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Manganese 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:

Chlorine (Cl) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 10 binding sites of Manganese where determined in the X-Ray Structure Dps From Kineococcus Radiotolerans in Complex with Mn (II) Ions., PDB code: 4a25:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4a25

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Manganese binding site 1 out of 10 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 Manganese with other atoms in the Mn 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:Mn1169

b:16.5
occ:1.00
 O A:HOH2052 2.0 22.0 1.0
OE2 A:GLU79 2.0 20.2 1.0
O A:HOH2045 2.2 14.5 1.0
NE2 B:HIS48 2.2 19.6 1.0
OD1 A:ASP75 2.3 19.4 1.0
OD2 A:ASP75 2.4 20.5 1.0
CG A:ASP75 2.7 20.3 1.0
CD A:GLU79 3.0 20.5 1.0
CD2 B:HIS48 3.1 20.1 1.0
CE1 B:HIS48 3.3 19.3 1.0
OE1 A:GLU79 3.5 19.3 1.0
NZ B:LYS45 3.7 19.9 1.0
O A:HOH2053 3.7 24.5 1.0
O A:HOH2014 4.0 15.6 1.0
OD2 B:ASP64 4.0 19.3 1.0
NE2 B:HIS60 4.1 19.7 1.0
CE1 B:HIS60 4.1 20.3 1.0
CG A:GLU79 4.2 20.2 1.0
CB A:ASP75 4.2 19.2 1.0
O A:HOH2047 4.3 23.4 1.0
CG B:HIS48 4.3 20.6 1.0
ND1 B:HIS48 4.3 18.7 1.0
NE1 B:TRP49 4.5 22.6 1.0
O A:HOH2046 4.6 26.5 1.0
CD1 B:TRP49 4.7 23.4 1.0
OD1 B:ASP64 4.7 22.4 1.0
CG B:ASP64 4.7 20.6 1.0
CE B:LYS45 5.0 21.7 1.0

Manganese binding site 2 out of 10 in 4a25

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Manganese binding site 2 out of 10 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 Manganese with other atoms in the Mn 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:Mn1170

b:19.5
occ:0.70
 O A:HOH2075 1.9 21.0 1.0
O A:HOH2087 2.0 19.4 1.0
O A:HOH2073 2.0 20.4 1.0
OD2 C:ASP144 2.0 31.5 1.0
OD1 A:ASP144 2.3 32.9 1.0
CG C:ASP144 2.9 30.8 1.0
OD2 A:ASP144 3.0 33.8 1.0
CG A:ASP144 3.0 31.0 1.0
OD1 C:ASP144 3.2 33.1 1.0
MN A:MN1171 3.4 30.2 0.5
CB C:ASP144 4.3 28.4 1.0
CB A:ASP144 4.5 28.0 1.0
O A:ASP144 4.8 26.1 1.0
O C:ASP144 4.8 25.9 1.0
O A:HOH2074 4.9 27.6 1.0

Manganese binding site 3 out of 10 in 4a25

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Manganese binding site 3 out of 10 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 Manganese with other atoms in the Mn 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
A:Mn1171

b:30.2
occ:0.50
 O A:HOH2074 2.0 27.6 1.0
O A:HOH2076 2.0 23.5 1.0
OD1 C:ASP144 2.1 33.1 1.0
OD1 A:ASP144 2.1 32.9 1.0
ND1 A:HIS147 2.9 29.9 1.0
CG C:ASP144 3.2 30.8 1.0
CG A:ASP144 3.2 31.0 1.0
MN A:MN1170 3.4 19.5 0.7
O A:HOH2088 3.5 25.9 1.0
CE1 A:HIS147 3.6 32.1 1.0
OD2 C:ASP144 3.6 31.5 1.0
CB A:ASP144 3.8 28.0 1.0
CA A:ASP144 3.9 27.2 1.0
CG A:HIS147 4.0 28.9 1.0
ND1 C:HIS147 4.2 27.8 1.0
OD2 A:ASP144 4.3 33.8 1.0
CB A:HIS147 4.4 27.1 1.0
O A:HOH2073 4.4 20.4 1.0
CB C:ASP144 4.5 28.4 1.0
O A:HOH2087 4.7 19.4 1.0
O A:ASP144 4.7 26.1 1.0
N A:ASP144 4.8 26.7 1.0
NE2 A:HIS147 4.8 32.4 1.0
O A:HOH2075 4.8 21.0 1.0
CE1 C:HIS147 4.8 29.7 1.0
C A:ASP144 4.8 25.9 1.0

Manganese binding site 4 out of 10 in 4a25

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Manganese binding site 4 out of 10 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 Manganese with other atoms in the Mn 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
A:Mn1172

b:32.3
occ:0.33
 OD1 A:ASN55 2.1 31.3 1.0
OD2 A:ASP58 2.1 29.5 1.0
CG A:ASP58 2.9 28.8 1.0
CG A:ASN55 3.1 31.1 1.0
ND2 A:ASN55 3.5 30.2 1.0
CB A:ASP58 3.6 28.3 1.0
OD1 A:ASP58 3.8 27.0 1.0
O A:HOH2030 4.3 3.8 0.3
CB A:ASN55 4.4 31.2 1.0
N A:ASP58 4.4 27.2 1.0
CA A:ASP58 4.6 27.1 1.0
CA A:ASN55 4.7 31.1 1.0

Manganese binding site 5 out of 10 in 4a25

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Manganese binding site 5 out of 10 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 Manganese with other atoms in the Mn 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
B:Mn1171

b:19.6
occ:1.00
 O A:HOH2025 2.0 17.1 1.0
OE2 B:GLU79 2.1 27.4 1.0
NE2 A:HIS48 2.2 24.0 1.0
OD1 B:ASP75 2.2 24.6 1.0
OD2 B:ASP75 2.3 24.7 1.0
O A:HOH2023 2.3 13.2 1.0
CG B:ASP75 2.6 24.9 1.0
CD B:GLU79 3.0 28.4 1.0
CD2 A:HIS48 3.1 24.5 1.0
CE1 A:HIS48 3.2 23.8 1.0
OE1 B:GLU79 3.4 27.7 1.0
O B:HOH2035 3.6 26.1 1.0
NZ A:LYS45 3.8 19.5 1.0
NE2 A:HIS60 4.0 25.4 1.0
OD2 A:ASP64 4.0 21.1 1.0
CB B:ASP75 4.1 23.2 1.0
O B:HOH2034 4.2 20.0 1.0
CE1 A:HIS60 4.2 24.5 1.0
CG B:GLU79 4.2 26.6 1.0
CG A:HIS48 4.2 24.1 1.0
ND1 A:HIS48 4.3 23.4 1.0
NE1 A:TRP49 4.5 25.1 1.0
CD1 A:TRP49 4.7 27.0 1.0
CG A:ASP64 4.7 23.2 1.0
OD1 A:ASP64 4.8 24.2 1.0

Manganese binding site 6 out of 10 in 4a25

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Manganese binding site 6 out of 10 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 Manganese with other atoms in the Mn 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
B:Mn1172

b:15.2
occ:0.70
 OD2 B:ASP58 2.0 21.7 1.0
OD1 C:ASN55 2.1 24.0 1.0
OD1 B:ASN55 2.1 22.3 1.0
OD2 C:ASP58 2.1 23.6 1.0
CG B:ASP58 3.0 21.1 1.0
CG C:ASP58 3.0 22.3 1.0
CG C:ASN55 3.1 24.6 1.0
CG B:ASN55 3.1 23.0 1.0
ND2 C:ASN55 3.5 22.2 1.0
ND2 B:ASN55 3.6 22.6 1.0
CB C:ASP58 3.6 22.2 1.0
CB B:ASP58 3.7 20.3 1.0
OD1 B:ASP58 3.8 20.5 1.0
OD1 C:ASP58 3.8 21.9 1.0
O B:HOH2020 4.3 7.3 1.0
CB C:ASN55 4.4 25.5 1.0
CB B:ASN55 4.4 22.7 1.0
N C:ASP58 4.5 20.7 1.0
N B:ASP58 4.5 19.6 1.0
CA C:ASP58 4.7 20.9 1.0
CA C:ASN55 4.7 24.9 1.0
CA B:ASP58 4.7 19.7 1.0
CA B:ASN55 4.7 22.4 1.0

