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Chlorine in PDB 4bvh: Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose

Protein crystallography data

The structure of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose, PDB code: 4bvh was solved by M.Gertz, M.Weyand, C.Steegborn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.44 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.710, 66.530, 201.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.159 / 22.581

Other elements in 4bvh:

The structure of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose (pdb code 4bvh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose, PDB code: 4bvh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4bvh

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Chlorine binding site 1 out of 5 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1393

b:33.7
occ:1.00
CL A:OCZ1393 0.0 33.7 1.0
CAB A:OCZ1393 1.9 30.9 1.0
CAA A:OCZ1393 2.8 27.7 1.0
CAC A:OCZ1393 2.8 30.9 1.0
CG2 A:ILE291 3.3 36.3 1.0
CD1 A:PHE180 3.3 36.8 1.0
CB A:PHE180 3.5 35.0 1.0
CD1 A:PHE293 3.5 42.0 1.0
CG A:PHE180 3.6 37.9 1.0
O A:VAL292 3.7 39.8 1.0
CE1 A:PHE293 3.8 46.5 1.0
C7D A:OAD1394 4.0 35.7 0.7
CAD A:OCZ1393 4.1 28.0 1.0
CAF A:OCZ1393 4.1 25.3 1.0
CE1 A:PHE180 4.2 33.9 1.0
CA A:PHE180 4.3 35.1 1.0
O A:PHE180 4.3 39.2 1.0
CA A:PHE293 4.5 45.7 1.0
C A:VAL292 4.5 39.6 1.0
CAE A:OCZ1393 4.6 26.1 1.0
CD2 A:PHE180 4.6 36.4 1.0
CD1 A:ILE230 4.7 18.5 1.0
N A:PHE293 4.8 41.4 1.0
CB A:ILE291 4.8 32.7 1.0
CG A:PHE293 4.8 40.3 1.0
C A:PHE180 4.8 37.1 1.0
C6D A:OAD1394 4.8 41.3 0.7

Chlorine binding site 2 out of 5 in 4bvh

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Chlorine binding site 2 out of 5 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1397

b:56.9
occ:1.00
NE2 A:GLN170 4.0 51.2 1.0
CD A:GLN170 4.7 54.8 1.0
OE1 A:GLN170 4.8 54.5 1.0

Chlorine binding site 3 out of 5 in 4bvh

Go back to Chlorine Binding Sites List in 4bvh
Chlorine binding site 3 out of 5 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1392

b:31.3
occ:1.00
CL B:OCZ1392 0.0 31.3 1.0
CAB B:OCZ1392 1.8 23.7 1.0
CAA B:OCZ1392 2.8 24.4 1.0
CAC B:OCZ1392 2.8 22.9 1.0
CD1 B:PHE180 3.4 35.9 1.0
CD1 B:ILE291 3.7 33.9 1.0
O B:VAL292 3.8 28.6 1.0
CG B:PHE180 3.8 35.2 1.0
CB B:PHE180 3.9 35.3 1.0
CAD B:OCZ1392 4.1 20.6 1.0
CE1 B:PHE180 4.1 39.5 1.0
CAF B:OCZ1392 4.1 21.8 1.0
CG1 B:ILE291 4.4 28.1 1.0
C B:VAL292 4.4 28.6 1.0
CA B:PHE293 4.5 36.6 1.0
CAE B:OCZ1392 4.5 20.6 1.0
N B:PHE293 4.7 30.3 1.0
CA B:PHE180 4.7 33.4 1.0
CB B:ILE291 4.7 25.2 1.0
CD1 B:ILE230 4.8 19.1 1.0
CD2 B:PHE180 4.8 40.6 1.0
CG B:PHE293 4.9 39.6 1.0
CD1 B:PHE293 4.9 43.9 1.0
O B:PHE180 4.9 40.1 1.0

Chlorine binding site 4 out of 5 in 4bvh

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Chlorine binding site 4 out of 5 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1397

b:72.8
occ:1.00
O B:HOH2058 3.8 29.8 1.0
CG1 B:VAL387 4.2 23.7 1.0
O B:PRO206 4.3 18.9 1.0
O B:HOH2057 4.3 36.3 1.0
O B:HOH2044 4.4 41.6 1.0
O B:HOH2016 4.5 36.3 1.0
CE2 B:TYR211 4.5 19.8 1.0
CG2 B:VAL208 4.5 20.1 1.0
N B:VAL208 4.6 15.0 1.0
CA B:ASN207 4.6 15.2 1.0
CG2 B:THR391 4.8 33.8 1.0
C B:ASN207 4.8 15.9 1.0
CD2 B:TYR211 4.9 17.2 1.0

Chlorine binding site 5 out of 5 in 4bvh

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Chlorine binding site 5 out of 5 in the Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human SIRT3 in Complex with the Inhibitor Ex-527 and 2'-O-Acetyl-Adp-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1394

b:24.3
occ:1.00
CL C:OCZ1394 0.0 24.3 1.0
CAB C:OCZ1394 1.9 17.7 1.0
CAC C:OCZ1394 2.8 16.9 1.0
CAA C:OCZ1394 2.9 14.7 1.0
CG2 C:ILE291 3.5 25.4 1.0
CD1 C:PHE180 3.6 37.3 1.0
CG C:PHE180 3.7 34.4 1.0
CB C:PHE180 3.7 43.7 1.0
O C:VAL292 3.8 19.8 1.0
CA C:PHE293 4.1 25.5 1.0
CAD C:OCZ1394 4.1 16.3 1.0
CAF C:OCZ1394 4.1 13.0 1.0
CE1 C:PHE180 4.3 36.5 1.0
C7D C:OAD1395 4.3 22.1 1.0
CD2 C:PHE293 4.3 29.5 1.0
CD2 C:PHE180 4.4 37.9 1.0
O C:PHE180 4.4 36.5 1.0
C C:VAL292 4.5 19.6 1.0
CG C:PHE293 4.5 27.1 1.0
O6D C:OAD1395 4.5 35.3 1.0
N C:PHE293 4.6 21.0 1.0
CAE C:OCZ1394 4.6 13.5 1.0
CE2 C:PHE293 4.7 37.1 1.0
N C:PHE294 4.7 30.2 1.0
C6D C:OAD1395 4.7 25.8 1.0
C C:PHE293 4.8 27.4 1.0
CD1 C:ILE230 4.8 14.2 1.0
CB C:PHE293 4.9 23.3 1.0
CA C:PHE180 4.9 44.5 1.0
CD1 C:PHE293 4.9 30.4 1.0
CB C:ILE291 4.9 23.4 1.0
CZ C:PHE180 5.0 35.4 1.0

Reference:

M.Gertz, F.Fischer, G.T.T.Nguyen, M.Lakshminarasimhan, M.Schutkowski, M.Weyand, C.Steegborn. Ex-527 Inhibits Sirtuins By Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism Proc.Natl.Acad.Sci.Usa V. 110 E2772 2013.
ISSN: ISSN 0027-8424
PubMed: 23840057
DOI: 10.1073/PNAS.1303628110
Page generated: Sat Dec 12 10:27:43 2020

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