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Manganese in PDB 4unc: The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6), PDB code: 4unc 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) 46.273 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.803, 70.409, 107.172, 90.00, 119.77, 90.00
R / Rfree (%) 18.47 / 22.45

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) (pdb code 4unc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6), PDB code: 4unc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 4unc

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Manganese binding site 1 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1188

b:43.9
occ:1.00
 OP1 B:DA14 2.0 47.4 1.0
O A:HOH2004 2.0 35.2 1.0
OP3 K:DC16 2.2 53.8 1.0
OD2 A:ASP21 2.2 42.8 1.0
O A:ALA116 2.3 43.4 1.0
OP2 K:DC16 2.5 49.5 1.0
P K:DC16 2.9 52.1 1.0
CG A:ASP21 3.1 41.7 1.0
OD1 A:ASP21 3.2 44.8 1.0
C A:ALA116 3.4 40.0 1.0
P B:DA14 3.4 44.1 1.0
CA A:ALA116 3.8 38.3 1.0
O5' K:DC16 3.9 45.1 1.0
NZ A:LYS120 3.9 45.0 1.0
MN A:MN1190 4.0 44.8 0.7
O3' B:DA13 4.0 44.6 1.0
OP1 K:DC16 4.0 48.7 1.0
C5' B:DA14 4.2 45.2 1.0
C4' B:DA14 4.2 47.7 1.0
O A:VAL115 4.3 41.8 1.0
NE2 A:GLN42 4.3 53.9 1.0
O5' B:DA14 4.4 52.3 1.0
OP2 B:DA14 4.4 50.9 1.0
CB A:ASP21 4.5 38.1 1.0
OE1 A:GLN42 4.5 57.8 1.0
N A:GLU117 4.6 39.1 1.0
O3' B:DA14 4.7 46.9 1.0
CB A:ALA116 4.7 36.1 1.0
C5' K:DC16 4.7 45.1 1.0
OE1 A:GLU117 4.7 51.4 1.0
C3' B:DA14 4.8 47.4 1.0
CD A:GLN42 4.8 53.5 1.0
CE A:LYS120 4.8 55.1 1.0
N A:ALA116 5.0 39.9 1.0

Manganese binding site 2 out of 9 in 4unc

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Manganese binding site 2 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1189

b:41.0
occ:1.00
 OE2 A:GLU117 1.9 43.6 1.0
OP1 C:DC15 2.1 39.2 1.0
O A:HOH2003 2.2 33.7 1.0
OP1 J:DG15 2.3 46.5 1.0
O A:GLY20 2.4 39.8 1.0
OP2 J:DG15 2.7 40.5 1.0
P J:DG15 2.9 42.9 1.0
CD A:GLU117 3.1 41.9 1.0
C A:GLY20 3.4 41.2 1.0
P C:DC15 3.5 39.0 1.0
OE1 A:GLU117 3.7 51.4 1.0
O C:HOH2004 3.7 46.8 1.0
O3' C:DA14 3.8 42.3 1.0
MN A:MN1190 3.8 44.8 0.7
ND2 A:ASN129 3.8 38.2 1.0
CA A:GLY20 3.9 38.3 1.0
O5' J:DG15 3.9 46.6 1.0
O A:ILE19 4.0 37.0 1.0
CG A:GLU117 4.1 39.8 1.0
OP3 J:DG15 4.1 42.4 1.0
C5' C:DC15 4.3 42.1 1.0
C4' C:DC15 4.3 42.7 1.0
O5' C:DC15 4.4 41.7 1.0
C5' J:DG15 4.5 40.1 1.0
OP2 C:DC15 4.5 38.1 1.0
N A:ASP21 4.6 35.2 1.0
OD1 A:ASP21 4.7 44.8 1.0
N A:GLY20 4.9 34.6 1.0
C A:ILE19 4.9 36.9 1.0
CG A:ASN129 4.9 41.3 1.0
O A:HOH2021 4.9 38.0 1.0

