Atomistry » Magnesium » PDB 4ams-4av6 » 4aqx
Atomistry »
  Magnesium »
    PDB 4ams-4av6 »
      4aqx »

Magnesium in PDB 4aqx: Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium

Protein crystallography data

The structure of Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium, PDB code: 4aqx was solved by J.Valton, F.Daboussi, S.Leduc, P.Redondo, R.Macmaster, R.Molina, G.Montoya, P.Duchateau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.793 / 2.20
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.839, 71.401, 179.054, 90.00, 90.00, 90.00
R / Rfree (%) 20.15 / 24.18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium (pdb code 4aqx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium, PDB code: 4aqx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4aqx

Go back to Magnesium Binding Sites List in 4aqx
Magnesium binding site 1 out of 3 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium


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 I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1525

b:31.7
occ:1.00
OP1 F:DG615 2.1 34.7 1.0
O3' C:DA514 2.1 34.5 0.9
O3' E:5CM614 2.1 38.7 1.0
OP2 D:DG515 2.1 35.3 0.9
OD1 A:ASP20 2.2 34.9 1.0
OD1 B:ASP20 2.2 35.8 1.0
C3' E:5CM614 3.2 43.6 1.0
C3' C:DA514 3.3 35.1 0.9
P F:DG615 3.3 34.9 1.0
CG A:ASP20 3.3 38.0 1.0
P D:DG515 3.3 35.8 0.9
CG B:ASP20 3.4 39.2 1.0
O5' F:DG615 3.6 38.0 1.0
O5' D:DG515 3.7 28.7 0.9
MG D:MG1526 3.8 30.7 1.0
OD2 A:ASP20 3.8 31.5 1.0
O C:HOH2014 3.9 40.8 1.0
OP3 F:DG615 3.9 28.4 1.0
MG F:MG1625 3.9 40.2 1.0
C4' E:5CM614 3.9 36.4 1.0
OP1 D:DG515 3.9 33.9 0.9
OD2 B:ASP20 3.9 31.7 1.0
O A:GLY19 4.0 30.9 1.0
C4' C:DA514 4.0 30.1 0.9
O B:GLY19 4.0 32.6 1.0
O C:HOH2016 4.2 42.9 1.0
C2' E:5CM614 4.4 41.3 1.0
C2' C:DA514 4.5 27.7 0.9
OP2 F:DG615 4.5 37.4 1.0
OP3 D:DG515 4.5 29.1 0.9
CB A:ASP20 4.5 29.6 1.0
CB B:ASP20 4.6 35.3 1.0
C A:GLY19 4.6 35.6 1.0
CA A:ASP20 4.6 33.9 1.0
CA B:ASP20 4.6 30.2 1.0
C B:GLY19 4.7 34.3 1.0
C5' E:5CM614 4.8 37.0 1.0
OP2 E:5CM614 4.8 37.9 1.0
OP1 C:DA514 4.8 33.5 0.9
C1' E:5CM614 4.9 43.6 1.0
N A:ASP20 4.9 30.1 1.0
C5' C:DA514 4.9 31.1 0.9
C5' F:DG615 5.0 29.4 1.0

Magnesium binding site 2 out of 3 in 4aqx

Go back to Magnesium Binding Sites List in 4aqx
Magnesium binding site 2 out of 3 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium


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 I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1526

