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Magnesium in PDB 4d6o: The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2), PDB code: 4d6o was solved by R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.489 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.888, 70.672, 107.143, 90.00, 119.80, 90.00
R / Rfree (%) 18.56 / 22.01

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) (pdb code 4d6o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2), PDB code: 4d6o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4d6o

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Magnesium binding site 1 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1186

b:29.2
occ:1.00
 O A:HOH2003 2.1 37.6 1.0
OP1 B:DA14 2.1 41.8 1.0
O A:ALA116 2.2 33.2 1.0
OD2 A:ASP21 2.3 38.8 1.0
OP2 C:DC16 2.3 39.6 1.0
OD1 A:ASP21 2.8 40.4 1.0
O A:HOH2037 2.8 44.6 1.0
CG A:ASP21 2.9 37.5 1.0
C A:ALA116 3.3 34.8 1.0
O A:HOH2002 3.6 28.9 1.0
P B:DA14 3.6 47.5 1.0
P C:DC16 3.7 42.7 1.0
CA A:ALA116 3.8 32.9 1.0
O5' C:DC16 4.2 42.8 1.0
OE1 A:GLN42 4.2 48.5 1.0
O3' B:DA13 4.3 44.9 1.0
O A:VAL115 4.3 33.2 1.0
NZ A:LYS120 4.3 47.5 1.0
CB A:ASP21 4.4 30.8 1.0
C4' B:DA14 4.4 44.0 1.0
C5' B:DA14 4.4 41.8 1.0
C5' C:DC16 4.4 38.3 1.0
N A:GLU117 4.4 32.8 1.0
OP1 C:DC16 4.5 43.9 1.0
NE2 A:GLN42 4.5 54.1 1.0
OP2 B:DA14 4.5 41.8 1.0
O5' B:DA14 4.5 44.1 1.0
CB A:ALA116 4.7 28.1 1.0
CD A:GLN42 4.8 41.9 1.0
O3' C:DC15 4.8 39.5 1.0
OE1 A:GLU117 4.8 45.0 1.0
CA A:GLU117 4.8 37.3 1.0
N A:ALA116 5.0 32.8 1.0

Magnesium binding site 2 out of 6 in 4d6o

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Magnesium binding site 2 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1187

b:42.7
occ:1.00
 OP1 C:DC15 2.0 35.4 1.0
OP2 B:DG15 2.1 41.4 1.0
OE2 A:GLU117 2.1 43.8 1.0
O A:GLY20 2.3 39.0 1.0
O A:HOH2057 2.6 48.0 1.0
CD A:GLU117 3.0 42.2 1.0
OE1 A:GLU117 3.2 45.0 1.0
C A:GLY20 3.3 40.4 1.0
P B:DG15 3.3 41.9 1.0
P C:DC15 3.4 32.8 1.0
CA A:GLY20 3.8 32.5 1.0
O A:HOH2002 3.8 28.9 1.0
O5' B:DG15 3.8 39.1 1.0
C5' B:DG15 3.8 36.1 1.0
O3' C:DA14 3.9 30.4 1.0
ND2 A:ASN129 3.9 31.2 1.0
O A:ILE19 3.9 34.3 1.0
OP1 B:DG15 4.0 40.3 1.0
CG A:GLU117 4.3 43.0 1.0
C4' C:DC15 4.4 32.5 1.0
OP2 C:DC15 4.4 34.0 1.0
C5' C:DC15 4.4 32.0 1.0
O5' C:DC15 4.5 36.5 1.0
N A:ASP21 4.5 31.8 1.0
O3' B:DA14 4.5 42.7 1.0
C A:ILE19 4.7 36.2 1.0
N A:GLY20 4.8 35.6 1.0
C4' B:DG15 4.8 39.2 1.0
CA A:ASP21 4.8 30.1 1.0
OD1 A:ASP21 4.9 40.4 1.0
CG A:ASN129 5.0 33.9 1.0

