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Manganese in PDB 4una: The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 2 Days Incubation in 5MM Mn (State 4)

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 2 Days Incubation in 5MM Mn (State 4), PDB code: 4una 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) 46.285 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.517, 70.153, 106.704, 90.00, 119.83, 90.00
R / Rfree (%) 18.98 / 21.91

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 2 Days Incubation in 5MM Mn (State 4) (pdb code 4una). 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 2 Days Incubation in 5MM Mn (State 4), PDB code: 4una:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1188

b:53.3
occ:1.00
 OP1 B:DA14 2.0 57.2 1.0
OP3 K:DC16 2.1 52.6 1.0
O A:HOH2003 2.1 46.8 1.0
OD2 A:ASP21 2.2 47.5 1.0
O A:ALA116 2.3 45.4 1.0
OP2 K:DC16 2.7 53.3 1.0
P K:DC16 3.0 59.6 1.0
CG A:ASP21 3.0 45.3 1.0
OD1 A:ASP21 3.2 47.2 1.0
C A:ALA116 3.3 46.4 1.0
P B:DA14 3.4 53.3 1.0
CA A:ALA116 3.6 49.2 1.0
NZ A:LYS120 3.7 58.2 1.0
O5' B:DA14 3.7 61.1 1.0
MN A:MN1190 3.8 53.5 0.8
O5' K:DC16 4.0 50.3 1.0
OP1 K:DC16 4.1 49.0 1.0
O A:VAL115 4.2 47.0 1.0
O3' B:DA13 4.2 53.4 1.0
NE2 A:GLN42 4.2 56.1 1.0
CB A:ALA116 4.4 39.1 1.0
CB A:ASP21 4.5 46.2 1.0
N A:GLU117 4.5 41.4 1.0
OP2 B:DA14 4.5 55.2 1.0
OE1 A:GLN42 4.5 61.6 1.0
C4' B:DA14 4.5 53.9 1.0
C5' B:DA14 4.7 46.8 1.0
CD A:GLN42 4.7 59.6 1.0
N A:ALA116 4.8 40.8 1.0
OE1 A:GLU117 4.8 47.2 1.0
C5' K:DC16 4.9 49.0 1.0
C A:VAL115 4.9 44.5 1.0
CE A:LYS120 5.0 57.4 1.0
CA A:GLU117 5.0 42.3 1.0

Manganese binding site 2 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1189

b:48.0
occ:1.00
 OP1 C:DC15 2.1 43.5 1.0
OE2 A:GLU117 2.2 42.3 1.0
O A:GLY20 2.3 46.5 1.0
O A:HOH2002 2.4 41.6 1.0
OP1 B:DG15 2.4 55.5 1.0
O A:HOH2035 2.8 55.7 1.0
CD A:GLU117 3.1 43.3 1.0
P B:DG15 3.3 59.9 1.0
OE1 A:GLU117 3.4 47.2 1.0
C A:GLY20 3.4 47.5 1.0
P C:DC15 3.5 47.6 1.0
O5' B:DG15 3.5 55.3 1.0
OP2 B:DG15 3.6 44.0 1.0
ND2 A:ASN129 3.7 35.8 1.0
CA A:GLY20 3.9 41.8 1.0
O3' C:DA14 3.9 45.3 1.0
MN A:MN1190 4.0 53.5 0.8
O A:ILE19 4.1 39.9 1.0
C5' C:DC15 4.3 44.7 1.0
C4' C:DC15 4.4 47.9 1.0
CG A:GLU117 4.4 48.4 1.0
O5' C:DC15 4.4 47.3 1.0
OP2 C:DC15 4.5 44.5 1.0
N A:ASP21 4.6 45.3 1.0
C5' B:DG15 4.7 46.6 1.0
OD1 A:ASP21 4.7 47.2 1.0
O3' B:DA14 4.7 52.5 1.0
O A:HOH2024 4.7 44.9 1.0
CG A:ASN129 4.9 44.6 1.0
CA A:ASP21 4.9 45.9 1.0
N A:GLY20 4.9 37.5 1.0
C A:ILE19 4.9 40.2 1.0
C4' B:DG15 4.9 49.3 1.0

