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Manganese in PDB 2vs8: The Crystal Structure of I-Dmoi in Complex with Dna and Mn

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Dna and Mn, PDB code: 2vs8 was solved by M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.76 / 2.1
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.134, 70.634, 106.955, 90.00, 119.85, 90.00
R / Rfree (%) 20.1 / 24.8

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi in Complex with Dna and Mn (pdb code 2vs8). 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 in Complex with Dna and Mn, PDB code: 2vs8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 2vs8

Go back to Manganese Binding Sites List in 2vs8
Manganese binding site 1 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Dna and 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 in Complex with Dna and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1188

b:40.8
occ:1.00
 OD2 A:ASP21 1.9 34.0 1.0
O A:ALA116 2.1 28.0 1.0
OP1 B:DA14 2.1 38.2 1.0
OP1 E:DC16 2.2 52.4 1.0
O A:HOH2044 2.5 37.4 1.0
OP3 E:DC16 2.7 50.8 1.0
CG A:ASP21 2.9 31.4 1.0
P E:DC16 3.0 52.4 1.0
OD1 A:ASP21 3.1 35.7 1.0
C A:ALA116 3.2 28.3 1.0
P B:DA14 3.6 40.0 1.0
CA A:ALA116 3.8 28.4 1.0
O A:HOH2002 3.8 22.7 1.0
O E:HOH2002 3.9 44.0 1.0
O5' E:DC16 4.0 47.4 1.0
O A:VAL115 4.1 32.0 1.0
OP2 E:DC16 4.1 51.5 1.0
O3' B:DA13 4.2 43.6 1.0
CB A:ASP21 4.3 28.9 1.0
C4' B:DA14 4.3 40.4 1.0
N A:GLU117 4.3 28.8 1.0
NE2 A:GLN42 4.4 47.7 1.0
OE1 A:GLN42 4.4 47.7 1.0
C5' B:DA14 4.4 41.2 1.0
O5' B:DA14 4.5 42.2 1.0
O3' B:DA14 4.5 40.5 1.0
OP2 B:DA14 4.6 43.9 1.0
CA A:GLU117 4.7 30.3 1.0
CD A:GLN42 4.7 45.6 1.0
CB A:ALA116 4.7 27.4 1.0
C3' B:DA14 4.8 39.6 1.0
N A:ALA116 4.8 29.6 1.0
C5' E:DC16 4.9 43.3 1.0
C A:VAL115 4.9 31.6 1.0
NZ A:LYS120 5.0 44.3 1.0

Manganese binding site 2 out of 6 in 2vs8

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Manganese binding site 2 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Dna and 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 in Complex with Dna and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1189

b:40.5
occ:1.00
 OP1 C:DG15 1.6 38.0 1.0
OP1 D:DC15 2.1 36.0 1.0
O A:HOH2082 2.1 34.2 1.0
O A:GLY20 2.3 32.3 1.0
OE2 A:GLU117 2.5 33.1 1.0
OE1 A:GLU117 2.8 31.1 1.0
CD A:GLU117 3.0 31.0 1.0
P C:DG15 3.1 39.5 1.0
C A:GLY20 3.3 30.5 1.0
P D:DC15 3.4 31.4 1.0
OP3 C:DG15 3.5 38.9 1.0
CA A:GLY20 3.7 29.9 1.0
O3' D:DA14 3.7 32.7 1.0
ND2 A:ASN129 3.8 27.8 1.0
O A:HOH2002 3.9 22.7 1.0
O A:ILE19 4.0 30.1 1.0
O5' C:DG15 4.0 34.6 1.0
O C:HOH2003 4.0 38.9 1.0
OP2 C:DG15 4.1 40.2 1.0
C4' D:DC15 4.3 34.0 1.0
C5' D:DC15 4.3 33.6 1.0
O5' D:DC15 4.3 29.7 1.0
C5' C:DG15 4.5 34.3 1.0
CG A:GLU117 4.5 30.9 1.0
N A:ASP21 4.5 29.3 1.0
OP2 D:DC15 4.5 30.2 1.0
O A:HOH2046 4.6 42.1 1.0
OD1 A:ASP21 4.7 35.7 1.0
N A:GLY20 4.8 29.5 1.0
C A:ILE19 4.8 30.8 1.0
CG A:ASN129 4.8 29.0 1.0
CA A:ASP21 5.0 28.6 1.0