Magnesium binding site 3 out of 6 in 4d6o

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Magnesium binding site 3 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1196

b:25.3
occ:1.00
 O D:HOH2009 2.1 33.7 1.0
OP2 F:DC16 2.1 34.8 1.0
O D:ALA116 2.2 31.6 1.0
OP1 E:DA14 2.2 33.7 1.0
OD2 D:ASP21 2.4 36.4 1.0
O D:HOH2064 2.6 41.9 1.0
OD1 D:ASP21 2.8 36.5 1.0
CG D:ASP21 2.9 34.8 1.0
C D:ALA116 3.3 35.7 1.0
P F:DC16 3.5 39.6 1.0
O D:HOH2007 3.5 27.5 1.0
P E:DA14 3.7 35.8 1.0
NZ D:LYS120 3.8 52.5 1.0
CA D:ALA116 3.9 33.2 1.0
O5' F:DC16 4.1 39.4 1.0
OE1 D:GLN42 4.2 44.2 1.0
C5' E:DA14 4.2 30.6 1.0
OP1 F:DC16 4.2 38.8 1.0
NE2 D:GLN42 4.3 37.1 1.0
O D:VAL115 4.3 35.4 1.0
O3' E:DA13 4.3 38.6 1.0
C5' F:DC16 4.3 39.1 1.0
C4' E:DA14 4.4 36.0 1.0
CB D:ASP21 4.5 33.3 1.0
N D:GLU117 4.5 36.7 1.0
O5' E:DA14 4.5 36.8 1.0
O D:HOH2004 4.6 56.2 1.0
O3' F:DC15 4.6 42.1 1.0
CD D:GLN42 4.6 39.3 1.0
OP2 E:DA14 4.7 31.5 1.0
CB D:ALA116 4.7 28.1 1.0
OE1 D:GLU117 4.7 46.0 1.0
CA D:GLU117 4.9 39.0 1.0
N D:ALA116 5.0 29.0 1.0

Magnesium binding site 4 out of 6 in 4d6o

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Magnesium binding site 4 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1197

b:36.7
occ:1.00
 OE2 D:GLU117 2.0 42.0 1.0
OP1 F:DC15 2.0 37.5 1.0
OP2 E:DG15 2.0 38.9 1.0
O D:HOH2006 2.3 37.7 1.0
O D:GLY20 2.3 37.6 1.0
O D:HOH2008 2.3 41.5 1.0
CD D:GLU117 2.8 44.1 1.0
OE1 D:GLU117 3.0 46.0 1.0
C D:GLY20 3.3 38.9 1.0
P E:DG15 3.4 38.8 1.0
P F:DC15 3.5 39.5 1.0
O D:HOH2007 3.6 27.5 1.0
ND2 D:ASN129 3.8 37.0 1.0
CA D:GLY20 3.8 33.4 1.0
O5' E:DG15 3.9 43.7 1.0
O3' F:DA14 4.0 41.3 1.0
O D:ILE19 4.1 34.4 1.0
OP1 E:DG15 4.1 37.9 1.0
C5' E:DG15 4.2 38.4 1.0
C4' F:DC15 4.2 39.4 1.0
CG D:GLU117 4.2 39.9 1.0
C5' F:DC15 4.2 38.7 1.0
O5' F:DC15 4.4 41.1 1.0
OP2 F:DC15 4.5 37.6 1.0
N D:ASP21 4.5 31.7 1.0
O3' E:DA14 4.5 35.4 1.0
CA D:ASP21 4.8 30.4 1.0
OD1 D:ASP21 4.8 36.5 1.0
O D:HOH2069 4.8 46.8 1.0
N D:GLY20 4.9 31.8 1.0
O3' F:DC15 4.9 42.1 1.0
C D:ILE19 4.9 31.7 1.0
CG D:ASN129 4.9 38.3 1.0
C3' F:DC15 4.9 39.9 1.0

