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Cobalt in PDB 2xdb: A Processed Non-Coding Rna Regulates A Bacterial Antiviral System

Enzymatic activity of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System

All present enzymatic activity of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System:
3.1.27.3;

Protein crystallography data

The structure of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System, PDB code: 2xdb was solved by T.R.Blower, X.Y.Pei, F.L.Short, P.C.Fineran, D.P.Humphreys, B.F.Luisi, G.P.C.Salmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 2.55
Space group I 41 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.650, 183.650, 183.650, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.2

Cobalt Binding Sites:

The binding sites of Cobalt atom in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System (pdb code 2xdb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System, PDB code: 2xdb:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 2xdb

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Cobalt binding site 1 out of 6 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1166

b:0.4
occ:1.00
 N A:GLY75 3.4 43.6 1.0
NE2 A:HIS72 3.6 55.5 1.0
CA A:GLY75 4.2 48.5 1.0
CA A:ASN74 4.2 47.0 1.0
C A:ASN74 4.3 51.2 1.0
O A:HOH2025 4.3 79.9 1.0
CE2 A:PHE120 4.4 43.5 1.0
CD2 A:HIS72 4.4 55.6 1.0
CE1 A:HIS72 4.5 61.6 1.0
O A:GLU73 4.7 48.7 1.0
CD2 A:PHE120 4.9 39.6 1.0

Cobalt binding site 2 out of 6 in 2xdb

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Cobalt binding site 2 out of 6 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1167

b:0.4
occ:1.00
 ND2 A:ASN74 2.7 53.8 1.0
N A:ASN74 2.8 48.6 1.0
O A:HOH2039 2.9 57.0 1.0
O A:LYS116 3.2 55.3 1.0
CB A:ASN74 3.5 49.0 1.0
CG A:ASN74 3.5 56.4 1.0
CG A:GLU73 3.6 61.2 1.0
CA A:GLU73 3.6 45.6 1.0
OE1 A:GLN119 3.7 49.6 1.0
C A:GLU73 3.7 46.9 1.0
CA A:ASN74 3.7 47.0 1.0
CD A:GLN119 3.9 52.1 1.0
CB A:GLN119 3.9 46.6 1.0
CD A:LYS116 4.0 52.5 1.0
C A:LYS116 4.0 53.6 1.0
CB A:GLU73 4.0 49.4 1.0
CA A:LYS116 4.1 49.3 1.0
N A:PHE120 4.3 44.7 1.0
CG A:GLN119 4.4 48.6 1.0
NE2 A:GLN119 4.4 51.0 1.0
CB A:LYS116 4.4 49.2 1.0
CB A:PHE120 4.6 39.3 1.0
O A:ASN74 4.6 55.2 1.0
CD A:GLU73 4.6 68.5 1.0
C A:ASN74 4.7 51.2 1.0
OD1 A:ASN74 4.7 60.0 1.0
C A:GLN119 4.7 48.7 1.0
O A:HIS72 4.7 51.5 1.0
OE2 A:GLU73 4.8 66.8 1.0
CA A:PHE120 4.8 41.4 1.0
CG A:LYS116 4.9 51.6 1.0
O A:GLU73 4.9 48.7 1.0
CA A:GLN119 4.9 49.3 1.0
O A:HOH2037 4.9 61.8 1.0
N A:GLU73 4.9 46.4 1.0
NZ A:LYS116 4.9 56.4 1.0

Cobalt binding site 3 out of 6 in 2xdb

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Cobalt binding site 3 out of 6 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co1033

b:0.4
occ:1.00
 O4' G:U22 3.4 41.1 1.0
O4' G:C14 3.5 47.9 1.0
C1' G:U22 3.6 49.4 1.0
O2' G:A13 3.6 49.1 1.0
N3 G:A13 3.8 70.1 1.0
N1 G:U22 4.0 56.7 1.0
C4' G:C14 4.1 50.5 1.0
C2' G:A13 4.1 44.6 1.0
C1' G:C14 4.3 52.1 1.0
C2 G:A13 4.4 68.1 1.0
C6 G:U22 4.5 52.3 1.0
C2 G:U22 4.5 61.1 1.0
C5' G:C14 4.6 58.7 1.0
C1' G:A13 4.6 54.6 1.0
O5' G:G21 4.6 52.0 1.0
C4' G:U22 4.7 43.9 1.0
O2 G:U22 4.7 64.4 1.0
C4 G:A13 4.9 64.0 1.0
C2' G:U22 4.9 49.3 1.0
O2' G:U22 5.0 51.5 1.0

Cobalt binding site 4 out of 6 in 2xdb

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Cobalt binding site 4 out of 6 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co1034

b:0.3
occ:1.00
 O2 G:U18 2.5 0.3 1.0
O2' G:U16 2.9 59.8 1.0
C2 G:U18 3.2 0.5 1.0
OP1 G:U18 3.3 0.8 1.0
N3 G:U18 3.3 0.7 1.0
O3' G:U16 3.4 71.2 1.0
C4' G:U16 3.8 46.0 1.0
C3' G:U16 3.9 50.5 1.0
C2' G:U16 4.0 50.3 1.0
C5' G:U17 4.2 92.7 1.0
OP2 G:U17 4.2 86.3 1.0
NE2 A:GLN141 4.4 68.4 1.0
P G:U17 4.4 88.0 1.0
N1 G:U18 4.5 0.1 1.0
OE1 A:GLN141 4.5 71.5 1.0
C4 G:U18 4.6 0.7 1.0
O4' G:U16 4.7 50.1 1.0
P G:U18 4.8 0.8 1.0
C5' G:U16 4.8 44.2 1.0
C3' G:U17 4.8 0.5 1.0
O5' G:U17 4.8 86.0 1.0
C4' G:U17 4.8 0.1 1.0
CD A:GLN141 4.9 62.4 1.0
C1' G:U16 4.9 52.8 1.0

Cobalt binding site 5 out of 6 in 2xdb

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Cobalt binding site 5 out of 6 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co1035

b:0.2
occ:1.00
 N7 G:G2 2.6 60.7 1.0
C8 G:G2 3.4 59.4 1.0
C5 G:G2 3.7 57.5 1.0
O6 G:G2 3.9 52.4 1.0
OG A:SER64 4.0 55.8 1.0
O G:HOH2006 4.2 81.6 1.0
OP2 G:G2 4.2 76.6 1.0
C6 G:G2 4.2 56.2 1.0
N7 G:A1 4.2 74.6 1.0
C5 G:A1 4.3 72.2 1.0
C8 G:A1 4.6 76.3 1.0
C6 G:A1 4.6 66.9 1.0
N7 G:G3 4.6 52.5 1.0
C4 G:A1 4.7 73.1 1.0
N9 G:G2 4.7 56.2 1.0
C4 G:G2 4.8 60.2 1.0
N9 G:A1 4.8 75.1 1.0
N6 G:A1 4.9 61.3 1.0

Cobalt binding site 6 out of 6 in 2xdb

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Cobalt binding site 6 out of 6 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co1036

b:0.7
occ:1.00
 C4 G:U18 4.4 0.7 1.0
O4 G:U18 4.4 0.8 1.0
O A:HOH2047 4.5 50.8 1.0
N3 G:U18 4.6 0.7 1.0
C5 G:U18 4.7 0.2 1.0
NZ A:LYS143 4.9 80.5 1.0

Reference:

T.R.Blower, X.Y.Pei, F.L.Short, P.C.Fineran, D.P.Humphreys, B.F.Luisi, G.P.C.Salmond. A Processed Noncoding Rna Regulates An Altruistic Bacterial Antiviral System. Nat.Struct.Mol.Biol. V. 18 185 2011.
ISSN: ISSN 1545-9993
PubMed: 21240270
DOI: 10.1038/NSMB.1981
Page generated: Sun Dec 13 10:39:10 2020

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