Manganese binding site 3 out of 6 in 2vs8

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Manganese binding site 3 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Dna and 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 in Complex with Dna and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1196

b:38.5
occ:1.00
 OP2 H:DG15 1.6 36.1 1.0
O F:HOH2080 1.9 33.1 1.0
OE2 F:GLU117 1.9 35.0 1.0
OP1 I:DC15 2.3 39.7 1.0
O F:GLY20 2.5 28.1 1.0
CD F:GLU117 2.7 38.1 1.0
OE1 F:GLU117 3.0 41.4 1.0
P H:DG15 3.1 43.9 1.0
C F:GLY20 3.4 28.8 1.0
P I:DC15 3.6 39.7 1.0
OP3 H:DG15 3.7 45.8 1.0
CA F:GLY20 3.8 29.0 1.0
O5' H:DG15 3.9 40.7 1.0
O J:HOH2002 3.9 22.7 1.0
OD1 F:ASN129 3.9 37.1 1.0
OP1 H:DG15 4.0 45.8 1.0
O F:ILE19 4.1 29.9 1.0
O3' I:DA14 4.1 42.5 1.0
CG F:GLU117 4.1 36.8 1.0
O F:HOH2060 4.2 45.0 1.0
C5' H:DG15 4.2 37.0 1.0
C4' I:DC15 4.3 39.1 1.0
O H:HOH2005 4.5 38.9 1.0
O5' I:DC15 4.5 39.7 1.0
C5' I:DC15 4.5 38.2 1.0
N F:ASP21 4.6 27.9 1.0
OP2 I:DC15 4.6 38.7 1.0
OD1 F:ASP21 4.8 31.3 1.0
CG F:ASN129 4.8 36.1 1.0
O3' I:DC15 4.8 40.3 1.0
N F:GLY20 4.9 28.8 1.0
C F:ILE19 4.9 29.3 1.0
C3' I:DC15 4.9 38.2 1.0
CA F:ASP21 5.0 27.7 1.0

Manganese binding site 4 out of 6 in 2vs8

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Manganese binding site 4 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Dna and 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 in Complex with Dna and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1197

b:38.6
occ:1.00
 OP1 G:DA14 2.0 28.9 1.0
OD2 F:ASP21 2.1 31.1 1.0
O F:ALA116 2.2 29.9 1.0
OP3 J:DC16 2.2 48.0 1.0
OP2 J:DC16 2.6 43.6 1.0
O F:HOH2059 2.6 35.6 1.0
P J:DC16 2.9 48.2 1.0
CG F:ASP21 2.9 30.1 1.0
OD1 F:ASP21 3.1 31.3 1.0
C F:ALA116 3.3 31.5 1.0
P G:DA14 3.5 31.6 1.0
O J:HOH2002 3.7 22.7 1.0
CA F:ALA116 3.8 31.6 1.0
OP1 J:DC16 3.9 43.5 1.0
O5' J:DC16 4.0 44.8 1.0
NZ F:LYS120 4.1 47.3 1.0
OE1 F:GLN42 4.1 36.3 1.0
O3' G:DA13 4.2 32.6 1.0
O F:VAL115 4.2 34.5 1.0
C4' G:DA14 4.2 32.3 1.0
CB F:ASP21 4.3 28.2 1.0
C5' G:DA14 4.4 29.2 1.0
NE2 F:GLN42 4.4 36.3 1.0
N F:GLU117 4.4 32.8 1.0
O5' G:DA14 4.4 31.7 1.0
OP2 G:DA14 4.5 32.0 1.0
O3' G:DA14 4.6 35.3 1.0
CD F:GLN42 4.6 36.5 1.0
O G:HOH2005 4.7 53.9 1.0
C3' G:DA14 4.7 31.7 1.0
C5' J:DC16 4.8 43.9 1.0
CB F:ALA116 4.8 30.3 1.0
N F:ALA116 4.9 32.3 1.0
O F:HOH2022 4.9 55.2 1.0
CA F:GLU117 4.9 34.5 1.0
C F:VAL115 5.0 33.4 1.0
OE1 F:GLU117 5.0 41.4 1.0

