Atomistry » Manganese » PDB 3cev-3ea3 » 3cm5
Atomistry »
  Manganese »
    PDB 3cev-3ea3 »
      3cm5 »

Manganese in PDB 3cm5: Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn

Protein crystallography data

The structure of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn, PDB code: 3cm5 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.81
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 125.132, 165.432, 64.589, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 23.9

Other elements in 3cm5:

The structure of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn (pdb code 3cm5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn, PDB code: 3cm5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3cm5

Go back to Manganese Binding Sites List in 3cm5
Manganese binding site 1 out of 2 in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:38.9
occ:1.00
OD2 A:ASP15 2.0 40.9 1.0
OE2 A:GLU17 2.0 39.2 1.0
OD2 A:ASP184 2.0 39.0 1.0
O A:HOH315 2.5 41.4 1.0
CG A:ASP15 3.0 39.0 1.0
CD A:GLU17 3.1 39.6 1.0
CG A:ASP184 3.1 40.0 1.0
OD1 A:ASP15 3.3 40.4 1.0
OE1 A:GLU17 3.6 41.0 1.0
O A:PHE16 3.7 37.5 1.0
CB A:ASP184 3.7 39.6 1.0
OD1 A:ASP184 4.1 40.0 1.0
CB A:ASP15 4.3 38.3 1.0
CG A:GLU17 4.4 38.0 1.0
CA A:HIS179 4.5 41.1 1.0
ND1 A:HIS179 4.5 40.3 1.0
CA A:ALA181 4.7 40.5 1.0
C A:PHE16 4.7 37.3 1.0
C A:HIS179 4.9 41.0 1.0
O A:HIS179 5.0 40.9 1.0

Manganese binding site 2 out of 2 in 3cm5

Go back to Manganese Binding Sites List in 3cm5
Manganese binding site 2 out of 2 in the Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Cell-Death Related Nuclease 4 (Crn-4) Bound with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:43.6
occ:1.00
OD2 B:ASP15 2.0 36.6 1.0
OD2 B:ASP184 2.0 41.3 1.0
OE2 B:GLU17 2.2 34.7 1.0
O B:HOH320 2.7 24.5 1.0
CG B:ASP15 2.8 36.6 1.0
OD1 B:ASP15 3.0 37.8 1.0
CG B:ASP184 3.2 40.2 1.0
CD B:GLU17 3.4 35.3 1.0
O B:PHE16 3.8 36.0 1.0
CB B:ASP184 3.8 39.1 1.0
OE1 B:GLU17 4.1 36.8 1.0
OD1 B:ASP184 4.2 40.0 1.0
CB B:ASP15 4.2 35.3 1.0
CA B:HIS179 4.4 43.4 1.0
CG B:GLU17 4.5 34.6 1.0
CA B:ALA181 4.6 41.2 1.0
ND1 B:HIS179 4.8 46.7 1.0
C B:PHE16 4.8 35.0 1.0
C B:HIS179 4.9 43.0 1.0
N B:HIS179 5.0 43.6 1.0

Reference:

Y.-Y.Hsiao, A.Nakagawa, Z.Shi, S.Mitani, D.Xue, H.S.Yuan. Crystal Structure of Crn-4: Implications For Domain Function in Apoptotic Dna Degradation Mol.Cell.Biol. V. 29 448 2009.
ISSN: ISSN 0270-7306
PubMed: 18981218
DOI: 10.1128/MCB.01006-08
Page generated: Tue Dec 15 04:08:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy