A:ARG89 4.0 25.2 0.5
O2B A:GDP274 4.0 19.9 1.0
O A:PRO80 4.0 18.6 1.0
N A:GLY21 4.0 17.1 1.0
O A:PRO20 4.2 16.4 1.0
O A:GLY19 4.2 14.8 1.0
N A:PRO80 4.2 19.0 1.0
CA A:GLY81 4.3 22.3 1.0
C A:PRO20 4.3 16.0 1.0
NE A:ARG89 4.5 23.4 0.5
N A:LEU22 4.6 17.2 1.0
C A:GLY21 4.6 15.9 1.0
O1B A:GDP274 4.7 17.6 1.0
CB A:VAL79 4.8 18.6 1.0
O A:HOH237 4.9 22.2 1.0
CA A:VAL79 4.9 17.5 1.0
CG1 A:VAL79 4.9 20.2 1.0
PB A:GDP274 4.9 20.4 1.0
NH1 A:ARG89 4.9 32.5 0.5
N A:GLN82 5.0 24.9 1.0
CD A:LYS25 5.0 10.6 1.0

Magnesium binding site 2 out of 6 in 3t1o

Go back to Magnesium Binding Sites List in 3t1o
Magnesium binding site 2 out of 6 in the Mgla Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mgla Bound to Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg198

b:28.5
occ:1.00
 O A:ASP104 2.6 24.4 1.0
O A:ALA106 2.8 22.2 1.0
ND2 A:ASN113 2.9 18.0 1.0
CA A:LEU110 3.4 22.7 1.0
N A:LEU110 3.5 20.0 1.0
CD1 A:LEU110 3.6 21.8 1.0
C A:SER105 3.7 23.0 1.0
CD1 A:LEU149 3.7 28.9 1.0
C A:ALA106 3.7 23.8 1.0
C A:ASP104 3.7 21.9 1.0
CB A:LEU110 3.8 23.0 1.0
O A:SER105 3.8 22.1 1.0
C A:ARG109 3.8 20.0 1.0
CG2 A:VAL154 3.9 19.8 1.0
CA A:SER105 4.0 21.7 1.0
N A:ALA106 4.0 22.9 1.0
O A:ARG109 4.2 18.0 1.0
CG A:ASN113 4.3 17.1 1.0
N A:SER105 4.3 23.5 1.0
CG A:LEU110 4.4 23.9 1.0
CG A:LEU149 4.4 30.6 1.0
CA A:ALA106 4.4 23.5 1.0
N A:PRO107 4.6 23.1 1.0
CG1 A:VAL154 4.6 19.7 1.0
CB A:ARG109 4.6 19.8 1.0
CA A:ARG109 4.7 17.7 1.0
N A:ARG109 4.8 21.3 1.0
CB A:LEU149 4.8 29.1 1.0
C A:LEU110 4.8 23.0 1.0
CA A:PRO107 4.8 24.3 1.0
CB A:VAL154 4.9 21.2 1.0
CA A:ASP104 4.9 22.0 1.0
OD1 A:ASN113 5.0 17.4 1.0
O A:PRO107 5.0 26.0 1.0

Magnesium binding site 3 out of 6 in 3t1o

Go back to Magnesium Binding Sites List in 3t1o
Magnesium binding site 3 out of 6 in the Mgla Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mgla Bound to Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg199

b:34.4
occ:1.00
 O A:LEU129 2.6 19.6 1.0
O A:ARG121 2.8 14.4 1.0
N A:ALA125 3.3 17.1 1.0
CA A:THR130 3.4 20.8 1.0
C A:LEU129 3.6 21.1 1.0
CB A:LEU124 3.6 16.0 1.0
CG A:ARG121 3.6 20.1 1.0
CB A:ALA125 3.7 18.7 1.0
C A:ARG121 3.7 16.3 1.0
CA A:ALA125 3.8 18.6 1.0
C A:LEU124 3.9 16.6 1.0
C A:THR130 4.0 20.3 1.0
N A:THR130 4.0 19.8 1.0
CA A:ARG121 4.0 15.5 1.0
N A:LEU131 4.1 21.7 1.0
CA A:LEU124 4.3 16.6 1.0
O A:HOH225 4.3 20.1 1.0
CB A:ARG121 4.4 16.8 1.0
CB A:THR130 4.5 20.4 1.0
O A:LEU124 4.7 16.6 1.0
CD A:ARG121 4.8 30.9 1.0
O A:THR130 4.8 19.8 1.0
N A:LEU124 4.9 14.4 1.0
NE A:ARG121 4.9 32.7 1.0
CG2 A:THR130 4.9 23.5 1.0
CG A:LEU124 4.9 17.1 1.0
N A:GLU122 4.9 15.4 1.0
CA A:LEU129 5.0 21.1 1.0

