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Sodium in PDB 4br6: Crystal Structure of Chaetomium Thermophilum Mnsod

Enzymatic activity of Crystal Structure of Chaetomium Thermophilum Mnsod

All present enzymatic activity of Crystal Structure of Chaetomium Thermophilum Mnsod:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Chaetomium Thermophilum Mnsod, PDB code: 4br6 was solved by T.Haikarainen, C.Frioux, L.-Q.Zhnag, D.-C.Li, A.C.Papageorgiou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.959 / 2.00
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 69.140, 69.140, 300.430, 90.00, 90.00, 120.00
R / Rfree (%) 11.96 / 17.77

Other elements in 4br6:

The structure of Crystal Structure of Chaetomium Thermophilum Mnsod also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Chaetomium Thermophilum Mnsod (pdb code 4br6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Chaetomium Thermophilum Mnsod, PDB code: 4br6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4br6

Go back to Sodium Binding Sites List in 4br6
Sodium binding site 1 out of 6 in the Crystal Structure of Chaetomium Thermophilum Mnsod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Chaetomium Thermophilum Mnsod within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:27.2
occ:1.00
 OD1 A:ASN137 2.3 36.4 1.0
OD1 A:ASP103 2.3 36.3 1.0
OD1 D:ASN137 2.3 31.2 1.0
OD1 D:ASP103 2.4 37.1 1.0
O A:HOH2313 2.6 33.0 1.0
CG D:ASP103 3.3 32.4 1.0
CG A:ASN137 3.4 30.1 1.0
CG A:ASP103 3.4 29.1 1.0
CG D:ASN137 3.5 30.4 1.0
O A:HOH2312 3.5 28.8 1.0
O A:HOH2311 3.6 58.7 1.0
OD2 A:ASP103 3.9 28.8 1.0
O A:HOH2260 3.9 71.8 1.0
OD2 D:ASP103 4.0 30.8 1.0
ND2 D:ASN137 4.1 28.9 1.0
ND2 A:ASN137 4.1 26.6 1.0
CB D:ASP103 4.3 27.5 1.0
O A:HOH2215 4.3 31.0 1.0
CA D:ASP103 4.4 30.0 1.0
O D:ALA102 4.5 36.0 1.0
O A:HOH2273 4.5 33.8 1.0
CB A:ASN137 4.5 27.9 1.0
CB D:ASN137 4.6 31.6 1.0
CB A:ASP103 4.7 28.5 1.0
CA A:ASN137 4.9 29.0 1.0
C D:ALA102 5.0 31.6 1.0
N D:ASP103 5.0 32.5 1.0

Sodium binding site 2 out of 6 in 4br6

Go back to Sodium Binding Sites List in 4br6
Sodium binding site 2 out of 6 in the Crystal Structure of Chaetomium Thermophilum Mnsod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Chaetomium Thermophilum Mnsod within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:30.2
occ:1.00
 O A:LEU168 2.6 22.6 1.0
O A:HOH2298 3.0 21.2 1.0
O A:HOH2294 3.2 19.1 1.0
C A:LEU168 3.5 21.4 1.0
O A:HOH2314 3.6 37.4 1.0
O A:GLN169 3.7 23.3 1.0
CG A:GLU171 3.7 21.3 1.0
O A:HOH2293 3.9 25.6 1.0
OE2 A:GLU171 3.9 22.9 1.0
C A:GLN169 3.9 19.3 1.0
CD A:GLU171 4.0 26.4 1.0
CA A:GLN169 4.0 18.8 1.0
N A:GLN169 4.1 22.3 1.0
O A:HOH2295 4.2 59.0 1.0
O A:HOH2166 4.3 29.4 1.0
O A:TYR167 4.4 19.0 1.0
CD2 B:LEU168 4.4 16.2 1.0
CA A:LEU168 4.6 18.0 1.0
O A:HOH2170 4.6 40.0 1.0
OE1 A:GLU171 4.7 24.4 1.0
N A:TYR170 4.8 21.2 1.0
N A:GLU171 4.8 18.4 1.0

Sodium binding site 3 out of 6 in 4br6

Go back to Sodium Binding Sites List in 4br6
Sodium binding site 3 out of 6 in the Crystal Structure of Chaetomium Thermophilum Mnsod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Chaetomium Thermophilum Mnsod within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na901

b:31.7
occ:1.00
 O A:HOH2316 2.8 28.6 1.0
OG1 A:THR142 3.0 21.8 1.0
O A:HOH2315 3.2 29.8 1.0
O A:THR142 3.3 21.1 1.0
C A:THR142 3.5 18.6 1.0
N A:ALA144 3.7 15.7 1.0
N A:ARG143 3.8 21.6 1.0
C A:ARG143 3.8 14.8 1.0
CA A:ARG143 3.8 16.0 1.0
CB A:THR142 3.9 19.1 1.0
O A:HOH2267 4.1 21.3 1.0
O A:HOH2272 4.3 16.9 1.0
CA A:THR142 4.3 20.4 1.0
O A:ARG143 4.5 18.3 1.0
CA A:ALA144 4.5 14.6 1.0
O A:HOH2238 4.6 14.8 1.0
CB A:ALA144 4.7 18.3 1.0
O A:HOH2266 4.9 37.2 1.0
O A:HOH2268 5.0 30.3 1.0