Manganese binding site 3 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1190

b:53.5
occ:0.77
 OP1 B:DG15 2.1 55.5 1.0
OD1 A:ASP21 2.3 47.2 1.0
OE1 A:GLU117 2.4 47.2 1.0
OP3 K:DC16 2.4 52.6 1.0
O3' C:DC15 2.6 46.7 1.0
O3' B:DA14 2.8 52.5 1.0
P B:DG15 3.1 59.9 1.0
CG A:ASP21 3.5 45.3 1.0
CD A:GLU117 3.5 43.3 1.0
C3' C:DC15 3.6 50.3 1.0
P K:DC16 3.6 59.6 1.0
C3' B:DA14 3.7 52.2 1.0
MN A:MN1188 3.8 53.3 1.0
C4' C:DC15 3.9 47.9 1.0
O A:ALA116 3.9 45.4 1.0
O5' K:DC16 3.9 50.3 1.0
O5' B:DG15 4.0 55.3 1.0
MN A:MN1189 4.0 48.0 1.0
O A:GLY20 4.0 46.5 1.0
C4' B:DA14 4.0 53.9 1.0
OP1 K:DC16 4.0 49.0 1.0
OE2 A:GLU117 4.1 42.3 1.0
OD2 A:ASP21 4.1 47.5 1.0
OP2 B:DG15 4.2 44.0 1.0
C A:ALA116 4.6 46.4 1.0
CA A:ASP21 4.6 45.9 1.0
CB A:ASP21 4.6 46.2 1.0
CG A:GLU117 4.6 48.4 1.0
C A:GLY20 4.6 47.5 1.0
OP2 K:DC16 4.7 53.3 1.0
CA A:GLU117 4.8 42.3 1.0
O4' B:DA14 4.8 54.9 1.0
O4' C:DC15 4.8 48.4 1.0
C5' C:DC15 4.9 44.7 1.0
C2' C:DC15 4.9 50.6 1.0
OP1 B:DA14 4.9 57.2 1.0
N A:ASP21 5.0 45.3 1.0

Manganese binding site 4 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1189

b:48.5
occ:1.00
 OE2 D:GLU117 1.9 46.6 1.0
OP1 F:DC15 2.1 46.9 1.0
O D:HOH2003 2.1 52.4 1.0
OP2 E:DG15 2.2 53.3 1.0
O D:GLY20 2.3 47.9 1.0
O D:HOH2002 2.4 41.6 1.0
CD D:GLU117 2.9 49.6 1.0
C D:GLY20 3.3 46.1 1.0
OE1 D:GLU117 3.4 55.1 1.0
P E:DG15 3.4 55.5 1.0
P F:DC15 3.6 48.8 1.0
ND2 D:ASN129 3.7 44.7 1.0
CA D:GLY20 3.8 41.6 1.0
MN D:MN1191 3.8 54.8 0.8
OP1 E:DG15 3.9 47.6 1.0
O5' E:DG15 4.0 46.8 1.0
O3' F:DA14 4.1 50.1 1.0
O D:ILE19 4.1 40.4 1.0
C5' E:DG15 4.2 44.1 1.0
CG D:GLU117 4.2 46.8 1.0
C4' F:DC15 4.3 53.1 1.0
O D:HOH2027 4.3 48.4 1.0
C5' F:DC15 4.3 46.3 1.0
O5' F:DC15 4.5 50.9 1.0
N D:ASP21 4.5 42.0 1.0
OD1 D:ASP21 4.5 46.5 1.0
OP2 F:DC15 4.6 47.8 1.0
O3' E:DA14 4.7 47.1 1.0
CG D:ASN129 4.8 49.4 1.0
CA D:ASP21 4.9 43.8 1.0
N D:GLY20 4.9 39.6 1.0
C D:ILE19 4.9 40.1 1.0
O3' F:DC15 5.0 51.2 1.0
C3' F:DC15 5.0 53.3 1.0

Manganese binding site 5 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1190

