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Zinc in PDB 4rmj: Human SIRT2 in Complex with Adp Ribose and Nicotinamide

Protein crystallography data

The structure of Human SIRT2 in Complex with Adp Ribose and Nicotinamide, PDB code: 4rmj was solved by T.Rumpf, M.Schiedel, B.Karaman, C.Roessler, B.J.North, A.Lehotzky, J.Olah, K.I.Ladwein, K.Schmidtkunz, M.Gajer, M.Pannek, C.Steegborn, D.A.Sinclair, S.Gerhardt, J.Ovadi, M.Schutkowski, W.Sippl, O.Einsle, M.Jung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.20 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.600, 77.960, 114.280, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24

Other elements in 4rmj:

The structure of Human SIRT2 in Complex with Adp Ribose and Nicotinamide also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide (pdb code 4rmj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide, PDB code: 4rmj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4rmj

Go back to Zinc Binding Sites List in 4rmj
Zinc binding site 1 out of 2 in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SIRT2 in Complex with Adp Ribose and Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:54.0
occ:1.00
SG A:CYS200 2.3 56.7 1.0
SG A:CYS224 2.3 50.5 1.0
SG A:CYS221 2.4 46.7 1.0
SG A:CYS195 2.4 49.0 1.0
CB A:CYS200 3.1 59.4 1.0
CB A:CYS221 3.2 49.0 1.0
CB A:CYS195 3.2 50.6 1.0
CB A:CYS224 3.4 53.0 1.0
N A:CYS224 3.7 53.6 1.0
CA A:CYS224 4.1 51.6 1.0
CB A:ASP223 4.4 62.4 1.0
CA A:CYS200 4.5 60.3 1.0
N A:ARG201 4.6 62.9 1.0
CA A:CYS221 4.7 48.9 1.0
C A:ASP223 4.7 58.9 1.0
CA A:CYS195 4.7 47.7 1.0
N A:HIS202 4.7 64.8 1.0
CB A:SER226 4.7 47.3 1.0
CB A:SER197 4.7 54.8 1.0
CB A:HIS202 4.7 74.0 1.0
C A:CYS224 4.8 51.2 1.0
C A:CYS200 4.9 60.6 1.0
N A:SER226 4.9 45.3 1.0
CA A:ASP223 4.9 61.4 1.0
N A:ASP223 5.0 63.0 1.0

Zinc binding site 2 out of 2 in 4rmj

Go back to Zinc Binding Sites List in 4rmj
Zinc binding site 2 out of 2 in the Human SIRT2 in Complex with Adp Ribose and Nicotinamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SIRT2 in Complex with Adp Ribose and Nicotinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:53.0
occ:1.00
SG B:CYS221 2.3 50.2 1.0
SG B:CYS200 2.3 59.5 1.0
SG B:CYS195 2.3 54.1 1.0
SG B:CYS224 2.4 55.4 1.0
CB B:CYS200 3.2 60.7 1.0
CB B:CYS195 3.3 51.7 1.0
CB B:CYS221 3.3 52.8 1.0
CB B:CYS224 3.4 57.0 1.0
N B:CYS224 3.9 61.5 1.0
CA B:CYS224 4.2 58.5 1.0
CB B:HIS202 4.4 64.5 1.0
N B:HIS202 4.5 62.0 1.0
CA B:CYS200 4.5 65.0 1.0
N B:ARG201 4.6 66.2 1.0
CB B:ASP223 4.6 65.4 1.0
CA B:CYS195 4.7 50.0 1.0
CA B:CYS221 4.7 54.1 1.0
C B:CYS224 4.7 57.2 1.0
CB B:SER197 4.7 55.7 1.0
C B:CYS200 4.7 66.5 1.0
CB B:SER226 4.8 53.2 1.0
N B:GLN225 4.9 57.0 1.0
OG B:SER226 4.9 54.6 1.0
C B:ASP223 5.0 65.9 1.0

Reference:

T.Rumpf, M.Schiedel, B.Karaman, C.Roessler, B.J.North, A.Lehotzky, J.Olah, K.I.Ladwein, K.Schmidtkunz, M.Gajer, M.Pannek, C.Steegborn, D.A.Sinclair, S.Gerhardt, J.Ovadi, M.Schutkowski, W.Sippl, O.Einsle, M.Jung. Selective SIRT2 Inhibition By Ligand-Induced Rearrangement of the Active Site. Nat Commun V. 6 6263 2015.
ISSN: ESSN 2041-1723
PubMed: 25672491
DOI: 10.1038/NCOMMS7263
Page generated: Wed Dec 16 05:46:02 2020

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