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Chlorine in PDB 4a25: X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.

Protein crystallography data

The structure of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions., PDB code: 4a25 was solved by A.Ilari, A.Fiorillo, M.Ardini, S.Stefanini, E.Chiancone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.24 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 150.474, 150.474, 86.618, 90.00, 90.00, 120.00
R / Rfree (%) 19.42 / 23.226

Other elements in 4a25:

The structure of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. also contains other interesting chemical elements:

Manganese (Mn) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. (pdb code 4a25). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions., PDB code: 4a25:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4a25

Go back to Chlorine Binding Sites List in 4a25
Chlorine binding site 1 out of 6 in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1173

b:24.1
occ:1.00
 NH1 A:ARG71 3.2 20.9 1.0
NZ A:LYS45 3.3 19.5 1.0
CE A:LYS45 3.4 23.0 1.0
O B:ARG71 3.6 21.1 1.0
O A:HOH2042 3.7 20.8 1.0
C B:ARG71 3.9 21.1 1.0
O B:HOH2028 4.1 23.8 1.0
CB B:ARG71 4.1 20.4 1.0
CB B:ASP75 4.1 23.2 1.0
CZ A:ARG71 4.1 22.4 1.0
NH2 A:ARG71 4.1 21.0 1.0
N B:GLY72 4.2 20.2 1.0
CA B:GLY72 4.3 20.0 1.0
CA B:ARG71 4.5 21.0 1.0
CG B:ASP75 4.7 24.9 1.0
O A:HOH2023 4.7 13.2 1.0
OD1 B:ASP75 4.8 24.6 1.0
O A:HOH2041 4.9 28.6 1.0
CD A:LYS45 4.9 22.0 1.0

Chlorine binding site 2 out of 6 in 4a25

Go back to Chlorine Binding Sites List in 4a25
Chlorine binding site 2 out of 6 in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1174

b:28.0
occ:0.33
 O A:HOH2030 2.6 3.8 0.3
NH1 A:ARG57 3.2 26.3 1.0
CD1 A:LEU61 4.1 22.1 1.0
CZ A:ARG57 4.3 27.1 1.0
OD1 A:ASP58 4.3 27.0 1.0
NH2 A:ARG57 4.5 27.1 1.0

Chlorine binding site 3 out of 6 in 4a25

Go back to Chlorine Binding Sites List in 4a25
Chlorine binding site 3 out of 6 in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1173

b:24.1
occ:1.00
 NH1 B:ARG71 3.1 22.4 1.0
O A:ARG71 3.5 18.6 1.0
CE B:LYS45 3.5 21.7 1.0
NZ B:LYS45 3.6 19.9 1.0
O A:HOH2040 3.6 22.4 1.0
C A:ARG71 3.8 19.0 1.0
O A:HOH2037 3.9 24.4 1.0
CZ B:ARG71 4.0 22.4 1.0
NH2 B:ARG71 4.0 21.3 1.0
CB A:ARG71 4.1 19.9 1.0
N A:GLY72 4.1 18.5 1.0
CB A:ASP75 4.1 19.2 1.0
CA A:GLY72 4.2 18.3 1.0
CA A:ARG71 4.5 19.9 1.0
CG A:ASP75 4.7 20.3 1.0
CD B:LYS45 5.0 21.3 1.0
OD1 A:ASP75 5.0 19.4 1.0
CG A:ARG71 5.0 21.1 1.0

Chlorine binding site 4 out of 6 in 4a25

Go back to Chlorine Binding Sites List in 4a25
Chlorine binding site 4 out of 6 in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1174

b:16.1
occ:1.00
 O B:HOH2020 2.6 7.3 1.0
NH1 B:ARG57 3.2 18.5 1.0
NH1 C:ARG57 3.2 18.5 1.0
O B:HOH2021 3.3 22.8 1.0
O C:HOH2030 3.5 25.4 1.0
CD1 C:LEU61 3.9 18.4 1.0
CD1 B:LEU61 3.9 17.7 1.0
OD1 C:ASP58 4.2 21.9 1.0
CZ C:ARG57 4.2 20.9 1.0
CZ B:ARG57 4.2 21.2 1.0
OD1 B:ASP58 4.3 20.5 1.0
O C:HOH2010 4.4 24.0 1.0
NH2 C:ARG57 4.4 22.3 1.0
NH2 B:ARG57 4.4 22.0 1.0

Chlorine binding site 5 out of 6 in 4a25

Go back to Chlorine Binding Sites List in 4a25
Chlorine binding site 5 out of 6 in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1172

b:22.2
occ:1.00
 NH1 C:ARG71 3.2 22.5 1.0
NZ C:LYS45 3.3 17.9 1.0
O D:HOH2007 3.4 25.4 1.0
CE C:LYS45 3.4 21.3 1.0
O D:ARG71 3.6 19.2 1.0
O C:HOH2044 3.6 16.7 1.0
C D:ARG71 3.8 18.8 1.0
O D:HOH2030 3.9 24.9 1.0
CB D:ASP75 4.0 20.4 1.0
N D:GLY72 4.1 18.2 1.0
CZ C:ARG71 4.1 23.2 1.0
NH2 C:ARG71 4.1 21.1 1.0
CB D:ARG71 4.2 19.4 1.0
CA D:GLY72 4.2 17.9 1.0
CG D:ASP75 4.5 21.1 1.0
CA D:ARG71 4.6 19.0 1.0
OD1 D:ASP75 4.7 20.1 1.0
O C:HOH2024 4.8 10.4 1.0
CD C:LYS45 4.9 21.1 1.0
O C:HOH2042 5.0 26.1 1.0

Chlorine binding site 6 out of 6 in 4a25

Go back to Chlorine Binding Sites List in 4a25
Chlorine binding site 6 out of 6 in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1172

b:22.5
occ:1.00
 NH1 D:ARG71 3.2 20.3 1.0
CE D:LYS45 3.4 20.7 1.0
NZ D:LYS45 3.4 17.0 1.0
O C:ARG71 3.5 18.9 1.0
O C:HOH2041 3.5 16.2 1.0
C C:ARG71 3.8 19.6 1.0
NH2 D:ARG71 4.0 20.4 1.0
CZ D:ARG71 4.0 20.1 1.0
CB C:ASP75 4.1 19.7 1.0
N C:GLY72 4.2 19.8 1.0
CB C:ARG71 4.2 20.8 1.0
O C:HOH2039 4.2 21.5 1.0
CA C:GLY72 4.2 20.0 1.0
CA C:ARG71 4.6 19.8 1.0
CG C:ASP75 4.6 21.1 1.0
O C:HOH2046 4.8 8.3 1.0
OD1 C:ASP75 4.8 21.3 1.0
CD D:LYS45 4.9 19.8 1.0

Reference:

M.Ardini, A.Fiorillo, M.Fittipaldi, S.Stefanini, D.Gatteschi, A.Llari, E.Chiancone. Kineococcus Radiotolerans Dps Forms A Heteronuclear Mn-Fe Ferroxidase Center That May Explain the Mn-Dependent Protection Against Oxidative Stress. Biochim.Biophys.Acta V.1830 3745 2013.
ISSN: ISSN 0006-3002
PubMed: 23396000
DOI: 10.1016/J.BBAGEN.2013.02.003
Page generated: Fri Jul 11 12:42:28 2025

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