b:48.2
occ:1.00
 O D:HOH2004 1.9 43.5 1.0
OP1 E:DA14 2.1 48.3 1.0
OD2 D:ASP21 2.2 40.8 1.0
OP3 M:DC16 2.3 53.5 1.0
OP2 M:DC16 2.3 47.1 1.0
O D:ALA116 2.4 42.4 1.0
P M:DC16 2.9 56.8 1.0
CG D:ASP21 3.0 40.2 1.0
OD1 D:ASP21 3.1 46.5 1.0
C D:ALA116 3.4 44.5 1.0
P E:DA14 3.5 44.8 1.0
NZ D:LYS120 3.8 64.1 1.0
CA D:ALA116 3.8 41.0 1.0
MN D:MN1191 3.8 54.8 0.8
C5' E:DA14 3.9 46.0 1.0
O5' M:DC16 3.9 53.6 1.0
OP1 M:DC16 4.0 55.2 1.0
O3' E:DA13 4.1 47.7 1.0
NE2 D:GLN42 4.2 45.7 1.0
O D:VAL115 4.2 47.6 1.0
O5' E:DA14 4.2 41.8 1.0
C4' E:DA14 4.3 47.9 1.0
OE1 D:GLN42 4.3 48.7 1.0
CB D:ASP21 4.4 42.5 1.0
OE1 D:GLU117 4.5 55.1 1.0
N D:GLU117 4.6 45.7 1.0
OP2 E:DA14 4.6 45.0 1.0
C5' M:DC16 4.6 49.7 1.0
CB D:ALA116 4.6 38.1 1.0
CD D:GLN42 4.6 48.7 1.0
CE D:LYS120 4.8 63.1 1.0
N D:ALA116 4.9 41.0 1.0
C D:VAL115 5.0 43.1 1.0
CA D:GLU117 5.0 49.2 1.0

Manganese binding site 6 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1191

b:54.8
occ:0.75
 OP2 M:DC16 2.1 47.1 1.0
OE1 D:GLU117 2.2 55.1 1.0
OD1 D:ASP21 2.2 46.5 1.0
OP2 E:DG15 2.3 53.3 1.0
O3' F:DC15 2.4 51.2 1.0
O3' E:DA14 2.7 47.1 1.0
P E:DG15 3.1 55.5 1.0
CD D:GLU117 3.3 49.6 1.0
CG D:ASP21 3.4 40.2 1.0
P M:DC16 3.4 56.8 1.0
C3' F:DC15 3.4 53.3 1.0
C3' E:DA14 3.6 40.5 1.0
OE2 D:GLU117 3.7 46.6 1.0
MN D:MN1190 3.8 48.2 1.0
MN D:MN1189 3.8 48.5 1.0
O5' M:DC16 3.9 53.6 1.0
O E:HOH2001 3.9 53.9 1.0
C4' E:DA14 3.9 47.9 1.0
C4' F:DC15 3.9 53.1 1.0
O D:ALA116 4.0 42.4 1.0
O D:GLY20 4.0 47.9 1.0
OD2 D:ASP21 4.0 40.8 1.0
O5' E:DG15 4.1 46.8 1.0
OP1 M:DC16 4.2 55.2 1.0
OP1 E:DG15 4.2 47.6 1.0
OP3 M:DC16 4.5 53.5 1.0
CA D:ASP21 4.5 43.8 1.0
CB D:ASP21 4.5 42.5 1.0
C D:GLY20 4.5 46.1 1.0
CG D:GLU117 4.6 46.8 1.0
C D:ALA116 4.6 44.5 1.0
C5' E:DA14 4.7 46.0 1.0
C2' F:DC15 4.8 51.4 1.0
CA D:GLU117 4.8 49.2 1.0
N D:ASP21 4.9 42.0 1.0
O4' F:DC15 4.9 53.8 1.0
O D:HOH2003 4.9 52.4 1.0
OP1 F:DC15 4.9 46.9 1.0
C5' F:DC15 5.0 46.3 1.0
C2' E:DA14 5.0 46.5 1.0

Manganese binding site 7 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1180

b:42.3
occ:1.00
 OP1 H:DA14 2.0 45.6 1.0
OP3 O:DC16 2.1 41.5 1.0
O G:ALA116 2.2 33.6 1.0
O G:HOH2002 2.2 39.4 1.0
OD2 G:ASP21 2.4 39.6 1.0
OP2 O:DC16 2.6 43.2 1.0
P O:DC16 2.8 58.0 1.0
OD1 G:ASP21 3.0 35.4 1.0
CG G:ASP21 3.1 39.8 1.0
C G:ALA116 3.3 41.5 1.0
P H:DA14 3.5 49.9 1.0
OE1 G:GLN42 3.7 55.6 1.0
CA G:ALA116 3.7 38.2 1.0
NZ G:LYS120 3.9 51.1 1.0
O5' O:DC16 3.9 45.2 1.0
OP1 O:DC16 3.9 54.6 1.0
MN G:MN1182 4.0 54.4 0.8
C5' H:DA14 4.0 42.4 1.0
O3' H:DA13 4.2 49.8 1.0
C4' H:DA14 4.3 47.3 1.0
NE2 G:GLN42 4.3 49.8 1.0
O5' H:DA14 4.3 47.4 1.0
O G:VAL115 4.3 40.5 1.0
CD G:GLN42 4.3 52.7 1.0
OP2 H:DA14 4.4 39.6 1.0
N G:GLU117 4.4 40.4 1.0
CB G:ALA116 4.5 38.7 1.0
CB G:ASP21 4.6 38.1 1.0
C5' O:DC16 4.8 42.8 1.0
CA G:GLU117 4.8 43.6 1.0
N G:ALA116 4.9 37.3 1.0
CG G:GLU117 5.0 45.9 1.0

