Atomistry » Magnesium » PDB 3srf-3t2b » 3t1o
Atomistry »
  Magnesium »
    PDB 3srf-3t2b »
      3t1o »

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

Go back to Magnesium Binding Sites List in 3t1o
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy