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Manganese in PDB 5o6i: Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi

Protein crystallography data

The structure of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi, PDB code: 5o6i was solved by R.Molina, M.J.Marcaida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.14 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.000, 70.480, 107.320, 90.00, 119.81, 90.00
R / Rfree (%) 19.6 / 22.8

Other elements in 5o6i:

The structure of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi (pdb code 5o6i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi, PDB code: 5o6i:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 5o6i

Go back to Manganese Binding Sites List in 5o6i
Manganese binding site 1 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn201

b:40.7
occ:1.00
 O D:HOH120 2.4 31.4 1.0
OP1 C:DA14 2.5 31.5 1.0
O A:ALA116 2.5 24.7 1.0
OP2 D:DC16 2.5 27.7 1.0
OD2 A:ASP21 2.5 34.1 1.0
O A:HOH317 2.6 32.5 1.0
OD1 A:ASP21 2.7 27.5 1.0
CG A:ASP21 2.9 31.8 1.0
O A:HOH304 3.5 24.5 1.0
C A:ALA116 3.5 29.3 1.0
P D:DC16 3.8 35.8 1.0
CA A:ALA116 3.9 28.7 1.0
P C:DA14 3.9 31.6 1.0
O5' D:DC16 3.9 36.4 1.0
O D:HOH111 4.0 44.7 1.0
OE1 A:GLN42 4.2 39.8 1.0
O A:VAL115 4.3 33.3 1.0
C5' C:DA14 4.3 28.3 1.0
O A:HOH352 4.3 46.0 1.0
C4' C:DA14 4.4 35.1 1.0
NZ A:LYS120 4.4 42.4 1.0
CB A:ASP21 4.4 29.5 1.0
O3' C:DA13 4.4 35.4 1.0
NE2 A:GLN42 4.4 29.5 1.0
O5' C:DA14 4.6 35.2 1.0
CD A:GLN42 4.7 33.1 1.0
N A:GLU117 4.7 32.9 1.0
CB A:ALA116 4.7 27.9 1.0
OP1 D:DC16 4.7 39.2 1.0
O3' D:DC15 4.8 37.0 1.0
OE1 A:GLU117 4.9 35.0 1.0
OP2 C:DA14 4.9 37.9 1.0
N A:ALA116 5.0 28.0 1.0

Manganese binding site 2 out of 6 in 5o6i

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Manganese binding site 2 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn202

b:40.8
occ:1.00
 OP2 C:DG15 2.4 34.1 1.0
OP1 D:DC15 2.4 37.9 1.0
O A:GLY20 2.4 34.2 1.0
OE2 A:GLU117 2.4 41.0 1.0
O C:HOH118 2.6 45.5 1.0
O A:HOH316 2.6 34.7 1.0
OE1 A:GLU117 2.9 35.0 1.0
CD A:GLU117 3.0 39.0 1.0
C A:GLY20 3.4 36.1 1.0
P C:DG15 3.7 27.9 1.0
ND2 A:ASN129 3.7 32.5 1.0
O A:HOH304 3.7 24.5 1.0
P D:DC15 3.8 40.0 1.0
CA A:GLY20 3.9 28.3 1.0
O A:ILE19 4.0 35.4 1.0
O5' C:DG15 4.1 33.6 1.0
C5' C:DG15 4.1 31.9 1.0
O3' D:DA14 4.2 34.7 1.0
C4' D:DC15 4.3 35.2 1.0
CG A:GLU117 4.4 31.5 1.0
C5' D:DC15 4.4 35.2 1.0
OP1 C:DG15 4.4 35.4 1.0
N A:ASP21 4.6 31.5 1.0
O5' D:DC15 4.7 39.8 1.0
O3' C:DA14 4.8 34.6 1.0
CG A:ASN129 4.8 37.6 1.0
OP2 D:DC15 4.8 39.9 1.0
C A:ILE19 4.9 29.5 1.0
N A:GLY20 4.9 33.1 1.0
O3' D:DC15 4.9 37.0 1.0
CA A:ASP21 5.0 30.9 1.0