Manganese binding site 8 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1181

b:44.0
occ:1.00
 OE2 G:GLU117 1.8 53.4 1.0
OP1 I:DC15 2.0 35.4 1.0
OP2 H:DG15 2.1 39.7 1.0
O G:GLY20 2.4 38.3 1.0
O G:HOH2001 2.4 37.2 1.0
O G:HOH2030 2.8 51.3 1.0
CD G:GLU117 2.8 42.9 1.0
OE1 G:GLU117 3.4 50.2 1.0
P I:DC15 3.4 39.0 1.0
C G:GLY20 3.5 42.1 1.0
P H:DG15 3.5 50.0 1.0
MN G:MN1182 3.7 54.4 0.8
ND2 G:ASN129 3.8 40.0 1.0
O3' I:DA14 3.9 40.9 1.0
O5' H:DG15 3.9 50.1 1.0
CA G:GLY20 4.0 38.8 1.0
CG G:GLU117 4.0 45.9 1.0
O G:ILE19 4.1 39.9 1.0
C5' H:DG15 4.1 42.8 1.0
C5' I:DC15 4.2 42.1 1.0
O5' I:DC15 4.3 48.9 1.0
C4' I:DC15 4.4 45.1 1.0
O G:HOH2020 4.4 40.7 1.0
OP1 H:DG15 4.4 51.5 1.0
OP2 I:DC15 4.5 41.6 1.0
O3' H:DA14 4.5 48.7 1.0
N G:ASP21 4.6 37.1 1.0
CG G:ASN129 4.9 40.9 1.0
OD1 G:ASP21 4.9 35.4 1.0
CA G:ASP21 4.9 40.5 1.0
C G:ILE19 5.0 41.4 1.0
C4' H:DG15 5.0 43.1 1.0
N G:GLY20 5.0 39.7 1.0

Manganese binding site 9 out of 9 in 4una

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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 2 Days Incubation in 5MM Mn (State 4)


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 2 Days Incubation in 5MM Mn (State 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1182

b:54.4
occ:0.79
 OP3 O:DC16 2.6 41.5 1.0
O3' H:DA14 2.6 48.7 1.0
OD1 G:ASP21 2.6 35.4 1.0
O3' I:DC15 2.7 46.0 1.0
OP2 H:DG15 2.8 39.7 1.0
OE2 G:GLU117 2.9 53.4 1.0
CG G:GLU117 3.1 45.9 1.0
P H:DG15 3.2 50.0 1.0
CD G:GLU117 3.4 42.9 1.0
C3' I:DC15 3.6 46.6 1.0
C3' H:DA14 3.6 48.5 1.0
MN G:MN1181 3.7 44.0 1.0
O G:GLY20 3.7 38.3 1.0
C4' I:DC15 3.8 45.1 1.0
P O:DC16 3.8 58.0 1.0
CG G:ASP21 3.8 39.8 1.0
O5' O:DC16 3.9 45.2 1.0
C4' H:DA14 4.0 47.3 1.0
MN G:MN1180 4.0 42.3 1.0
O5' H:DG15 4.0 50.1 1.0
O G:ALA116 4.0 33.6 1.0
OP1 O:DC16 4.3 54.6 1.0
OP1 H:DG15 4.4 51.5 1.0
CB G:GLU117 4.4 47.6 1.0
C G:GLY20 4.5 42.1 1.0
OD2 G:ASP21 4.6 39.6 1.0
CA G:ASP21 4.6 40.5 1.0
C5' I:DC15 4.6 42.1 1.0
C G:ALA116 4.7 41.5 1.0
OE1 G:GLU117 4.7 50.2 1.0
OP1 I:DC15 4.7 35.4 1.0
CA G:GLU117 4.8 43.6 1.0
CB G:ASP21 4.8 38.1 1.0
O4' I:DC15 4.9 44.2 1.0
C5' H:DA14 4.9 42.4 1.0
N G:ASP21 4.9 37.1 1.0
C2' H:DA14 5.0 50.4 1.0
OP2 O:DC16 5.0 43.2 1.0
C2' I:DC15 5.0 48.5 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 21:22:51 2024

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