Manganese binding site 3 out of 9 in 4unc

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Manganese binding site 3 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1190

b:44.8
occ:0.72
 OP2 J:DG15 2.2 40.5 1.0
OE1 A:GLU117 2.2 51.4 1.0
OD1 A:ASP21 2.3 44.8 1.0
O3' B:DA14 2.6 46.9 1.0
OP3 K:DC16 2.6 53.8 1.0
O3' C:DC15 2.7 46.0 1.0
CD A:GLU117 3.0 41.9 1.0
OE2 A:GLU117 3.3 43.6 1.0
CG A:ASP21 3.5 41.7 1.0
P J:DG15 3.5 42.9 1.0
O A:GLY20 3.6 39.8 1.0
C3' C:DC15 3.6 38.3 1.0
C3' B:DA14 3.7 47.4 1.0
MN A:MN1189 3.8 41.0 1.0
O5' J:DG15 3.8 46.6 1.0
P K:DC16 3.8 52.1 1.0
MN A:MN1188 4.0 43.9 1.0
O5' K:DC16 4.0 45.1 1.0
C4' C:DC15 4.0 42.7 1.0
O A:ALA116 4.0 43.4 1.0
OD2 A:ASP21 4.1 42.8 1.0
C A:GLY20 4.4 41.2 1.0
C4' B:DA14 4.4 47.7 1.0
CG A:GLU117 4.4 39.8 1.0
OP1 K:DC16 4.4 48.7 1.0
O B:HOH2004 4.5 48.1 1.0
CA A:ASP21 4.5 37.9 1.0
OP3 J:DG15 4.5 42.4 1.0
OP1 J:DG15 4.5 46.5 1.0
CB A:ASP21 4.6 38.1 1.0
C A:ALA116 4.6 40.0 1.0
CA A:GLU117 4.8 42.5 1.0
N A:ASP21 4.8 35.2 1.0
OP2 K:DC16 4.9 49.5 1.0
CB A:GLU117 4.9 42.8 1.0
O4' C:DC15 5.0 41.4 1.0
OP1 C:DC15 5.0 39.2 1.0
C2' B:DA14 5.0 44.7 1.0

Manganese binding site 4 out of 9 in 4unc

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Manganese binding site 4 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1197

b:43.9
occ:1.00
 O D:HOH2006 2.0 35.4 1.0
OP1 E:DA14 2.0 41.1 1.0
OP2 M:DC16 2.1 54.1 1.0
OD2 D:ASP21 2.2 41.4 1.0
O D:ALA116 2.3 37.9 1.0
OP3 M:DC16 2.4 47.7 1.0
P M:DC16 2.7 54.1 1.0
CG D:ASP21 3.1 38.2 1.0
OD1 D:ASP21 3.3 42.0 1.0
C D:ALA116 3.4 45.5 1.0
P E:DA14 3.5 42.4 1.0
NZ D:LYS120 3.6 52.8 1.0
OP1 M:DC16 3.8 49.0 1.0
O5' M:DC16 3.9 53.0 1.0
MN D:MN1199 3.9 46.6 0.8
CA D:ALA116 3.9 42.5 1.0
O3' E:DA13 4.0 48.0 1.0
OE1 D:GLN42 4.2 58.7 1.0
O D:VAL115 4.2 42.8 1.0
NE2 D:GLN42 4.2 49.4 1.0
C5' E:DA14 4.2 42.8 1.0
C4' E:DA14 4.3 41.7 1.0
O5' E:DA14 4.4 42.3 1.0
CB D:ASP21 4.5 37.2 1.0
OP2 E:DA14 4.5 42.4 1.0
CD D:GLN42 4.6 53.0 1.0
N D:GLU117 4.6 45.3 1.0
C5' M:DC16 4.6 51.4 1.0
O3' E:DA14 4.7 43.8 1.0
OE1 D:GLU117 4.8 46.2 1.0
CB D:ALA116 4.8 33.2 1.0
C3' E:DA14 4.8 42.6 1.0
N D:ALA116 5.0 39.1 1.0
CA D:GLU117 5.0 48.6 1.0

Manganese binding site 5 out of 9 in 4unc

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Manganese binding site 5 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1198

