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Manganese in PDB 4w8y: Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)

Protein crystallography data

The structure of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form), PDB code: 4w8y was solved by C.Benda, J.Ebert, M.Baumgaertner, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.72 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.400, 167.925, 100.908, 90.00, 98.91, 90.00
R / Rfree (%) 22.3 / 25.9

Other elements in 4w8y:

The structure of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) (pdb code 4w8y). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form), PDB code: 4w8y:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4w8y

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Manganese binding site 1 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:0.6
occ:1.00
 OD1 A:ASP14 2.2 0.3 1.0
NE2 A:HIS25 2.2 0.8 1.0
CD2 A:HIS25 3.0 0.3 1.0
CG A:ASP14 3.2 0.4 1.0
CE1 A:HIS25 3.3 0.5 1.0
MN A:MN903 3.5 0.9 1.0
OD2 A:ASP14 3.5 1.0 1.0
NZ A:LYS18 3.8 0.9 1.0
OE2 A:GLU26 4.2 0.1 1.0
CG A:HIS25 4.2 0.7 1.0
ND1 A:HIS25 4.3 0.5 1.0
CD2 A:HIS13 4.4 0.4 1.0
CD A:GLU26 4.5 0.3 1.0
CB A:ASP14 4.5 0.3 1.0
CG A:GLU26 4.6 0.6 1.0
O A:HIS13 4.6 99.9 1.0
NE2 A:HIS13 4.6 0.6 1.0
CE A:LYS18 4.7 0.1 1.0
CA A:ASP14 4.9 0.3 1.0

Manganese binding site 2 out of 8 in 4w8y

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Manganese binding site 2 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn903

b:0.9
occ:1.00
 OD2 A:ASP14 2.1 1.0 1.0
NE2 A:HIS13 2.2 0.6 1.0
CD2 A:HIS13 3.0 0.4 1.0
CG A:ASP14 3.1 0.4 1.0
CE1 A:HIS13 3.3 0.3 1.0
NE2 A:HIS207 3.4 0.5 1.0
OD1 A:ASP14 3.4 0.3 1.0
MN A:MN902 3.5 0.6 1.0
OD2 A:ASP50 3.8 0.9 1.0
NZ A:LYS18 3.9 0.9 1.0
CE1 A:HIS207 4.2 0.4 1.0
CG A:ASP50 4.2 0.3 1.0
OD1 A:ASP50 4.2 0.7 1.0
CG A:HIS13 4.2 0.8 1.0
ND1 A:HIS13 4.3 0.2 1.0
CD2 A:HIS207 4.4 0.4 1.0
CB A:ASP14 4.4 0.3 1.0

Manganese binding site 3 out of 8 in 4w8y

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Manganese binding site 3 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn904

b:76.8
occ:1.00
 OD2 A:ASP673 2.1 74.8 1.0
OD1 A:ASP600 2.1 77.5 1.0
CG A:ASP600 3.1 73.1 1.0
CG A:ASP673 3.1 74.0 1.0
OD2 A:ASP674 3.2 78.7 1.0
OD2 A:ASP600 3.3 85.6 1.0
OD1 A:ASP673 3.5 79.1 1.0
CG A:ASP674 3.7 70.8 1.0
OD1 A:ASP674 4.1 72.4 1.0
CB A:ASP673 4.3 72.8 1.0
N A:GLY601 4.4 74.1 1.0
CB A:ASP674 4.4 75.1 1.0
CB A:ASP600 4.5 70.2 1.0
N A:ASP674 4.6 66.7 1.0
O A:GLY601 4.7 0.3 1.0
CA A:ASP600 4.9 67.6 1.0
CB A:MET604 4.9 75.1 1.0
CA A:ASP674 5.0 67.0 1.0

Manganese binding site 4 out of 8 in 4w8y

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Manganese binding site 4 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn905

b:0.2
occ:1.00
 OE2 A:GLU694 2.1 93.9 1.0
OE1 A:GLU656 2.2 87.4 1.0
OE2 A:GLU700 2.2 0.9 1.0
CD A:GLU700 2.7 0.5 1.0
OE1 A:GLU700 2.8 0.9 1.0
CD A:GLU656 3.1 86.6 1.0
CD A:GLU694 3.1 90.9 1.0
OE2 A:GLU656 3.5 86.1 1.0
OE1 A:GLU694 3.9 94.6 1.0
CG A:GLU700 3.9 0.3 1.0
CG A:GLU694 4.0 84.0 1.0
NZ A:LYS697 4.1 0.2 1.0
CG A:GLU656 4.3 82.8 1.0
CB A:GLU700 4.6 0.8 1.0

Manganese binding site 5 out of 8 in 4w8y

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Manganese binding site 5 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn902

b:0.4
occ:1.00
 OD2 B:ASP14 2.1 0.4 1.0
NE2 B:HIS13 2.2 0.6 1.0
NE2 B:HIS207 2.2 0.2 1.0
CE1 B:HIS13 2.8 0.8 1.0
CE1 B:HIS207 3.1 0.6 1.0
CD2 B:HIS207 3.2 100.0 1.0
CG B:ASP14 3.4 0.8 1.0
CD2 B:HIS13 3.4 0.9 1.0
NZ B:LYS18 4.0 0.7 1.0
ND1 B:HIS13 4.1 0.5 1.0
OD1 B:ASP14 4.2 0.8 1.0
ND1 B:HIS207 4.3 0.2 1.0
CB B:ASP14 4.3 0.9 1.0
CG B:HIS207 4.3 97.2 1.0
OG1 B:THR211 4.3 0.5 1.0
OD1 B:ASP50 4.3 0.1 1.0
MN B:MN903 4.3 1.0 1.0
CG B:HIS13 4.4 0.7 1.0
OD2 B:ASP50 4.8 0.2 1.0
CG B:ASP50 4.9 0.0 1.0

Manganese binding site 6 out of 8 in 4w8y

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Manganese binding site 6 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn903

b:1.0
occ:1.00
 OD1 B:ASP14 2.1 0.8 1.0
NE2 B:HIS25 2.3 0.5 1.0
NZ B:LYS18 2.8 0.7 1.0
CG B:ASP14 2.9 0.8 1.0
CE1 B:HIS25 2.9 0.6 1.0
OD2 B:ASP14 3.0 0.4 1.0
CD2 B:HIS25 3.3 0.7 1.0
CE B:LYS18 3.8 97.3 1.0
ND1 B:HIS25 4.1 0.3 1.0
CG B:HIS25 4.3 0.6 1.0
CB B:ASP14 4.3 0.9 1.0
MN B:MN902 4.3 0.4 1.0
CD B:LYS18 4.5 95.2 1.0
NE2 B:HIS13 4.7 0.6 1.0
CD2 B:HIS13 4.7 0.9 1.0
OE1 B:GLU26 4.7 0.2 1.0
CA B:ASP14 5.0 99.6 1.0

Manganese binding site 7 out of 8 in 4w8y

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Manganese binding site 7 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn904

b:82.2
occ:1.00
 OD2 B:ASP673 2.1 80.0 1.0
OD1 B:ASP600 2.2 87.1 1.0
CG B:ASP600 3.0 80.4 1.0
CG B:ASP673 3.1 77.1 1.0
OD2 B:ASP600 3.2 88.9 1.0
OD1 B:ASP673 3.5 85.6 1.0
OD1 B:ASP674 4.0 84.9 1.0
CG B:ASP674 4.3 80.3 1.0
CB B:ASP673 4.3 73.5 1.0
CB B:ASP674 4.4 75.9 1.0
N B:GLY601 4.4 77.8 1.0
CB B:ASP600 4.5 78.2 1.0
N B:ASP674 4.6 75.1 1.0
CG B:MET604 4.6 93.1 1.0
O B:GLY601 4.8 86.8 1.0
CA B:ASP600 4.9 71.7 1.0
CA B:ASP674 5.0 73.2 1.0
CB B:MET604 5.0 95.7 1.0
OD2 B:ASP674 5.0 80.9 1.0

Manganese binding site 8 out of 8 in 4w8y

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Manganese binding site 8 out of 8 in the Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Full Length CMR2 From Pyrococcus Furiosus (Manganese Bound Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn905

b:0.8
occ:1.00
 OE2 B:GLU694 2.1 0.7 1.0
OE2 B:GLU700 2.2 0.5 1.0
OE1 B:GLU656 2.2 93.3 1.0
CD B:GLU694 3.1 96.9 1.0
CD B:GLU700 3.2 0.7 1.0
CD B:GLU656 3.3 84.7 1.0
OE1 B:GLU700 3.7 0.7 1.0
OE2 B:GLU656 3.8 82.0 1.0
OE1 B:GLU694 3.9 93.9 1.0
CG B:GLU694 4.0 88.8 1.0
CG B:GLU700 4.2 0.6 1.0
OG B:SER659 4.4 81.8 1.0
NZ B:LYS697 4.5 0.2 1.0
CG B:GLU656 4.5 78.0 1.0
CB B:GLU656 4.9 74.8 1.0

Reference:

C.Benda, J.Ebert, R.A.Scheltema, H.B.Schiller, M.Baumgartner, F.Bonneau, M.Mann, E.Conti. Structural Model of A Crispr Rna-Silencing Complex Reveals the Rna-Target Cleavage Activity in CMR4. Mol.Cell V. 56 43 2014.
ISSN: ISSN 1097-2765
PubMed: 25280103
DOI: 10.1016/J.MOLCEL.2014.09.002
Page generated: Sat Oct 5 21:30:29 2024

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