Manganese binding site 7 out of 10 in 4a25

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Manganese binding site 7 out of 10 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 Manganese with other atoms in the Mn binding site number 7 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:Mn1171

b:16.0
occ:1.00
 OE2 C:GLU79 2.0 21.6 1.0
NE2 D:HIS48 2.1 19.0 1.0
O C:HOH2053 2.2 18.6 1.0
O C:HOH2046 2.2 8.3 1.0
OD2 C:ASP75 2.4 19.9 1.0
OD1 C:ASP75 2.4 21.3 1.0
CG C:ASP75 2.7 21.1 1.0
CD C:GLU79 3.0 22.2 1.0
CE1 D:HIS48 3.1 19.2 1.0
CD2 D:HIS48 3.2 19.1 1.0
OE1 C:GLU79 3.4 20.7 1.0
NZ D:LYS45 3.8 17.0 1.0
O D:HOH2024 4.0 24.6 1.0
O C:HOH2048 4.0 30.6 1.0
OD2 D:ASP64 4.1 19.6 1.0
CE1 D:HIS60 4.1 20.4 1.0
NE2 D:HIS60 4.1 19.4 1.0
O C:HOH2049 4.1 18.9 1.0
O C:HOH2047 4.1 24.8 1.0
ND1 D:HIS48 4.2 19.1 1.0
CB C:ASP75 4.2 19.7 1.0
CG C:GLU79 4.2 19.9 1.0
CG D:HIS48 4.3 19.8 1.0
NE1 D:TRP49 4.4 23.4 1.0
CD1 D:TRP49 4.6 23.9 1.0
OD1 D:ASP64 4.7 21.8 1.0
CG D:ASP64 4.8 19.1 1.0

Manganese binding site 8 out of 10 in 4a25

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Manganese binding site 8 out of 10 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 Manganese with other atoms in the Mn binding site number 8 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:Mn1169

b:17.1
occ:1.00
 O C:HOH2026 1.8 17.5 1.0
O C:HOH2024 2.1 10.4 1.0
OE2 D:GLU79 2.1 21.1 1.0
NE2 C:HIS48 2.2 19.1 1.0
OD2 D:ASP75 2.4 20.7 1.0
OD1 D:ASP75 2.4 20.1 1.0
CG D:ASP75 2.7 21.1 1.0
CD D:GLU79 3.1 22.6 1.0
CD2 C:HIS48 3.1 20.3 1.0
CE1 C:HIS48 3.2 19.6 1.0
O D:HOH2037 3.4 28.2 1.0
OE1 D:GLU79 3.5 20.2 1.0
NZ C:LYS45 3.7 17.9 1.0
CE1 C:HIS60 4.0 20.4 1.0
OD2 C:ASP64 4.0 19.1 1.0
O D:HOH2036 4.1 21.9 1.0
NE2 C:HIS60 4.1 19.7 1.0
CB D:ASP75 4.2 20.4 1.0
CG C:HIS48 4.3 19.7 1.0
ND1 C:HIS48 4.3 18.7 1.0
CG D:GLU79 4.3 21.2 1.0
O D:HOH2038 4.4 27.4 1.0
NE1 C:TRP49 4.4 23.7 1.0
O C:HOH2037 4.7 24.3 1.0
CD1 C:TRP49 4.7 26.6 1.0
OD1 C:ASP64 4.7 22.6 1.0
CG C:ASP64 4.7 21.1 1.0

Manganese binding site 9 out of 10 in 4a25

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Manganese binding site 9 out of 10 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 Manganese with other atoms in the Mn binding site number 9 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:Mn1170

b:31.0
occ:0.33
 OD1 D:ASP144 2.2 33.2 1.0
O D:HOH2060 2.2 17.3 1.0
CG D:ASP144 3.0 31.5 1.0
OD2 D:ASP144 3.1 33.4 1.0
MN D:MN1171 3.2 30.5 0.1
CB D:ASP144 4.4 29.1 1.0
O D:ASP144 4.7 28.7 1.0
O D:HOH2059 5.0 24.7 1.0

Manganese binding site 10 out of 10 in 4a25

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Manganese binding site 10 out of 10 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 Manganese with other atoms in the Mn binding site number 10 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:Mn1171

b:30.5
occ:0.15
 OD2 D:ASP144 1.8 33.4 1.0
O D:HOH2059 2.4 24.7 1.0
CG D:ASP144 2.8 31.5 1.0
MN D:MN1170 3.2 31.0 0.3
OD1 D:ASP144 3.3 33.2 1.0
ND1 D:HIS147 3.7 31.2 1.0
CB D:ASP144 3.9 29.1 1.0
CE1 D:HIS147 4.3 33.5 1.0
CA D:ASP144 4.4 29.4 1.0
O D:HOH2060 4.5 17.3 1.0
O D:HOH2057 4.7 20.5 1.0
CG D:HIS147 4.9 30.5 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: Sat Oct 5 18:43:27 2024

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