b:47.0
occ:1.00
 OE2 D:GLU117 2.0 45.4 1.0
OP2 L:DG15 2.1 41.2 1.0
OP1 F:DC15 2.2 48.6 1.0
O D:HOH2005 2.2 41.2 1.0
O D:GLY20 2.4 45.0 1.0
OP3 L:DG15 2.5 51.8 1.0
P L:DG15 2.8 48.7 1.0
CD D:GLU117 2.9 42.4 1.0
OE1 D:GLU117 3.2 46.2 1.0
C D:GLY20 3.4 43.4 1.0
P F:DC15 3.5 43.5 1.0
O5' L:DG15 3.8 42.3 1.0
O3' F:DA14 3.8 48.3 1.0
CA D:GLY20 3.8 40.9 1.0
OD1 D:ASN129 3.8 46.8 1.0
MN D:MN1199 3.9 46.6 0.8
OP1 L:DG15 4.1 45.5 1.0
O D:ILE19 4.1 41.9 1.0
CG D:GLU117 4.3 46.4 1.0
C4' F:DC15 4.3 46.3 1.0
C5' L:DG15 4.3 42.6 1.0
C5' F:DC15 4.4 44.0 1.0
O5' F:DC15 4.5 47.6 1.0
OP2 F:DC15 4.5 46.6 1.0
OD1 D:ASP21 4.6 42.0 1.0
N D:ASP21 4.6 41.0 1.0
O D:HOH2028 4.6 50.5 1.0
CG D:ASN129 4.8 48.7 1.0
N D:GLY20 4.9 36.0 1.0
O3' F:DC15 4.9 50.5 1.0
C D:ILE19 4.9 39.3 1.0
C3' F:DC15 5.0 48.9 1.0
CA D:ASP21 5.0 39.3 1.0

Manganese binding site 6 out of 9 in 4unc

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Manganese binding site 6 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1199

b:46.6
occ:0.82
 OE1 D:GLU117 2.1 46.2 1.0
OP3 L:DG15 2.2 51.8 1.0
OD1 D:ASP21 2.3 42.0 1.0
OP2 M:DC16 2.3 54.1 1.0
O3' E:DA14 2.5 43.8 1.0
O3' F:DC15 2.5 50.5 1.0
CD D:GLU117 3.3 42.4 1.0
CG D:ASP21 3.4 38.2 1.0
P M:DC16 3.5 54.1 1.0
C3' F:DC15 3.6 48.9 1.0
C3' E:DA14 3.6 42.6 1.0
P L:DG15 3.6 48.7 1.0
O E:HOH2002 3.7 52.7 1.0
O5' M:DC16 3.8 53.0 1.0
MN D:MN1198 3.9 47.0 1.0
O5' L:DG15 3.9 42.3 1.0
MN D:MN1197 3.9 43.9 1.0
OE2 D:GLU117 3.9 45.4 1.0
O D:ALA116 3.9 37.9 1.0
O D:GLY20 3.9 45.0 1.0
OD2 D:ASP21 4.0 41.4 1.0
C4' F:DC15 4.0 46.3 1.0
OP1 M:DC16 4.2 49.0 1.0
C4' E:DA14 4.2 41.7 1.0
OP1 L:DG15 4.3 45.5 1.0
CG D:GLU117 4.5 46.4 1.0
OP2 L:DG15 4.5 41.2 1.0
C D:GLY20 4.5 43.4 1.0
CA D:ASP21 4.5 39.3 1.0
CB D:ASP21 4.6 37.2 1.0
C D:ALA116 4.6 45.5 1.0
OP3 M:DC16 4.7 47.7 1.0
CA D:GLU117 4.7 48.6 1.0
C2' E:DA14 4.8 43.2 1.0
CB D:GLU117 4.9 44.9 1.0
C2' F:DC15 4.9 47.7 1.0
N D:ASP21 4.9 41.0 1.0
O4' F:DC15 4.9 54.8 1.0

Manganese binding site 7 out of 9 in 4unc

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Manganese binding site 7 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1181

b:46.6
occ:1.00
 OP3 O:DC16 2.1 46.5 1.0
OP1 H:DA14 2.1 52.5 1.0
OD2 G:ASP21 2.2 46.8 1.0
O G:HOH2003 2.2 44.6 1.0
O G:ALA116 2.2 44.0 1.0
OP2 O:DC16 2.4 52.5 1.0
P O:DC16 2.8 60.8 1.0
CG G:ASP21 3.1 39.3 1.0
OD1 G:ASP21 3.3 40.1 1.0
C G:ALA116 3.3 43.6 1.0
P H:DA14 3.6 48.3 1.0
CA G:ALA116 3.8 43.8 1.0
OP1 O:DC16 3.8 56.2 1.0
MN G:MN1183 3.9 48.6 0.7
O5' O:DC16 4.0 51.2 1.0
OE1 G:GLN42 4.0 58.1 1.0
O3' H:DA13 4.1 50.2 1.0
O G:VAL115 4.2 50.8 1.0
NE2 G:GLN42 4.3 53.1 1.0
C4' H:DA14 4.3 48.5 1.0
C5' H:DA14 4.4 43.0 1.0
OP2 H:DA14 4.4 44.9 1.0
CB G:ASP21 4.4 40.3 1.0
N G:GLU117 4.5 44.3 1.0
CD G:GLN42 4.5 54.8 1.0
O5' H:DA14 4.5 49.5 1.0
CB G:ALA116 4.7 41.7 1.0
O3' H:DA14 4.8 42.0 1.0
C5' O:DC16 4.8 44.9 1.0
CA G:GLU117 4.8 46.6 1.0
C3' H:DA14 4.8 46.3 1.0
N G:ALA116 4.9 43.1 1.0

