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Zinc in PDB 1yc2: SIR2AF2-Nad-Adpribose-Nicotinamide

Protein crystallography data

The structure of SIR2AF2-Nad-Adpribose-Nicotinamide, PDB code: 1yc2 was solved by J.L.Avalos, M.K.Bever, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.122, 181.562, 79.025, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.5

Zinc Binding Sites:

The binding sites of Zinc atom in the SIR2AF2-Nad-Adpribose-Nicotinamide (pdb code 1yc2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the SIR2AF2-Nad-Adpribose-Nicotinamide, PDB code: 1yc2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 1yc2

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Zinc binding site 1 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:34.9
occ:1.00
SG A:CYS129 2.4 33.9 1.0
SG A:CYS150 2.4 35.7 1.0
SG A:CYS153 2.4 38.1 1.0
SG A:CYS126 2.4 30.4 1.0
CB A:CYS129 3.1 32.1 1.0
CB A:CYS150 3.2 39.4 1.0
CB A:CYS126 3.3 28.9 1.0
CB A:CYS153 3.3 37.0 1.0
N A:CYS129 3.6 33.8 1.0
N A:CYS153 3.8 39.5 1.0
CA A:CYS129 3.9 34.1 1.0
CA A:CYS153 4.1 37.9 1.0
CB A:SER155 4.4 38.1 1.0
C A:CYS129 4.6 34.2 1.0
CB A:GLU131 4.6 38.1 1.0
N A:HIS130 4.7 34.2 1.0
CB A:LYS152 4.7 47.8 1.0
CA A:CYS150 4.7 40.4 1.0
CA A:CYS126 4.8 30.7 1.0
C A:ASP128 4.8 34.9 1.0
C A:CYS153 4.8 37.8 1.0
N A:SER155 4.8 39.0 1.0
CB A:ASP128 4.8 33.4 1.0
C A:LYS152 4.8 44.1 1.0
N A:GLY154 4.9 38.9 1.0
N A:GLU131 4.9 36.8 1.0

Zinc binding site 2 out of 9 in 1yc2

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Zinc binding site 2 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:35.4
occ:1.00
OE1 A:GLU180 2.0 43.0 1.0
NE2 C:HIS130 2.1 36.4 1.0
NE2 A:HIS17 2.2 42.2 1.0
NE2 A:HIS183 2.2 32.9 1.0
CD A:GLU180 2.7 41.3 1.0
OE2 A:GLU180 2.9 42.2 1.0
CE1 A:HIS17 2.9 42.4 1.0
CD2 C:HIS130 3.0 34.8 1.0
CE1 C:HIS130 3.1 35.4 1.0
CE1 A:HIS183 3.2 35.3 1.0
CD2 A:HIS183 3.2 33.2 1.0
CD2 A:HIS17 3.3 42.6 1.0
CG C:HIS130 4.1 36.4 1.0
ND1 A:HIS17 4.1 42.0 1.0
ND1 C:HIS130 4.2 37.0 1.0
CG A:GLU180 4.2 38.1 1.0
ND1 A:HIS183 4.3 33.3 1.0
CG A:HIS17 4.3 41.7 1.0
CG A:HIS183 4.4 33.7 1.0
CB A:LYS95 4.6 31.4 1.0
O A:HOH723 4.6 45.4 1.0
CA A:GLU180 4.7 30.1 1.0
O C:ASP128 4.8 38.1 1.0
CB A:GLU180 4.9 33.5 1.0

Zinc binding site 3 out of 9 in 1yc2

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Zinc binding site 3 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:37.2
occ:1.00
SG B:CYS150 2.3 36.2 1.0
SG B:CYS129 2.4 38.1 1.0
SG B:CYS153 2.4 45.0 1.0
SG B:CYS126 2.4 35.5 1.0
CB B:CYS150 3.1 35.7 1.0
CB B:CYS126 3.1 29.2 1.0
CB B:CYS129 3.2 34.8 1.0
CB B:CYS153 3.3 42.6 1.0
N B:CYS153 3.7 43.5 1.0
N B:CYS129 3.7 37.6 1.0
CA B:CYS129 4.0 35.9 1.0
CA B:CYS153 4.0 44.0 1.0
CB B:LYS152 4.6 46.2 1.0
C B:CYS129 4.6 35.4 1.0
CB B:SER155 4.6 44.1 1.0
CA B:CYS150 4.6 38.3 1.0
CB B:GLU131 4.6 39.0 1.0
CA B:CYS126 4.6 30.6 1.0
C B:LYS152 4.7 44.4 1.0
C B:CYS153 4.7 43.7 1.0
N B:HIS130 4.8 34.6 1.0
C B:ASP128 4.8 36.5 1.0
CB B:ASP128 4.8 38.9 1.0
N B:GLY154 4.8 44.2 1.0
N B:SER155 4.9 43.2 1.0
N B:GLU131 4.9 36.2 1.0

Zinc binding site 4 out of 9 in 1yc2

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Zinc binding site 4 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:31.4
occ:1.00
OE1 B:GLU180 2.1 31.7 1.0
NE2 B:HIS183 2.1 33.8 1.0
NE2 B:HIS17 2.3 33.4 1.0
CD B:GLU180 2.9 32.6 1.0
CE1 B:HIS183 3.0 36.3 1.0
OE2 B:GLU180 3.0 32.3 1.0
CD2 B:HIS183 3.1 32.7 1.0
CD2 B:HIS17 3.2 32.4 1.0
CE1 B:HIS17 3.3 33.9 1.0
ND1 B:HIS183 4.1 35.3 1.0
CG B:HIS183 4.2 34.5 1.0
CG B:GLU180 4.3 29.2 1.0
CG B:HIS17 4.4 32.6 1.0
ND1 B:HIS17 4.4 34.5 1.0
CA B:GLU180 4.7 27.8 1.0
O B:GLU180 4.9 28.6 1.0
NE B:ARG113 4.9 27.6 1.0
CB B:GLU180 4.9 29.7 1.0
CB B:LYS95 5.0 28.3 1.0
CB B:ALA96 5.0 24.5 1.0

Zinc binding site 5 out of 9 in 1yc2

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Zinc binding site 5 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn405

b:37.2
occ:1.00
SG C:CYS129 2.3 36.1 1.0
SG C:CYS126 2.4 29.9 1.0
SG C:CYS150 2.4 33.2 1.0
SG C:CYS153 2.4 41.4 1.0
CB C:CYS126 3.2 29.9 1.0
CB C:CYS150 3.2 34.0 1.0
CB C:CYS129 3.2 36.0 1.0
CB C:CYS153 3.3 39.4 1.0
N C:CYS129 3.7 35.7 1.0
N C:CYS153 3.8 41.5 1.0
CA C:CYS129 4.0 35.5 1.0
CA C:CYS153 4.1 40.5 1.0
CB C:SER155 4.4 37.2 1.0
C C:CYS129 4.6 35.4 1.0
CA C:CYS126 4.6 30.9 1.0
N C:HIS130 4.6 35.2 1.0
CA C:CYS150 4.7 37.6 1.0
C C:ASP128 4.8 37.8 1.0
C C:CYS153 4.8 39.2 1.0
CB C:GLU131 4.8 38.9 1.0
CB C:LYS152 4.8 44.9 1.0
C C:LYS152 4.8 43.5 1.0
CB C:ASP128 4.8 40.2 1.0
N C:GLU131 4.9 35.2 1.0
N C:SER155 4.9 36.8 1.0
N C:GLY154 4.9 39.9 1.0

Zinc binding site 6 out of 9 in 1yc2

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Zinc binding site 6 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn406

b:35.6
occ:1.00
OE2 C:GLU180 2.1 46.1 1.0
NE2 A:HIS130 2.1 36.9 1.0
NE2 C:HIS183 2.2 36.0 1.0
NE2 C:HIS17 2.3 40.7 1.0
CD C:GLU180 2.9 44.1 1.0
CE1 A:HIS130 3.0 37.0 1.0
OE1 C:GLU180 3.0 46.9 1.0
CE1 C:HIS183 3.0 35.3 1.0
CD2 C:HIS17 3.1 42.4 1.0
CD2 A:HIS130 3.2 34.9 1.0
CD2 C:HIS183 3.2 36.3 1.0
CE1 C:HIS17 3.4 43.1 1.0
ND1 A:HIS130 4.1 36.1 1.0
ND1 C:HIS183 4.2 36.9 1.0
CG C:GLU180 4.2 40.6 1.0
CG C:HIS17 4.3 42.5 1.0
CG A:HIS130 4.3 35.6 1.0
CG C:HIS183 4.3 36.7 1.0
ND1 C:HIS17 4.4 42.9 1.0
CA C:GLU180 4.6 35.8 1.0
O A:ASP128 4.7 38.2 1.0
O C:GLU180 4.8 33.4 1.0
CB C:GLU180 4.9 36.5 1.0
CB C:ALA96 4.9 35.5 1.0