b:30.7
occ:1.00
OD2 B:ASP20 2.0 31.7 1.0
O A:GLY19 2.1 30.9 1.0
OP2 E:5CM614 2.1 37.9 1.0
OP2 D:DG515 2.1 35.3 0.9
O A:HOH2004 2.1 33.0 1.0
OP3 D:DG515 2.3 29.1 0.9
P D:DG515 2.7 35.8 0.9
CG B:ASP20 2.9 39.2 1.0
C A:GLY19 3.2 35.6 1.0
OD1 B:ASP20 3.2 35.8 1.0
P E:5CM614 3.6 41.3 1.0
O5' D:DG515 3.7 28.7 0.9
CA A:GLY19 3.7 36.1 1.0
MG D:MG1525 3.8 31.7 1.0
O A:HOH2043 3.9 46.7 1.0
OP1 D:DG515 3.9 33.9 0.9
O3' E:DA613 4.1 36.5 0.8
C5' E:5CM614 4.2 37.0 1.0
NE2 B:GLN47 4.2 34.1 1.0
OE1 B:GLN47 4.2 42.6 1.0
OD1 A:ASP20 4.3 34.9 1.0
O A:ASP18 4.3 39.4 1.0
N A:ASP20 4.3 30.1 1.0
C5' D:DG515 4.3 31.6 0.9
CB B:ASP20 4.3 35.3 1.0
O5' E:5CM614 4.4 42.0 1.0
C4' E:5CM614 4.4 36.4 1.0
OP1 E:5CM614 4.5 47.2 1.0
CD B:GLN47 4.6 42.8 1.0
O A:HOH2051 4.6 48.4 1.0
O3' E:5CM614 4.7 38.7 1.0
CA A:ASP20 4.8 33.9 1.0
C3' E:5CM614 4.8 43.6 1.0
N A:GLY19 4.9 34.1 1.0
O3' C:DA514 4.9 34.5 0.9

Magnesium binding site 3 out of 3 in 4aqx

Go back to Magnesium Binding Sites List in 4aqx
Magnesium binding site 3 out of 3 in the Crystal Structure of I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium


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 I-Crei Complexed with Its Target Methylated at Position Plus 2 (in the B Strand) in the Presence of Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1625

b:40.2
occ:1.00
OD2 A:ASP20 2.1 31.5 1.0
OP1 C:DA514 2.1 33.5 0.9
O A:HOH2006 2.1 28.4 1.0
OP1 F:DG615 2.2 34.7 1.0
OP2 F:DG615 2.2 37.4 1.0
O B:GLY19 2.3 32.6 1.0
P F:DG615 2.6 34.9 1.0
CG A:ASP20 3.1 38.0 1.0
C B:GLY19 3.4 34.3 1.0
OD1 A:ASP20 3.4 34.9 1.0
P C:DA514 3.4 27.4 0.9
O B:HOH2031 3.6 41.1 1.0
O5' F:DG615 3.7 38.0 1.0
OP3 F:DG615 3.8 28.4 1.0
O3' C:DG513 3.9 26.2 0.9
CA B:GLY19 3.9 33.7 1.0
MG D:MG1525 3.9 31.7 1.0
OE1 A:GLN47 4.1 36.1 1.0
O B:ASP18 4.2 27.8 1.0
NE2 A:GLN47 4.2 33.1 1.0
C5' C:DA514 4.2 31.1 0.9
C4' C:DA514 4.4 30.1 0.9
OD1 B:ASP20 4.4 35.8 1.0
O5' C:DA514 4.4 34.2 0.9
C5' F:DG615 4.4 29.4 1.0
CB A:ASP20 4.4 29.6 1.0
OP2 C:DA514 4.5 30.2 0.9
N B:ASP20 4.5 35.6 1.0
CD A:GLN47 4.6 36.7 1.0
O3' C:DA514 4.6 34.5 0.9
O B:HOH2038 4.6 39.7 1.0
C3' C:DA514 4.8 35.1 0.9
CA B:ASP20 4.9 30.2 1.0
N B:GLY19 5.0 33.5 1.0
O3' E:5CM614 5.0 38.7 1.0

Reference:

J.Valton, F.Daboussi, S.Leduc, R.Molina, P.Redondo, R.Macmaster, G.Montoya, P.Duchateau. 5'-Cytosine-Phosphoguanine (Cpg) Methylation Impacts the Activity of Natural and Engineered Meganucleases. J.Biol.Chem. V. 287 30139 2012.
ISSN: ISSN 0021-9258
PubMed: 22740697
DOI: 10.1074/JBC.M112.379966
Page generated: Mon Dec 14 09:08:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy