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Manganese in PDB 5a0m: The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of Mn

Protein crystallography data

The structure of The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of Mn, PDB code: 5a0m was solved by J.Prieto, P.Redondo, N.Merino, M.Villate, F.J.Blanco, R.Molina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.897 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80.113, 80.565, 130.871, 90.00, 90.00, 90.00
R / Rfree (%) 18.62 / 24.86

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of Mn (pdb code 5a0m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of Mn, PDB code: 5a0m:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5a0m

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Manganese binding site 1 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of 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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1527

b:63.3
occ:1.00
 OD1 A:ASP344 2.0 62.3 1.0
OD1 A:ASP445 2.2 51.1 1.0
OP3 K:DC15 2.2 52.7 1.0
OP1 L:DC17 2.4 53.7 1.0
O3' D:DT16 2.6 53.3 1.0
O3' C:DA14 2.6 53.4 1.0
CG A:ASP344 3.1 59.9 1.0
CG A:ASP445 3.3 51.0 1.0
P L:DC17 3.4 57.0 1.0
O5' L:DC17 3.5 54.2 1.0
P K:DC15 3.5 56.1 1.0
C3' C:DA14 3.6 55.1 1.0
OD2 A:ASP344 3.7 62.2 1.0
C3' D:DT16 3.7 53.6 1.0
OP3 L:DC17 3.8 51.3 1.0
OP2 K:DC15 3.9 53.1 1.0
OD2 A:ASP445 3.9 55.0 1.0
O A:ASP444 4.0 65.8 1.0
MN A:MN1529 4.0 56.1 1.0
MN A:MN1528 4.1 56.4 1.0
O5' K:DC15 4.1 53.5 1.0
C4' C:DA14 4.1 54.5 1.0
C4' D:DT16 4.3 57.3 1.0
CB A:ASP344 4.4 56.4 1.0
O A:GLY343 4.4 54.4 1.0
CB A:ASP445 4.5 53.7 1.0
CA A:ASP445 4.5 56.1 1.0
C A:ASP444 4.6 66.6 1.0
OP1 K:DC15 4.6 59.2 1.0
CA A:ASP344 4.6 52.9 1.0
C5' C:DA14 4.7 58.1 1.0
C A:GLY343 4.7 53.9 1.0
O4' D:DT16 4.7 62.5 1.0
OP2 L:DC17 4.8 59.3 1.0
N A:ASP445 4.9 57.8 1.0
C5' L:DC17 4.9 57.3 1.0
OP1 C:DA14 4.9 48.2 1.0
C2' D:DT16 5.0 57.6 1.0
C2' C:DA14 5.0 49.3 1.0
N A:ASP344 5.0 53.1 1.0

Manganese binding site 2 out of 8 in 5a0m

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Manganese binding site 2 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of 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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1528

b:56.4
occ:1.00
 O A:GLY343 2.3 54.4 1.0
OD2 A:ASP445 2.3 55.0 1.0
OP3 K:DC15 2.4 52.7 1.0
OP1 K:DC15 2.6 59.2 1.0
P K:DC15 3.0 56.1 1.0
CG A:ASP445 3.1 51.0 1.0
C A:GLY343 3.2 53.9 1.0
OD1 A:ASP445 3.4 51.1 1.0
O5' K:DC15 3.4 53.5 1.0
O A:LEU342 3.5 55.9 1.0
CA A:GLY343 3.7 51.1 1.0
MN A:MN1527 4.1 63.3 1.0
OD1 A:ASP344 4.2 62.3 1.0
C A:LEU342 4.3 55.2 1.0
N A:GLY343 4.4 50.7 1.0
OP2 K:DC15 4.4 53.1 1.0
N A:ASP344 4.4 53.1 1.0
O A:ASN463 4.5 52.2 1.0
CB A:ASP445 4.5 53.7 1.0
OP2 D:DT16 4.6 58.2 1.0
CA A:ASP344 4.8 52.9 1.0
C5' K:DC15 4.8 51.8 1.0
OG A:SER466 4.9 73.6 1.0

Manganese binding site 3 out of 8 in 5a0m

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Manganese binding site 3 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of 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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1529

b:56.1
occ:1.00
 O A:ASP444 2.0 65.8 1.0
OD2 A:ASP344 2.1 62.2 1.0
OP1 C:DA14 2.3 48.2 1.0
OP1 L:DC17 2.3 53.7 1.0
OP2 L:DC17 3.0 59.3 1.0
C A:ASP444 3.0 66.6 1.0
P L:DC17 3.0 57.0 1.0
CG A:ASP344 3.1 59.9 1.0
CA A:ASP444 3.4 67.7 1.0
OD1 A:ASP344 3.6 62.3 1.0
P C:DA14 3.7 55.2 1.0
O5' L:DC17 3.8 54.2 1.0
O A:MET443 4.0 68.4 1.0
MN A:MN1527 4.0 63.3 1.0
NZ A:LYS523 4.0 71.3 1.0
C5' C:DA14 4.1 58.1 1.0
N A:ASP445 4.2 57.8 1.0
CB A:ASP444 4.2 71.5 1.0
NE1 A:TRP362 4.3 57.7 1.0
OP3 L:DC17 4.3 51.3 1.0
CD1 A:TRP362 4.3 58.9 1.0
CB A:ASP344 4.4 56.4 1.0
O5' C:DA14 4.4 58.1 1.0
O3' C:DA13 4.5 53.7 1.0
OD1 A:ASP445 4.5 51.1 1.0
N A:ASP444 4.5 70.8 1.0
C A:MET443 4.7 64.7 1.0
C4' C:DA14 4.7 54.5 1.0
OP2 C:DA14 4.7 59.7 1.0
CA A:ASP445 4.7 56.1 1.0
CG A:ASP444 4.8 81.8 1.0
H4' L:DC17 4.9 69.0 1.0
C5' L:DC17 5.0 57.3 1.0
H5' L:DC17 5.0 68.7 1.0

Manganese binding site 4 out of 8 in 5a0m

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Manganese binding site 4 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of 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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1529

b:57.1
occ:1.00
 OP2 J:DC15 2.1 56.3 1.0
OP1 J:DC15 2.4 47.6 1.0
O B:GLY343 2.4 51.9 1.0
OD2 B:ASP445 2.4 50.7 1.0
P J:DC15 2.5 52.0 1.0
O5' J:DC15 3.1 49.8 1.0
CG B:ASP445 3.2 48.2 1.0
OD1 B:ASP445 3.2 45.1 1.0
C B:GLY343 3.6 50.3 1.0
MN B:MN1530 3.8 49.1 1.0
O B:LEU342 3.8 50.5 1.0
OP3 J:DC15 3.9 45.7 1.0
OD1 B:ASP344 4.0 53.3 1.0
OG B:SER466 4.1 59.2 1.0
OP1 H:DT16 4.2 50.8 1.0
CA B:GLY343 4.3 45.8 1.0
O B:ASN463 4.5 42.8 1.0
C5' J:DC15 4.5 45.8 1.0
N B:ASP344 4.6 50.3 1.0
CB B:ASP445 4.6 45.1 1.0
C B:LEU342 4.7 50.3 1.0
CA B:ASP344 4.8 47.4 1.0
N B:GLY343 4.9 44.6 1.0
C5' H:DT16 5.0 48.2 1.0

Manganese binding site 5 out of 8 in 5a0m

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Manganese binding site 5 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of 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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1530

b:49.1
occ:1.00
 OD1 B:ASP344 2.0 53.3 1.0
OP1 J:DC15 2.2 47.6 1.0
OD1 B:ASP445 2.2 45.1 1.0
OP2 I:DC17 2.4 44.0 1.0
O3' E:DA14 2.7 42.7 1.0
O3' H:DT16 3.0 46.2 1.0
CG B:ASP344 3.1 50.3 1.0
CG B:ASP445 3.4 48.2 1.0
OD2 B:ASP344 3.4 52.3 1.0
P I:DC17 3.4 44.5 1.0
O5' I:DC17 3.5 45.8 1.0
O B:ASP444 3.5 46.8 1.0
P J:DC15 3.6 52.0 1.0
C3' E:DA14 3.6 41.3 1.0
C3' H:DT16 3.8 45.6 1.0
MN B:MN1529 3.8 57.1 1.0
MN B:MN1531 4.0 52.8 1.0
OD2 B:ASP445 4.1 50.7 1.0
C4' H:DT16 4.1 45.0 1.0
O5' J:DC15 4.1 49.8 1.0
OP1 I:DC17 4.2 48.9 1.0
C4' E:DA14 4.2 43.0 1.0
OP3 J:DC15 4.3 45.7 1.0
C B:ASP444 4.3 48.7 1.0
O B:GLY343 4.3 51.9 1.0
CB B:ASP344 4.4 45.9 1.0
CA B:ASP445 4.4 47.2 1.0
CB B:ASP445 4.5 45.1 1.0
OP2 J:DC15 4.6 56.3 1.0
OP3 I:DC17 4.7 47.7 1.0
CA B:ASP344 4.7 47.4 1.0
N B:ASP445 4.7 47.6 1.0
C B:GLY343 4.8 50.3 1.0
C5' I:DC17 4.8 46.3 1.0
C5' E:DA14 4.9 41.5 1.0
C2' E:DA14 5.0 41.3 1.0

Manganese binding site 6 out of 8 in 5a0m

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Manganese binding site 6 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of 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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1531

b:52.8
occ:1.00
 OD2 B:ASP344 2.1 52.3 1.0
O B:ASP444 2.2 46.8 1.0
OP2 I:DC17 2.2 44.0 1.0
OP1 E:DA14 2.2 37.9 1.0
OP3 I:DC17 2.7 47.7 1.0
P I:DC17 3.0 44.5 1.0
C B:ASP444 3.1 48.7 1.0
CG B:ASP344 3.2 50.3 1.0
CA B:ASP444 3.4 48.9 1.0
P E:DA14 3.7 42.5 1.0
OD1 B:ASP344 3.8 53.3 1.0
O5' I:DC17 3.9 45.8 1.0
MN B:MN1530 4.0 49.1 1.0
O B:MET443 4.1 45.9 1.0
C5' E:DA14 4.1 41.5 1.0
OP1 I:DC17 4.1 48.9 1.0
CB B:ASP444 4.2 48.9 1.0
NZ B:LYS523 4.3 49.0 1.0
NE1 B:TRP362 4.3 40.3 1.0
N B:ASP445 4.4 47.6 1.0
O5' E:DA14 4.4 44.0 1.0
O3' E:DA13 4.4 43.7 1.0
CD1 B:TRP362 4.4 40.8 1.0
CB B:ASP344 4.5 45.9 1.0
C4' E:DA14 4.6 43.0 1.0
N B:ASP444 4.6 46.6 1.0
C5' I:DC17 4.7 46.3 1.0
OD1 B:ASP445 4.7 45.1 1.0
C B:MET443 4.8 43.9 1.0
OP2 E:DA14 4.8 42.9 1.0
CA B:ASP445 4.9 47.2 1.0
OD1 B:ASP444 5.0 58.7 1.0

Manganese binding site 7 out of 8 in 5a0m

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Manganese binding site 7 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of Mn


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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1017

b:64.6
occ:1.00
 OP2 K:DC15 2.2 53.1 1.0
OP1 D:DT16 2.4 52.3 1.0
P K:DC15 3.5 56.1 1.0
P D:DT16 3.7 55.2 1.0
OP1 K:DC15 3.8 59.2 1.0
O4' K:DC15 3.8 50.6 1.0
O4' D:DA15 3.8 59.4 1.0
C4' D:DT16 4.0 57.3 1.0
C4' K:DC15 4.1 48.3 1.0
O3' C:DA14 4.1 53.4 1.0
O2 D:DT14 4.2 58.6 1.0
OP2 D:DT16 4.3 58.2 1.0
O4' D:DT16 4.3 62.5 1.0
C5' D:DT16 4.3 55.5 1.0
O5' D:DT16 4.4 56.2 1.0
OP3 K:DC15 4.4 52.7 1.0
N3 C:DA14 4.5 48.1 1.0
C4' D:DA15 4.5 54.1 1.0
O5' K:DC15 4.5 53.5 1.0
C5' K:DC15 4.5 51.8 1.0
C2' C:DA14 4.6 49.3 1.0
C1' D:DA15 4.7 58.5 1.0
N3 D:DA15 4.8 56.1 1.0
C3' C:DA14 5.0 55.1 1.0

Manganese binding site 8 out of 8 in 5a0m

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Manganese binding site 8 out of 8 in the The Crystal Structure of I-Scei in Complex with Its Target Dna in the Presence of Mn


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-Scei in Complex with Its Target Dna in the Presence of Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1017

b:61.1
occ:1.00
 OP3 J:DC15 2.3 45.7 1.0
OP1 H:DT16 2.7 50.8 1.0
O3' H:DA15 3.5 46.3 1.0
P H:DT16 3.7 42.5 1.0
P J:DC15 3.8 52.0 1.0
O4' J:DC15 3.9 48.2 1.0
N3 E:DA14 4.1 42.0 1.0
OP2 J:DC15 4.3 56.3 1.0
C4' J:DC15 4.4 44.5 1.0
OP1 J:DC15 4.4 47.6 1.0
N3 H:DA15 4.4 45.1 1.0
O4' H:DT16 4.4 47.9 1.0
O5' H:DT16 4.4 48.3 1.0
O3' E:DA14 4.4 42.7 1.0
O2 H:DT14 4.4 43.9 1.0
O4' H:DA15 4.5 48.7 1.0
C4' H:DT16 4.5 45.0 1.0
C1' H:DA15 4.6 45.9 1.0
C2 E:DA14 4.7 43.0 1.0
C2' E:DA14 4.8 41.3 1.0
C3' H:DA15 4.8 45.8 1.0
C4' H:DA15 4.8 43.6 1.0
C5' J:DC15 4.8 45.8 1.0
O5' J:DC15 4.8 49.8 1.0
C5' H:DT16 5.0 48.2 1.0
OP2 H:DT16 5.0 49.0 1.0

Reference:

J.Prieto, P.Redondo, N.Merino, M.Villate, G.Montoya, F.J.Blanco, R.Molina. Structure of the I-Scei Nuclease Complexed with Its Dsdna Target and Three Catalytic Metal Ions. Acta Crystallogr.,Sect.F V. 72 473 2016.
ISSN: ISSN 2053-230X
PubMed: 27303901
DOI: 10.1107/S2053230X16007512
Page generated: Sat Oct 5 23:18:35 2024

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