Manganese binding site 8 out of 9 in 4unc

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Manganese binding site 8 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1182

b:44.8
occ:1.00
 OP2 N:DG15 2.0 42.5 1.0
OP1 I:DC15 2.0 40.0 1.0
O G:HOH2002 2.2 37.9 1.0
OE2 G:GLU117 2.2 68.0 1.0
O G:GLY20 2.4 35.1 1.0
OP3 N:DG15 2.8 45.9 1.0
CD G:GLU117 2.9 48.7 1.0
P N:DG15 2.9 44.2 1.0
OE1 G:GLU117 2.9 52.4 1.0
P I:DC15 3.4 42.4 1.0
C G:GLY20 3.5 37.5 1.0
O I:HOH2005 3.6 40.0 1.0
O3' I:DA14 3.7 40.2 1.0
O5' N:DG15 3.9 47.8 1.0
MN G:MN1183 3.9 48.6 0.7
CA G:GLY20 3.9 35.9 1.0
ND2 G:ASN129 4.0 42.7 1.0
O G:ILE19 4.0 49.2 1.0
OP1 N:DG15 4.1 52.7 1.0
C5' I:DC15 4.2 45.1 1.0
C4' I:DC15 4.3 43.4 1.0
O5' I:DC15 4.3 44.4 1.0
CG G:GLU117 4.3 39.7 1.0
C5' N:DG15 4.4 47.2 1.0
OP2 I:DC15 4.5 42.5 1.0
O I:HOH2004 4.5 47.4 1.0
N G:ASP21 4.6 35.8 1.0
OD1 G:ASP21 4.6 40.1 1.0
C G:ILE19 4.9 42.9 1.0
N G:GLY20 4.9 44.9 1.0
CA G:ASP21 5.0 34.4 1.0

Manganese binding site 9 out of 9 in 4unc

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Manganese binding site 9 out of 9 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8 Days Incubation in 5MM Mn (State 6) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1183

b:48.6
occ:0.70
 OP3 N:DG15 2.2 45.9 1.0
OD1 G:ASP21 2.3 40.1 1.0
OE1 G:GLU117 2.3 52.4 1.0
OP3 O:DC16 2.5 46.5 1.0
O3' I:DC15 2.6 46.3 1.0
O3' H:DA14 2.6 42.0 1.0
O H:HOH2001 3.4 48.5 1.0
CG G:ASP21 3.5 39.3 1.0
CD G:GLU117 3.5 48.7 1.0
P N:DG15 3.6 44.2 1.0
C3' I:DC15 3.6 47.4 1.0
C3' H:DA14 3.8 46.3 1.0
P O:DC16 3.8 60.8 1.0
O G:GLY20 3.8 35.1 1.0
O5' O:DC16 3.9 51.2 1.0
MN G:MN1182 3.9 44.8 1.0
O G:ALA116 3.9 44.0 1.0
O5' N:DG15 3.9 47.8 1.0
MN G:MN1181 3.9 46.6 1.0
C4' I:DC15 4.0 43.4 1.0
OD2 G:ASP21 4.1 46.8 1.0
OP2 N:DG15 4.3 42.5 1.0
OE2 G:GLU117 4.3 68.0 1.0
C4' H:DA14 4.3 48.5 1.0
CG G:GLU117 4.4 39.7 1.0
OP1 O:DC16 4.4 56.2 1.0
C G:GLY20 4.4 37.5 1.0
OP1 N:DG15 4.5 52.7 1.0
CA G:ASP21 4.5 34.4 1.0
C G:ALA116 4.5 43.6 1.0
CB G:ASP21 4.6 40.3 1.0
CA G:GLU117 4.6 46.6 1.0
CB G:GLU117 4.7 52.7 1.0
OP2 O:DC16 4.8 52.5 1.0
N G:ASP21 4.9 35.8 1.0
N G:GLU117 4.9 44.3 1.0
C2' I:DC15 4.9 44.0 1.0
OP1 H:DA14 5.0 52.5 1.0
C5' I:DC15 5.0 45.1 1.0
O4' I:DC15 5.0 46.2 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: Sat Oct 5 21:23:19 2024

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