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Manganese in PDB 5ak9: The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn, PDB code: 5ak9 was solved by R.Molina, M.J.Marcaida, P.Redondo, M.Marenchino, M.D'abramo, G.Montoya, J.Prieto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.95 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.530, 70.880, 107.680, 90.00, 119.78, 90.00
R / Rfree (%) 17 / 22.2

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn (pdb code 5ak9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn, PDB code: 5ak9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5ak9

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Manganese binding site 1 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn


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 Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1188

b:35.4
occ:1.00
 OP1 B:DA14 2.3 28.9 1.0
OP2 D:DC16 2.3 19.4 1.0
O A:ALA116 2.4 29.3 1.0
OD2 A:ASP21 2.5 17.7 1.0
OD1 A:ASP21 2.8 21.6 1.0
CG A:ASP21 3.0 23.9 1.0
O A:HOH2005 3.4 9.0 1.0
C A:ALA116 3.5 23.0 1.0
P D:DC16 3.6 32.2 1.0
P B:DA14 3.7 27.1 1.0
O B:HOH2006 4.0 49.1 1.0
CA A:ALA116 4.1 16.7 1.0
O5' D:DC16 4.1 26.5 1.0
O A:HOH2039 4.3 37.2 1.0
C4' B:DA14 4.3 30.9 1.0
C5' B:DA14 4.4 32.4 1.0
C5' D:DC16 4.4 23.0 1.0
O3' B:DA13 4.4 28.5 1.0
OP1 D:DC16 4.5 32.9 1.0
CB A:ASP21 4.5 28.7 1.0
O A:HOH2006 4.5 24.1 1.0
O5' B:DA14 4.5 41.8 1.0
OP2 B:DA14 4.6 47.3 1.0
O A:VAL115 4.6 29.4 1.0
N A:GLU117 4.7 23.8 1.0
O3' D:DC15 4.7 27.4 1.0
CB A:ALA116 4.8 15.5 1.0
O3' B:DA14 4.9 18.5 1.0
C3' B:DA14 4.9 29.2 1.0
OE1 A:GLU117 5.0 28.1 1.0

Manganese binding site 2 out of 6 in 5ak9

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Manganese binding site 2 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn


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 Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1189

b:37.9
occ:1.00
 OP1 D:DC15 2.1 27.4 1.0
O A:GLY20 2.3 16.9 1.0
O A:HOH2004 2.3 37.1 1.0
OE2 A:GLU117 2.4 25.3 1.0
OP1 C:DG15 2.5 53.8 1.0
OP3 C:DG15 2.6 36.0 1.0
OE1 A:GLU117 3.0 28.1 1.0
CD A:GLU117 3.0 27.3 1.0
P C:DG15 3.1 42.0 1.0
C A:GLY20 3.4 21.5 1.0
P D:DC15 3.6 28.6 1.0
O A:HOH2005 3.8 9.0 1.0
O5' C:DG15 3.8 36.2 1.0
CA A:GLY20 3.9 31.0 1.0
ND2 A:ASN129 4.0 27.8 1.0
O A:ILE19 4.1 22.9 1.0
C5' C:DG15 4.2 35.8 1.0
O3' D:DA14 4.2 32.1 1.0
O C:HOH2002 4.2 54.6 1.0
C4' D:DC15 4.2 30.9 1.0
C5' D:DC15 4.3 29.5 1.0
O5' D:DC15 4.4 31.9 1.0
OP2 C:DG15 4.4 48.9 1.0
CG A:GLU117 4.4 26.1 1.0
O A:HOH2040 4.5 32.5 1.0
OP2 D:DC15 4.5 25.7 1.0
N A:ASP21 4.5 23.1 1.0
O3' B:DA14 4.8 18.5 1.0
OD1 A:ASP21 4.9 21.6 1.0
C A:ILE19 4.9 25.7 1.0
CA A:ASP21 4.9 28.0 1.0
N A:GLY20 4.9 32.0 1.0
C3' D:DC15 4.9 29.2 1.0
O3' D:DC15 5.0 27.4 1.0

Manganese binding site 3 out of 6 in 5ak9

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Manganese binding site 3 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn


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 Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1188

b:39.0
occ:1.00
 OP2 H:DC16 2.3 21.8 1.0
OP1 F:DA14 2.3 36.6 1.0
O E:ALA116 2.4 31.6 1.0
OD2 E:ASP21 2.5 32.8 1.0
O E:HOH2034 2.7 36.0 1.0
OD1 E:ASP21 2.8 28.1 1.0
O E:HOH2033 3.0 40.0 1.0
CG E:ASP21 3.0 30.6 1.0
C E:ALA116 3.4 22.7 1.0
O E:HOH2007 3.7 13.1 1.0
P H:DC16 3.7 28.0 1.0
P F:DA14 3.8 41.4 1.0
CA E:ALA116 3.8 15.7 1.0
O5' H:DC16 4.3 21.1 1.0
O E:HOH2032 4.3 35.8 1.0
O3' F:DA13 4.4 25.6 1.0
C4' F:DA14 4.4 43.5 1.0
O E:VAL115 4.4 38.0 1.0
C5' H:DC16 4.4 26.7 1.0
C5' F:DA14 4.4 39.0 1.0
OP1 H:DC16 4.5 36.5 1.0
CB E:ASP21 4.5 26.8 1.0
N E:GLU117 4.6 25.0 1.0
CB E:ALA116 4.6 9.8 1.0
O5' F:DA14 4.6 43.6 1.0
OP2 F:DA14 4.7 54.6 1.0
O3' F:DA14 4.8 35.0 1.0
O3' H:DC15 4.8 18.6 1.0
C3' F:DA14 4.9 40.5 1.0
N E:ALA116 5.0 24.4 1.0

Manganese binding site 4 out of 6 in 5ak9

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Manganese binding site 4 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn


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 Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1189

b:48.0
occ:1.00
 OP1 H:DC15 2.2 35.5 1.0
O E:GLY20 2.3 42.6 1.0
OE2 E:GLU117 2.4 40.9 1.0
O E:HOH2005 2.6 32.7 1.0
OP1 G:DG15 2.6 62.3 1.0
OP3 G:DG15 2.7 40.3 1.0
OE1 E:GLU117 3.0 34.7 1.0
CD E:GLU117 3.0 34.9 1.0
P G:DG15 3.2 54.6 1.0
C E:GLY20 3.3 27.4 1.0
O E:HOH2006 3.5 33.3 1.0
P H:DC15 3.5 30.3 1.0
CA E:GLY20 3.8 25.4 1.0
O5' G:DG15 3.9 30.3 1.0
O E:HOH2007 3.9 13.1 1.0
O E:ILE19 3.9 38.9 1.0
O3' H:DA14 4.0 24.3 1.0
ND2 E:ASN129 4.1 17.3 1.0
C5' G:DG15 4.3 29.6 1.0
CG E:GLU117 4.4 34.4 1.0
C4' H:DC15 4.4 22.0 1.0
C5' H:DC15 4.4 23.6 1.0
O5' H:DC15 4.5 36.2 1.0
N E:ASP21 4.5 19.9 1.0
OP2 H:DC15 4.5 37.4 1.0
OP2 G:DG15 4.5 69.4 1.0
O G:HOH2002 4.6 52.1 1.0
C E:ILE19 4.8 28.0 1.0
N E:GLY20 4.8 24.7 1.0
O3' F:DA14 4.9 35.0 1.0
CA E:ASP21 5.0 24.3 1.0

Manganese binding site 5 out of 6 in 5ak9

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Manganese binding site 5 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn


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 Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1187

b:41.6
occ:1.00
 OP1 K:DA14 2.3 40.2 1.0
O J:ALA116 2.4 33.9 1.0
OP2 N:DC16 2.4 26.9 1.0
OD2 J:ASP21 2.6 37.3 1.0
O J:HOH2059 2.7 44.7 1.0
OD1 J:ASP21 2.8 34.2 1.0
CG J:ASP21 3.1 34.0 1.0
C J:ALA116 3.4 32.8 1.0
O J:HOH2004 3.7 31.1 1.0
P K:DA14 3.7 30.3 1.0
O J:HOH2037 3.8 37.4 1.0
CA J:ALA116 3.8 23.2 1.0
P N:DC16 3.8 30.9 1.0
O5' N:DC16 4.4 29.4 1.0
O3' K:DA13 4.4 36.1 1.0
CB J:ALA116 4.4 12.9 1.0
O J:VAL115 4.4 32.4 1.0
C5' N:DC16 4.5 31.9 1.0
C4' K:DA14 4.5 34.6 1.0
O J:HOH2005 4.5 25.8 1.0
OP1 N:DC16 4.5 29.2 1.0
C5' K:DA14 4.5 26.1 1.0
CB J:ASP21 4.5 29.3 1.0
N J:GLU117 4.6 31.8 1.0
OP2 K:DA14 4.6 44.0 1.0
O5' K:DA14 4.7 34.1 1.0
O3' N:DC15 4.9 20.5 1.0
O3' K:DA14 4.9 34.8 1.0
N J:ALA116 5.0 27.7 1.0

Manganese binding site 6 out of 6 in 5ak9

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Manganese binding site 6 out of 6 in the The Crystal Structure of I-Dmoi Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn


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 Q42AK120M in Complex with Its Target Dna in the Presence of 2MM Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1188

b:40.8
occ:1.00
 OP1 N:DC15 2.1 29.4 1.0
O J:GLY20 2.3 36.4 1.0
OP1 L:DG15 2.5 56.6 1.0
OE1 J:GLU117 2.7 36.2 1.0
OE2 J:GLU117 2.7 34.7 1.0
OP3 L:DG15 2.7 30.8 1.0
O J:HOH2003 2.8 37.2 1.0
CD J:GLU117 3.0 37.9 1.0
P L:DG15 3.2 44.3 1.0
C J:GLY20 3.3 30.1 1.0
P N:DC15 3.6 28.4 1.0
CA J:GLY20 3.7 21.7 1.0
O J:HOH2004 3.8 31.1 1.0
O5' L:DG15 3.9 27.8 1.0
O J:ILE19 3.9 37.2 1.0
ND2 J:ASN129 4.1 22.4 1.0
O3' N:DA14 4.3 29.1 1.0
CG J:GLU117 4.3 40.8 1.0
C5' L:DG15 4.4 23.0 1.0
C4' N:DC15 4.4 27.4 1.0
C5' N:DC15 4.4 29.6 1.0
OP2 N:DC15 4.5 33.1 1.0
O5' N:DC15 4.5 35.6 1.0
OP2 L:DG15 4.5 44.1 1.0
N J:ASP21 4.5 26.4 1.0
O J:HOH2043 4.6 30.5 1.0
N J:GLY20 4.7 29.4 1.0
C J:ILE19 4.8 35.3 1.0
O3' K:DA14 4.9 34.8 1.0
CA J:ASP21 5.0 25.5 1.0

Reference:

R.Molina, M.J.Marcaida, P.Redondo, M.Marenchino, P.Duchateau, M.D'abramo, G.Montoya, J.Prieto. Engineering A Nickase on the Homing Endonuclease I-Dmoi Scaffold. J.Biol.Chem. V. 290 18534 2015.
ISSN: ISSN 0021-9258
PubMed: 26045557
DOI: 10.1074/JBC.M115.658666
Page generated: Sat Oct 5 23:24:24 2024

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