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Zinc in PDB 2xdd: 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: 2xdd 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) 34.90 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 182.850, 118.130, 41.900, 90.00, 92.78, 90.00
R / Rfree (%) 18.8 / 25.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System (pdb code 2xdd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System, PDB code: 2xdd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 2xdd

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Zinc binding site 1 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1163

b:70.4
occ:1.00
NE2 A:HIS72 2.4 60.2 1.0
CD2 A:HIS72 3.3 55.3 1.0
CE1 A:HIS72 3.4 57.0 1.0
ND1 A:HIS72 4.5 51.4 1.0
CG A:HIS72 4.5 48.4 1.0
CZ A:PHE120 4.7 35.7 1.0
CE2 A:PHE120 4.7 40.6 1.0
OE1 A:GLU63 4.7 0.5 1.0

Zinc binding site 2 out of 12 in 2xdd

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Zinc binding site 2 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1164

b:98.4
occ:1.00
OD2 A:ASP19 3.4 63.8 1.0
OD1 A:ASP19 3.6 90.7 1.0
CG A:ASP19 3.8 75.6 1.0

Zinc binding site 3 out of 12 in 2xdd

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Zinc binding site 3 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
B:Zn1163

b:88.7
occ:1.00
NE2 B:HIS72 2.6 77.9 1.0
CD2 B:HIS72 3.5 67.2 1.0
CE1 B:HIS72 3.5 80.1 1.0
CG B:HIS72 4.6 65.0 1.0
ND1 B:HIS72 4.6 73.0 1.0
OE1 B:GLU63 4.7 92.3 1.0
CZ B:PHE120 4.7 69.2 1.0
CE2 B:PHE120 4.8 72.8 1.0

Zinc binding site 4 out of 12 in 2xdd

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Zinc binding site 4 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
E:Zn1163

b:91.5
occ:1.00
NE2 E:HIS72 2.6 68.8 1.0
CD2 E:HIS72 3.3 73.5 1.0
CE1 E:HIS72 3.7 63.3 1.0
OE1 E:GLU63 4.1 0.8 1.0
CG E:HIS72 4.6 70.6 1.0
CZ E:PHE120 4.6 61.3 1.0
ND1 E:HIS72 4.7 66.1 1.0
CE2 E:PHE120 4.7 62.4 1.0
CD E:GLU63 4.8 0.4 1.0

Zinc binding site 5 out of 12 in 2xdd

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Zinc binding site 5 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
F:Zn1032

b:99.3
occ:1.00
N7 F:G2 3.1 88.8 1.0
OP2 F:G2 3.4 87.5 1.0
C8 F:G2 3.8 90.5 1.0
CE E:LYS62 4.0 0.8 1.0
N7 F:A1 4.0 87.0 1.0
OG E:SER64 4.1 0.3 1.0
O F:HOH2001 4.2 28.6 1.0
C8 F:A1 4.3 88.1 1.0
C5 F:G2 4.3 90.1 1.0
CG E:LYS62 4.5 0.9 1.0
O6 F:G2 4.5 86.3 1.0
C5 F:A1 4.6 89.4 1.0
CD E:LYS62 4.8 0.8 1.0
P F:G2 4.9 90.5 1.0
C6 F:G2 4.9 89.0 1.0

Zinc binding site 6 out of 12 in 2xdd

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Zinc binding site 6 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1032

b:0.8
occ:1.00
N7 G:G3 2.3 69.7 1.0
O G:HOH2001 2.8 64.5 1.0
C5 G:G3 3.0 65.2 1.0
O6 G:G3 3.2 57.4 1.0
C8 G:G3 3.2 75.7 1.0
C6 G:G3 3.3 57.1 1.0
O4 G:U4 3.6 55.1 1.0
C5 G:U4 4.0 62.1 1.0
C4 G:G3 4.1 67.5 1.0
C4 G:U4 4.2 50.2 1.0
N9 G:G3 4.2 71.3 1.0
O6 G:G21 4.4 75.2 1.0
N1 G:G3 4.6 57.4 1.0

Zinc binding site 7 out of 12 in 2xdd

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Zinc binding site 7 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1033

b:0.8
occ:1.00
N7 G:G2 3.0 71.1 1.0
O G:HOH2001 3.6 64.5 1.0
OP2 G:G2 3.7 83.7 1.0
C8 G:G2 3.9 79.0 1.0
OG A:SER64 4.0 78.3 1.0
C5 G:G2 4.1 65.5 1.0
O6 G:G2 4.2 54.1 1.0
C6 G:G2 4.6 57.3 1.0
N7 G:A1 4.7 62.0 1.0
C5 G:A1 4.7 62.6 1.0
N7 G:G3 4.8 69.7 1.0
CE A:LYS62 5.0 0.6 1.0
C6 G:A1 5.0 57.5 1.0