Sodium binding site 4 out of 6 in 4br6

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Sodium binding site 4 out of 6 in the Crystal Structure of Chaetomium Thermophilum Mnsod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Chaetomium Thermophilum Mnsod within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:29.2
occ:1.00
 O C:HOH2308 2.8 42.9 1.0
O C:HOH2307 2.9 41.0 1.0
O A:HOH2176 3.2 25.2 1.0
CB C:ASN65 3.6 17.7 1.0
N A:PRO62 3.6 18.6 1.0
CA A:PRO62 3.6 19.9 1.0
O A:HOH2081 3.7 34.3 1.0
CG C:ASN65 3.7 19.4 1.0
C A:ALA61 3.8 19.1 1.0
O A:ALA61 3.8 21.1 1.0
OD1 C:ASN65 3.8 22.3 1.0
CD A:PRO62 3.9 23.9 1.0
CG A:PRO62 3.9 20.7 1.0
CB A:ALA61 4.2 15.4 1.0
CB A:PRO62 4.2 20.5 1.0
O A:HOH2079 4.2 35.3 1.0
ND2 C:ASN65 4.3 20.8 1.0
O A:HOH2173 4.6 21.4 1.0
CA A:ALA61 4.6 21.4 1.0
CB A:ASN65 4.6 16.3 1.0
O C:HOH2156 4.6 20.5 1.0
O C:ALA61 4.7 21.4 1.0
C A:PRO62 4.8 18.1 1.0
O C:HOH2150 4.9 20.2 1.0
CA C:ASN65 5.0 18.3 1.0
C C:ALA61 5.0 17.6 1.0

Sodium binding site 5 out of 6 in 4br6

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Sodium binding site 5 out of 6 in the Crystal Structure of Chaetomium Thermophilum Mnsod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Chaetomium Thermophilum Mnsod within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na701

b:25.2
occ:1.00
 OH C:TYR34 2.9 22.5 1.0
CZ3 C:TRP162 3.2 19.3 1.0
O C:HOH2071 3.6 24.3 1.0
O C:HOH2309 3.6 14.9 1.0
CH2 C:TRP162 3.7 15.2 1.0
O C:HOH2032 3.7 23.5 1.0
CZ C:TYR34 3.9 17.4 1.0
CE3 C:TRP162 3.9 14.8 1.0
ND1 C:HIS30 4.2 16.9 1.0
OE2 D:GLU163 4.3 19.2 1.0
O D:HOH2270 4.3 37.9 1.0
CE1 C:HIS164 4.3 19.9 1.0
CE1 C:TYR34 4.4 16.9 1.0
O D:HOH2217 4.5 30.9 1.0
ND1 C:HIS164 4.5 16.0 1.0
O D:HOH2256 4.5 16.9 1.0
CZ C:PHE66 4.6 21.5 1.0
O D:HOH2266 4.6 12.2 1.0
CZ2 C:TRP162 4.8 18.7 1.0
O D:HOH2269 4.8 37.8 1.0
CE1 C:HIS30 4.8 16.6 1.0
CE2 C:TYR34 4.8 16.9 1.0
CD2 C:TRP162 4.9 12.2 1.0

Sodium binding site 6 out of 6 in 4br6

Go back to Sodium Binding Sites List in 4br6
Sodium binding site 6 out of 6 in the Crystal Structure of Chaetomium Thermophilum Mnsod


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Chaetomium Thermophilum Mnsod within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:25.4
occ:1.00
 CE2 D:TYR9 2.7 23.4 1.0
O D:TRP78 2.7 16.8 1.0
CZ D:TYR9 2.8 24.4 1.0
O D:HOH2029 2.9 24.5 1.0
O D:LEU81 3.2 19.9 1.0
C D:TRP78 3.4 17.3 1.0
CA D:TRP78 3.4 13.8 1.0
CB D:TRP78 3.5 15.9 1.0
O D:HOH2171 3.7 27.0 1.0
CB D:LEU81 3.8 16.4 1.0
CD2 D:TYR9 3.9 22.1 1.0
C D:LEU81 4.0 22.8 1.0
CE1 D:TYR9 4.0 19.1 1.0
CD2 D:LEU7 4.3 17.5 1.0
CA D:LEU81 4.4 17.8 1.0
CG D:TRP78 4.6 13.6 1.0
N D:GLU79 4.6 17.7 1.0
N D:LEU81 4.7 19.7 1.0
CE3 D:TRP78 4.7 17.9 1.0
N D:TRP78 4.8 18.7 1.0
CG D:TYR9 4.8 26.5 1.0
CD1 D:TYR9 4.9 20.1 1.0
CD1 D:LEU81 4.9 15.2 1.0
CE D:MET23 4.9 24.2 1.0
O D:HOH2021 4.9 31.0 1.0
CB D:LEU7 5.0 17.4 1.0
CD2 D:TRP78 5.0 15.2 1.0
CG D:LEU81 5.0 17.6 1.0
N D:ALA82 5.0 27.4 1.0

Reference:

T.Haikarainen, C.Frioux, L.Zhnag, D.Li, A.C.Papageorgiou. Crystal Structure and Biochemical Characterization of A Manganese Superoxide Dismutase From Chaetomium Thermophilum. Biochim.Biophys.Acta V.1844 422 2014.
ISSN: ISSN 0006-3002
PubMed: 24316252
DOI: 10.1016/J.BBAPAP.2013.11.014
Page generated: Mon Oct 7 14:33:10 2024

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