Magnesium binding site 4 out of 6 in 3t1o

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Magnesium binding site 4 out of 6 in the Mgla Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mgla Bound to Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg200

b:46.4
occ:1.00
 OD1 A:ASP58 2.6 34.2 1.0
O A:GLU43 2.8 23.6 1.0
CA A:GLY42 2.8 25.9 1.0
C A:GLY42 2.9 24.4 1.0
N A:ASP58 2.9 20.3 1.0
N A:GLU43 3.0 24.8 1.0
CG A:ASP58 3.2 28.3 1.0
N A:GLY42 3.3 23.5 1.0
O A:ASP58 3.4 22.9 1.0
O A:GLY42 3.6 24.6 1.0
C A:GLU43 3.6 23.8 1.0
OD2 A:ASP58 3.6 34.9 1.0
CA A:PHE57 3.7 19.1 1.0
C A:PHE57 3.8 20.1 1.0
CA A:ASP58 3.8 22.5 1.0
CB A:PHE57 3.8 17.3 1.0
CA A:GLU43 3.9 25.6 1.0
CB A:ASP58 4.0 23.0 1.0
C A:ASP58 4.0 22.8 1.0
C A:LYS41 4.6 25.8 1.0
N A:MET44 4.7 22.9 1.0
O A:PHE57 5.0 19.1 1.0
CG A:PHE57 5.0 18.3 1.0
CB A:GLU43 5.0 27.8 1.0

Magnesium binding site 5 out of 6 in 3t1o

Go back to Magnesium Binding Sites List in 3t1o
Magnesium binding site 5 out of 6 in the Mgla Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mgla Bound to Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg197

b:27.3
occ:1.00
 NH2 B:ARG89 2.5 13.7 0.5
O B:VAL79 2.6 15.7 1.0
O B:GLY81 2.8 21.7 1.0
NZ B:LYS25 2.8 14.6 1.0
CE B:LYS25 3.3 13.6 1.0
N B:GLY81 3.5 20.1 1.0
CA B:GLY21 3.5 15.3 1.0
C B:PRO80 3.6 18.1 1.0
CZ B:ARG89 3.7 21.6 0.5
C B:VAL79 3.7 16.0 1.0
CG1 B:VAL83 3.8 27.9 1.0
CA B:PRO80 3.8 17.1 1.0
N B:GLY21 3.8 16.2 1.0
C B:GLY81 3.9 22.5 1.0
O B:PRO20 4.0 16.2 1.0
O2B B:GDP274 4.0 13.9 1.0
O B:GLY19 4.1 14.3 1.0
C B:PRO20 4.1 16.9 1.0
O B:PRO80 4.1 18.0 1.0
N B:PRO80 4.3 16.3 1.0
CA B:GLY81 4.3 20.6 1.0
NE B:ARG89 4.4 19.6 0.5
NH1 B:ARG89 4.6 30.6 0.5
C B:GLY21 4.6 14.9 1.0
N B:LEU22 4.6 12.6 1.0
O1B B:GDP274 4.7 13.0 1.0
CG1 B:VAL79 4.8 14.9 1.0
CD B:LYS25 4.8 15.6 1.0
PB B:GDP274 4.8 16.2 1.0
O B:HOH204 4.9 20.8 1.0
CB B:VAL79 4.9 14.3 1.0
CA B:VAL79 5.0 14.0 1.0

Magnesium binding site 6 out of 6 in 3t1o

Go back to Magnesium Binding Sites List in 3t1o
Magnesium binding site 6 out of 6 in the Mgla Bound to Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mgla Bound to Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg198

b:30.0
occ:1.00
 OE1 B:GLU50 3.0 27.6 1.0
N B:GLU50 3.1 29.1 1.0
CG B:GLU50 3.1 33.0 1.0
CB B:GLU50 3.3 32.4 1.0
CD B:GLU50 3.5 34.2 1.0
CA B:GLU50 3.8 30.0 1.0
CG2 B:THR49 4.1 28.9 1.0
C B:THR49 4.1 28.6 1.0
CA B:THR49 4.3 27.7 1.0
OG1 B:THR49 4.4 31.9 1.0
CB B:THR49 4.4 29.4 1.0
OE2 B:GLU50 4.7 32.1 1.0
N B:ASP51 4.9 25.9 0.5
C B:GLU50 4.9 29.4 1.0

Reference:

M.Miertzschke, C.Koerner, I.R.Vetter, D.Keilberg, E.Hot, S.Leonardy, L.Sogaard-Andersen, A.Wittinghofer. Structural Analysis of the Ras-Like G Protein Mgla and Its Cognate Gap Mglb and Implications For Bacterial Polarity. Embo J. V. 30 4185 2011.
ISSN: ISSN 0261-4189
PubMed: 21847100
DOI: 10.1038/EMBOJ.2011.291
Page generated: Thu Aug 15 11:17:56 2024

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