Zinc binding site 8 out of 12 in 2xdd

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Zinc binding site 8 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1034

b:0.7
occ:1.00
N7 G:G10 2.8 73.9 1.0
O2' G:U8 3.6 85.0 1.0
C8 G:G10 3.6 79.8 1.0
O3' G:U8 3.6 95.7 1.0
OP2 G:G10 3.9 0.6 1.0
C5 G:G10 4.0 66.0 1.0
C5 G:U9 4.0 98.9 1.0
C6 G:U9 4.1 0.8 1.0
O6 G:G10 4.1 54.0 1.0
O6 G:G5 4.2 61.8 1.0
C4 G:U9 4.2 87.7 1.0
C2' G:U9 4.2 0.1 1.0
OP2 G:U9 4.3 0.7 1.0
N4 G:C11 4.3 56.8 1.0
O5' G:U9 4.3 0.5 1.0
P G:U9 4.4 0.3 1.0
N1 G:U9 4.4 0.7 1.0
C2' G:U8 4.4 90.3 1.0
C6 G:G10 4.5 59.0 1.0
N3 G:U9 4.5 88.8 1.0
C3' G:U9 4.5 0.1 1.0
C3' G:U8 4.6 91.0 1.0
C2 G:U9 4.7 0.8 1.0
C1' G:U8 4.7 82.4 1.0
O4 G:U9 4.7 78.1 1.0
C5 G:C11 4.8 65.8 1.0
N9 G:G10 4.9 77.1 1.0
C4 G:C11 5.0 59.7 1.0

Zinc binding site 9 out of 12 in 2xdd

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Zinc binding site 9 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1032

b:82.5
occ:1.00
N7 H:G2 2.8 61.0 1.0
O6 H:G2 3.5 37.2 1.0
OG B:SER64 3.6 68.1 1.0
C5 H:G2 3.7 56.0 1.0
C8 H:G2 3.9 76.9 1.0
C6 H:G2 3.9 43.5 1.0
OP2 H:G2 4.0 66.8 1.0
ZN H:ZN1035 4.4 89.5 1.0
N7 H:A1 4.6 61.8 1.0
C5 H:A1 4.7 59.4 1.0
N7 H:G3 4.8 46.1 1.0
C6 H:A1 4.9 52.9 1.0
O6 H:G3 4.9 26.4 1.0
CE B:LYS62 4.9 53.0 1.0
C4 H:G2 4.9 65.2 1.0
N6 H:A1 4.9 43.8 1.0
CB B:SER64 5.0 71.4 1.0

Zinc binding site 10 out of 12 in 2xdd

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Zinc binding site 10 out of 12 in the A Processed Non-Coding Rna Regulates A Bacterial Antiviral System


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of A Processed Non-Coding Rna Regulates A Bacterial Antiviral System within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1033

b:0.4
occ:1.00
OP2 H:U9 2.3 94.1 1.0
OP2 H:G10 2.9 93.8 1.0
P H:U9 3.5 93.3 1.0
O3' H:U8 3.7 64.9 1.0
C2' H:U9 4.1 82.9 1.0
O2' H:U8 4.1 42.4 1.0
C3' H:U9 4.1 98.3 1.0
O5' H:U9 4.2 96.1 1.0
P H:G10 4.2 0.5 1.0
O2' H:U9 4.4 76.2 1.0
O5' H:G10 4.6 85.0 1.0
N7 H:G10 4.6 41.3 1.0
OP1 H:U9 4.7 0.0 1.0
C3' H:U8 4.7 57.5 1.0
C8 H:G10 4.7 47.9 1.0
O3' H:U9 4.8 0.7 1.0
C6 H:U9 4.9 63.9 1.0

Reference:

P.C.Fineran, T.R.Blower, I.J.Foulds, D.P.Humphreys, K.S.Lilley, G.P.C.Salmond. The Phage Abortive Infection System, Toxin, Functions As A Protein-Rna Toxin-Antitoxin Pair. Proc.Natl.Acad.Sci.Usa V. 106 894 2009.
ISSN: ISSN 0027-8424
PubMed: 19124776
DOI: 10.1073/PNAS.0808832106
Page generated: Wed Dec 16 03:59:48 2020

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