Manganese binding site 5 out of 6 in 2vs8

Go back to Manganese Binding Sites List in 2vs8
Manganese binding site 5 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Dna and 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 in Complex with Dna and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mn1183

b:40.2
occ:1.00
 OD2 K:ASP21 2.0 30.5 1.0
OP2 L:DA14 2.1 40.3 1.0
O K:ALA116 2.1 29.5 1.0
OP3 O:DC16 2.3 46.9 1.0
OP1 O:DC16 2.4 47.1 1.0
P O:DC16 2.9 50.4 1.0
CG K:ASP21 2.9 30.9 1.0
C K:ALA116 3.2 30.4 1.0
OD1 K:ASP21 3.2 30.6 1.0
P L:DA14 3.4 38.7 1.0
CA K:ALA116 3.7 30.4 1.0
O3' L:DA13 3.8 39.7 1.0
O K:HOH2002 3.8 24.6 1.0
OP2 O:DC16 3.9 47.6 1.0
O5' O:DC16 4.0 45.4 1.0
NZ K:LYS120 4.0 47.7 1.0
O K:VAL115 4.0 31.9 1.0
OE1 K:GLN42 4.1 45.1 1.0
C4' L:DA14 4.3 40.0 1.0
CB K:ASP21 4.3 28.7 1.0
N K:GLU117 4.3 31.4 1.0
OP1 L:DA14 4.4 34.0 1.0
C5' L:DA14 4.4 38.6 1.0
O5' L:DA14 4.4 38.1 1.0
NE2 K:GLN42 4.5 42.8 1.0
CB K:ALA116 4.6 29.1 1.0
CD K:GLN42 4.6 43.2 1.0
CA K:GLU117 4.7 31.6 1.0
N K:ALA116 4.8 30.8 1.0
O3' L:DA14 4.8 42.0 1.0
C K:VAL115 4.9 32.1 1.0
C5' O:DC16 4.9 40.0 1.0
C3' L:DA14 4.9 39.8 1.0

Manganese binding site 6 out of 6 in 2vs8

Go back to Manganese Binding Sites List in 2vs8
Manganese binding site 6 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Dna and 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 in Complex with Dna and Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mn1184

b:39.1
occ:1.00
 OP1 M:DG15 1.7 31.6 1.0
O K:HOH2077 2.0 36.9 1.0
OP1 N:DC15 2.1 38.5 1.0
O K:GLY20 2.3 29.5 1.0
OE1 K:GLU117 2.3 36.5 1.0
OE2 K:GLU117 2.6 34.4 1.0
CD K:GLU117 2.8 34.4 1.0
P M:DG15 3.1 38.4 1.0
C K:GLY20 3.2 29.5 1.0
P N:DC15 3.5 34.1 1.0
OP3 M:DG15 3.5 40.5 1.0
CA K:GLY20 3.6 29.2 1.0
ND2 K:ASN129 3.8 29.0 1.0
O K:HOH2002 3.9 24.6 1.0
O K:ILE19 3.9 33.5 1.0
O3' N:DA14 4.0 36.8 1.0
O5' M:DG15 4.0 36.3 1.0
O M:HOH2003 4.1 41.0 1.0
OP2 M:DG15 4.2 39.5 1.0
CG K:GLU117 4.3 34.9 1.0
C4' N:DC15 4.3 33.2 1.0
O5' N:DC15 4.4 34.1 1.0
C5' M:DG15 4.4 33.6 1.0
C5' N:DC15 4.4 34.7 1.0
N K:ASP21 4.4 28.0 1.0
OP2 N:DC15 4.5 33.4 1.0
O K:HOH2049 4.6 38.7 1.0
OD1 K:ASP21 4.6 30.6 1.0
N K:GLY20 4.6 30.8 1.0
C K:ILE19 4.7 31.0 1.0
CG K:ASN129 4.8 31.4 1.0
O N:HOH2013 4.8 44.5 1.0
CA K:ASP21 4.9 28.3 1.0
O3' L:DA14 4.9 42.0 1.0
O3' N:DC15 5.0 34.5 1.0
C3' N:DC15 5.0 32.1 1.0

Reference:

M.J.Marcaida, J.Prieto, P.Redondo, A.D.Nadra, A.Alibes, L.Serrano, S.Grizot, P.Duchateau, F.Paques, F.J.Blanco, G.Montoya. Crystal Structure of I-Dmoi in Complex with Its Target Dna Provides New Insights Into Meganuclease Engineering. Proc.Nat.Acad.Sci.Usa V. 105 16888 2008.
ISSN: ISSN 0027-8424
PubMed: 18974222
DOI: 10.1073/PNAS.0804795105
Page generated: Sat Oct 5 15:19:55 2024

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