Zinc binding site 7 out of 9 in 1yc2

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Zinc binding site 7 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn407

b:27.2
occ:1.00
SG D:CYS126 2.3 25.0 1.0
SG D:CYS129 2.3 27.1 1.0
SG D:CYS150 2.3 28.3 1.0
SG D:CYS153 2.4 28.8 1.0
CB D:CYS150 3.1 30.2 1.0
CB D:CYS126 3.2 24.4 1.0
CB D:CYS153 3.2 27.9 1.0
CB D:CYS129 3.3 23.8 1.0
N D:CYS129 3.7 26.5 1.0
N D:CYS153 3.7 31.8 1.0
CA D:CYS153 4.0 29.6 1.0
CA D:CYS129 4.0 26.1 1.0
CB D:SER155 4.5 26.7 1.0
CA D:CYS150 4.6 31.6 1.0
C D:CYS153 4.6 29.1 1.0
C D:CYS129 4.6 26.4 1.0
CA D:CYS126 4.6 24.1 1.0
N D:GLY154 4.7 29.7 1.0
N D:SER155 4.8 26.8 1.0
N D:HIS130 4.8 27.0 1.0
CB D:LYS152 4.8 39.6 1.0
C D:LYS152 4.8 35.0 1.0
CB D:GLU131 4.8 32.0 1.0
C D:ASP128 4.8 26.4 1.0
CB D:ASP128 4.9 30.1 1.0
N D:GLU131 5.0 28.5 1.0

Zinc binding site 8 out of 9 in 1yc2

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Zinc binding site 8 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn408

b:35.9
occ:1.00
OE2 D:GLU180 2.2 42.5 1.0
NE2 D:HIS17 2.2 37.8 1.0
NE2 D:HIS183 2.2 42.9 1.0
CD D:GLU180 2.9 43.6 1.0
CE1 D:HIS183 3.0 44.8 1.0
CE1 D:HIS17 3.1 38.5 1.0
OE1 D:GLU180 3.1 44.0 1.0
CD2 D:HIS17 3.3 37.5 1.0
CD2 D:HIS183 3.3 43.5 1.0
ND1 D:HIS183 4.1 45.5 1.0
CG D:GLU180 4.2 40.2 1.0
ND1 D:HIS17 4.2 39.8 1.0
CG D:HIS183 4.3 42.2 1.0
CG D:HIS17 4.4 39.2 1.0
CA D:GLU180 4.5 34.2 1.0
CB D:GLU180 4.6 37.2 1.0
CB D:LYS95 4.8 29.9 1.0
O D:HOH723 4.9 40.5 1.0

Zinc binding site 9 out of 9 in 1yc2

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Zinc binding site 9 out of 9 in the SIR2AF2-Nad-Adpribose-Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of SIR2AF2-Nad-Adpribose-Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn409

b:36.3
occ:1.00
SG E:CYS129 2.3 36.6 1.0
SG E:CYS153 2.4 41.6 1.0
SG E:CYS150 2.4 39.2 1.0
SG E:CYS126 2.5 40.6 1.0
CB E:CYS129 3.1 37.9 1.0
CB E:CYS150 3.2 39.1 1.0
CB E:CYS153 3.3 38.2 1.0
CB E:CYS126 3.3 40.5 1.0
N E:CYS129 3.5 38.6 1.0
N E:CYS153 3.7 35.9 1.0
CA E:CYS129 3.9 39.2 1.0
CA E:CYS153 4.0 36.8 1.0
CB E:SER155 4.2 41.4 1.0
CB E:LYS152 4.6 40.6 1.0
C E:CYS129 4.6 39.9 1.0
CB E:ASP128 4.6 41.9 1.0
CA E:CYS150 4.7 41.1 1.0
C E:ASP128 4.7 39.6 1.0
C E:CYS153 4.7 36.8 1.0
C E:LYS152 4.7 37.0 1.0
N E:SER155 4.7 39.5 1.0
CB E:GLU131 4.7 47.5 1.0
CA E:CYS126 4.8 41.2 1.0
N E:GLY154 4.8 37.9 1.0
N E:HIS130 4.8 41.3 1.0
N E:GLU131 5.0 45.6 1.0

Reference:

J.L.Avalos, K.M.Bever, C.Wolberger. Mechanism of Sirtuin Inhibition By Nicotinamide: Altering the Nad(+) Cosubstrate Specificity of A SIR2 Enzyme. Mol.Cell V. 17 855 2005.
ISSN: ISSN 1097-2765
PubMed: 15780941
DOI: 10.1016/J.MOLCEL.2005.02.022
Page generated: Wed Dec 16 03:14:04 2020

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