Magnesium binding site 5 out of 6 in 4d6o

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Magnesium binding site 5 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1183

b:25.9
occ:1.00
 OP1 H:DA14 2.1 37.0 1.0
O G:ALA116 2.2 29.4 1.0
O G:HOH2006 2.3 38.2 1.0
OP1 I:DC16 2.3 37.8 1.0
OD2 G:ASP21 2.3 39.0 1.0
O G:HOH2034 2.6 39.7 1.0
OD1 G:ASP21 2.8 33.1 1.0
CG G:ASP21 2.9 33.8 1.0
C G:ALA116 3.3 32.5 1.0
O G:HOH2005 3.5 27.2 1.0
P H:DA14 3.6 38.5 1.0
P I:DC16 3.7 42.3 1.0
CA G:ALA116 3.8 33.4 1.0
NE2 G:GLN42 4.0 59.5 1.0
C5' H:DA14 4.2 33.2 1.0
O5' I:DC16 4.3 40.5 1.0
O3' H:DA13 4.3 41.2 1.0
C4' H:DA14 4.4 33.5 1.0
O G:VAL115 4.4 34.5 1.0
OE1 G:GLN42 4.4 78.0 1.0
O G:HOH2032 4.4 46.8 1.0
CB G:ASP21 4.4 29.9 1.0
O5' H:DA14 4.5 40.2 1.0
C5' I:DC16 4.5 39.1 1.0
OP2 I:DC16 4.5 46.4 1.0
CD G:GLN42 4.5 47.7 1.0
OP2 H:DA14 4.5 35.7 1.0
N G:GLU117 4.5 31.2 1.0
CB G:ALA116 4.6 29.6 1.0
O3' I:DC15 4.8 38.9 1.0
NZ G:LYS120 4.9 70.2 1.0
CA G:GLU117 4.9 39.6 1.0
CE G:LYS120 5.0 61.3 1.0

Magnesium binding site 6 out of 6 in 4d6o

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Magnesium binding site 6 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mg (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1184

b:39.9
occ:1.00
 OP1 H:DG15 2.0 36.3 1.0
OP1 I:DC15 2.1 34.8 1.0
O G:GLY20 2.1 35.9 1.0
O G:HOH2004 2.3 39.7 1.0
OE2 G:GLU117 2.3 48.5 1.0
OE1 G:GLU117 2.9 43.4 1.0
CD G:GLU117 2.9 42.0 1.0
C G:GLY20 3.2 37.6 1.0
P H:DG15 3.3 38.9 1.0
P I:DC15 3.5 33.8 1.0
O G:HOH2005 3.6 27.2 1.0
O5' H:DG15 3.7 41.6 1.0
CA G:GLY20 3.7 30.6 1.0
C5' H:DG15 3.9 38.4 1.0
ND2 G:ASN129 3.9 38.2 1.0
O3' I:DA14 4.0 30.2 1.0
O G:ILE19 4.0 35.9 1.0
OP2 H:DG15 4.1 35.4 1.0
C4' I:DC15 4.3 32.4 1.0
N G:ASP21 4.3 31.3 1.0
C5' I:DC15 4.4 35.5 1.0
CG G:GLU117 4.4 42.5 1.0
O G:HOH2038 4.4 52.9 1.0
O3' H:DA14 4.4 43.7 1.0
O5' I:DC15 4.5 37.9 1.0
OP2 I:DC15 4.5 32.6 1.0
CA G:ASP21 4.7 27.2 1.0
OD1 G:ASP21 4.8 33.1 1.0
N G:GLY20 4.8 34.5 1.0
C G:ILE19 4.8 35.8 1.0
C4' H:DG15 4.9 34.9 1.0
O3' I:DC15 5.0 38.9 1.0
O I:HOH2006 5.0 45.0 1.0

Reference:

R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya. Visualizing Phosphodiester-Bond Hydrolysis By An Endonuclease. Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25486305
DOI: 10.1038/NSMB.2932
Page generated: Mon Aug 11 07:24:38 2025

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