Manganese binding site 3 out of 6 in 5o6i

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Manganese binding site 3 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn201

b:44.1
occ:1.00
 OP1 G:DA14 2.4 34.1 1.0
O F:ALA116 2.4 31.5 1.0
OP2 I:DC16 2.5 36.4 1.0
OD2 F:ASP21 2.6 39.2 1.0
O F:HOH309 2.6 35.3 1.0
OD1 F:ASP21 2.8 39.4 1.0
O I:HOH116 2.8 40.4 1.0
CG F:ASP21 3.0 33.5 1.0
C F:ALA116 3.5 35.5 1.0
O F:HOH303 3.6 23.0 1.0
P I:DC16 3.9 37.2 1.0
P G:DA14 3.9 42.9 1.0
NE2 F:GLN42 3.9 37.5 1.0
CA F:ALA116 3.9 33.2 1.0
O I:HOH104 4.1 40.3 1.0
O F:VAL115 4.3 31.1 1.0
OE1 F:GLN42 4.3 43.3 1.0
O3' G:DA13 4.4 42.0 1.0
C5' G:DA14 4.4 34.9 1.0
C4' G:DA14 4.5 37.9 1.0
CB F:ASP21 4.5 36.1 1.0
CD F:GLN42 4.5 41.2 1.0
O5' I:DC16 4.5 36.1 1.0
C5' I:DC16 4.5 31.6 1.0
OP1 I:DC16 4.6 35.6 1.0
N F:GLU117 4.7 34.4 1.0
O5' G:DA14 4.7 46.0 1.0
CB F:ALA116 4.8 26.5 1.0
OP2 G:DA14 4.8 49.0 1.0
O3' I:DC15 4.9 38.9 1.0
OE1 F:GLU117 4.9 39.1 1.0

Manganese binding site 4 out of 6 in 5o6i

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Manganese binding site 4 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn202

b:42.1
occ:1.00
 OP1 I:DC15 2.4 32.5 1.0
OP2 G:DG15 2.4 37.4 1.0
O F:GLY20 2.4 36.6 1.0
OE2 F:GLU117 2.5 38.7 1.0
O F:HOH315 2.6 38.1 1.0
CD F:GLU117 3.2 34.7 1.0
OE1 F:GLU117 3.3 39.1 1.0
C F:GLY20 3.5 38.7 1.0
P G:DG15 3.6 36.4 1.0
P I:DC15 3.7 36.0 1.0
ND2 F:ASN129 3.8 31.8 1.0
C5' G:DG15 3.9 32.4 1.0
O F:ILE19 3.9 36.7 1.0
O F:HOH303 3.9 23.0 1.0
O5' G:DG15 4.0 38.2 1.0
O F:HOH345 4.0 38.4 1.0
CA F:GLY20 4.0 31.1 1.0
O3' I:DA14 4.1 36.2 1.0
OP1 G:DG15 4.2 43.3 1.0
C4' I:DC15 4.5 33.8 1.0
C5' I:DC15 4.5 33.3 1.0
CG F:GLU117 4.6 34.8 1.0
N F:ASP21 4.7 31.1 1.0
O5' I:DC15 4.7 41.2 1.0
OP2 I:DC15 4.7 41.8 1.0
C4' G:DG15 4.8 33.5 1.0
C F:ILE19 4.8 34.8 1.0
O3' G:DA14 4.8 39.4 1.0
CG F:ASN129 4.9 33.5 1.0
N F:GLY20 4.9 33.2 1.0

Manganese binding site 5 out of 6 in 5o6i

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Manganese binding site 5 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mn201

b:41.8
occ:1.00
 O K:HOH315 2.3 28.7 1.0
OP1 L:DA14 2.4 36.0 1.0
OP2 N:DC16 2.4 30.6 1.0
O K:ALA116 2.4 29.6 1.0
OD2 K:ASP21 2.6 38.9 1.0
OD1 K:ASP21 2.7 29.3 1.0
O K:HOH330 2.7 33.5 1.0
CG K:ASP21 3.0 33.0 1.0
O K:HOH302 3.4 23.8 1.0
C K:ALA116 3.5 29.2 1.0
CA K:ALA116 3.8 30.7 1.0
P N:DC16 3.8 35.9 1.0
P L:DA14 3.9 35.9 1.0
O N:HOH112 3.9 40.2 1.0
NZ K:LYS120 4.1 49.5 1.0
NE2 K:GLN42 4.2 36.0 1.0
O K:VAL115 4.3 37.2 1.0
C4' L:DA14 4.3 34.0 1.0
C5' L:DA14 4.3 30.6 1.0
O5' N:DC16 4.4 38.5 1.0
O3' L:DA13 4.4 37.4 1.0
OE1 K:GLN42 4.5 36.2 1.0
C5' N:DC16 4.5 34.6 1.0
CB K:ASP21 4.5 29.6 1.0
OP1 N:DC16 4.6 40.3 1.0
CB K:ALA116 4.6 26.8 1.0
O5' L:DA14 4.7 37.0 1.0
N K:GLU117 4.7 32.1 1.0
CD K:GLN42 4.7 38.2 1.0
O3' N:DC15 4.8 38.2 1.0
OP2 L:DA14 4.8 38.0 1.0
N K:ALA116 5.0 31.7 1.0
O3' L:DA14 5.0 38.3 1.0

Manganese binding site 6 out of 6 in 5o6i

Go back to Manganese Binding Sites List in 5o6i
Manganese binding site 6 out of 6 in the Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structures and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mn202

b:38.7
occ:1.00
 OP2 L:DG15 2.4 31.8 1.0
OP1 N:DC15 2.4 31.2 1.0
O K:GLY20 2.4 32.4 1.0
OE2 K:GLU117 2.5 45.3 1.0
O K:HOH326 2.6 38.1 1.0
O L:HOH124 2.7 43.7 1.0
OE1 K:GLU117 3.0 37.2 1.0
CD K:GLU117 3.0 38.7 1.0
C K:GLY20 3.5 30.4 1.0
P L:DG15 3.6 30.7 1.0
ND2 K:ASN129 3.7 33.9 1.0
O K:HOH302 3.7 23.8 1.0
P N:DC15 3.8 36.1 1.0
CA K:GLY20 3.9 31.4 1.0
O K:ILE19 4.0 33.8 1.0
C5' L:DG15 4.0 33.2 1.0
O5' L:DG15 4.0 40.8 1.0
O3' N:DA14 4.2 35.8 1.0
C5' N:DC15 4.3 32.3 1.0
C4' N:DC15 4.4 31.5 1.0
OP1 L:DG15 4.4 29.6 1.0
CG K:GLU117 4.5 36.2 1.0
O5' N:DC15 4.6 37.4 1.0
N K:ASP21 4.6 28.8 1.0
O3' L:DA14 4.8 38.3 1.0
OP2 N:DC15 4.8 38.3 1.0
CG K:ASN129 4.9 36.2 1.0
C K:ILE19 4.9 33.6 1.0
N K:GLY20 4.9 34.0 1.0
C4' L:DG15 5.0 34.4 1.0

Reference:

J.Alba, M.J.Marcaida, J.Prieto, G.Montoya, R.Molina, M.D'abramo. Structure and Dynamics of Mesophilic Variants From the Homing Endonuclease I-Dmoi. J. Comput. Aided Mol. Des. V. 31 1063 2017.
ISSN: ESSN 1573-4951
PubMed: 29177929
DOI: 10.1007/S10822-017-0087-5
Page generated: Sun Oct 6 02:12:19 2024

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