Sodium in PDB 6zs1: Chaetomium Thermophilum Cuzn-Superoxide Dismutase

Enzymatic activity of Chaetomium Thermophilum Cuzn-Superoxide Dismutase

All present enzymatic activity of Chaetomium Thermophilum Cuzn-Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of Chaetomium Thermophilum Cuzn-Superoxide Dismutase, PDB code: 6zs1 was solved by A.C.Papageorgiou, I.Mohsin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.59 / 1.56
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 89.11, 89.11, 310.37, 90, 90, 120
R / Rfree (%) 17.3 / 20.4

Other elements in 6zs1:

The structure of Chaetomium Thermophilum Cuzn-Superoxide Dismutase also contains other interesting chemical elements:

Zinc (Zn) 8 atoms
Copper (Cu) 4 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase (pdb code 6zs1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase, PDB code: 6zs1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in 6zs1

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Sodium binding site 1 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:30.5
occ:1.00
 O A:HOH884 2.6 27.3 1.0
O A:LEU85 2.7 14.5 1.0
O A:ASN87 2.8 15.6 1.0
O D:HOH833 3.3 28.6 1.0
N A:ASN87 3.6 15.8 1.0
C A:ASN87 3.7 14.4 1.0
CE A:MET100 3.7 23.6 1.0
SD A:MET100 3.7 21.8 1.0
O A:HOH910 3.9 30.9 1.0
C A:LEU85 3.9 11.6 1.0
O A:HOH750 4.0 17.4 1.0
C A:GLY86 4.0 13.3 1.0
CA A:GLY86 4.1 13.9 1.0
O A:HOH698 4.2 24.8 1.0
CA A:ASN87 4.3 14.2 1.0
N A:GLY86 4.5 13.7 1.0
O A:HOH918 4.6 20.3 1.0
N A:ILE88 4.7 16.1 1.0
O A:HOH913 4.8 22.6 1.0
O D:HOH665 4.8 21.0 1.0
O A:GLY86 4.8 14.3 1.0
CG A:PRO75 4.8 12.7 1.0
CH2 A:TRP33 5.0 20.6 1.0

Sodium binding site 2 out of 15 in 6zs1

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Sodium binding site 2 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:35.0
occ:1.00
 OG1 D:THR99 2.8 16.1 1.0
CD1 A:ILE30 2.9 28.5 1.0
O D:HOH835 3.0 42.7 1.0
O A:HOH643 3.2 35.7 1.0
CG2 D:THR99 3.7 14.3 1.0
CB D:THR99 3.7 14.4 1.0
O D:HOH699 4.0 19.4 1.0
OG1 D:THR32 4.1 20.6 0.6
CG1 A:ILE30 4.2 16.8 1.0
CG2 D:THR32 4.2 21.2 0.4
O A:HOH886 4.3 32.7 1.0
CG2 D:THR32 4.5 19.3 0.6
O A:HOH751 4.9 40.1 1.0
OG1 A:THR99 4.9 19.7 1.0
CB D:THR32 4.9 16.7 0.4
CB D:THR32 4.9 16.7 0.6
O D:HOH794 5.0 47.4 1.0

Sodium binding site 3 out of 15 in 6zs1

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Sodium binding site 3 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:38.1
occ:1.00
 CE A:LYS3 2.6 43.6 1.0
CG A:LYS3 2.7 28.9 1.0
O A:ALA4 3.0 17.6 1.0
O A:HOH898 3.0 38.9 1.0
CD A:LYS3 3.1 35.6 1.0
CB A:THR19 3.5 16.0 1.0
C A:ALA4 3.6 16.9 1.0
CB A:ALA153 3.7 19.7 1.0
CG2 A:THR19 3.8 13.9 1.0
N A:ALA4 3.9 13.5 1.0
NZ A:LYS3 4.0 50.3 1.0
CB A:VAL5 4.0 18.2 1.0
O F:HOH681 4.1 40.8 1.0
CB A:LYS3 4.1 17.7 1.0
O A:HOH820 4.2 39.3 1.0
O A:PHE20 4.2 14.1 1.0
CA A:THR19 4.3 13.4 1.0
CA A:ALA4 4.3 12.1 1.0
N A:VAL5 4.4 11.6 1.0
C A:LYS3 4.4 17.5 1.0
N A:PHE20 4.4 12.9 1.0
CA A:VAL5 4.5 11.9 1.0
OG1 A:THR19 4.6 22.4 1.0
CA A:LYS3 4.6 14.3 1.0
CG1 A:VAL5 4.7 18.4 1.0
OE2 A:GLU21 4.8 36.8 1.0
C A:THR19 4.8 14.3 1.0
CG2 A:VAL5 4.9 16.2 1.0
CG A:GLU21 4.9 20.0 1.0

Sodium binding site 4 out of 15 in 6zs1

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Sodium binding site 4 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:33.0
occ:1.00
 O B:VAL105 2.6 14.2 1.0
O B:ASP102 2.9 17.9 1.0
C B:HIS103 3.2 17.0 1.0
O B:HIS103 3.3 17.9 1.0
NZ B:LYS106 3.4 28.4 1.0
N B:THR29 3.5 12.8 1.0
O B:HOH768 3.5 28.7 1.0
CA B:PRO28 3.5 19.7 1.0
CA B:HIS103 3.6 14.6 1.0
C B:VAL105 3.6 11.9 1.0
O B:SER27 3.7 21.3 1.0
N B:LEU104 3.7 12.8 1.0
N B:VAL105 3.8 13.3 1.0
C B:ASP102 3.8 14.5 1.0
C B:LEU104 3.9 14.1 1.0
OG1 B:THR29 3.9 13.8 1.0
C B:PRO28 3.9 20.1 1.0
N B:HIS103 4.1 12.1 1.0
CG B:LYS106 4.1 18.1 1.0
CA B:LEU104 4.2 11.4 1.0
CA B:VAL105 4.3 13.3 1.0
CB B:THR29 4.3 11.8 1.0
NE2 B:GLN22 4.4 14.5 1.0
O B:HOH601 4.4 38.7 1.0
O B:LEU104 4.4 14.5 1.0
N B:PRO28 4.4 18.6 1.0
CB B:PRO28 4.5 18.4 1.0
N B:LYS106 4.5 12.9 1.0
C B:SER27 4.5 22.6 1.0
CA B:THR29 4.5 13.7 1.0
CE B:LYS106 4.6 35.1 1.0
CA B:LYS106 4.7 11.7 1.0
CD B:LYS106 4.9 24.6 1.0
CB B:HIS103 4.9 15.0 1.0

Sodium binding site 5 out of 15 in 6zs1

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Sodium binding site 5 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:38.2
occ:1.00
 CE B:LYS3 2.7 45.0 1.0
CG B:LYS3 2.7 27.6 1.0
O B:ALA4 2.9 18.6 1.0
O B:HOH883 3.0 36.1 1.0
CD B:LYS3 3.1 35.7 1.0
CB B:THR19 3.4 18.4 1.0
C B:ALA4 3.7 16.4 1.0
CG2 B:THR19 3.7 12.9 1.0
CB B:ALA153 3.8 21.0 1.0
N B:ALA4 3.9 12.7 1.0
NZ B:LYS3 4.0 51.8 1.0
CB B:VAL5 4.1 15.2 1.0
CB B:LYS3 4.1 16.0 1.0
O B:HOH791 4.1 38.4 1.0
O B:PHE20 4.2 13.5 1.0
CA B:THR19 4.2 14.3 1.0
O E:HOH621 4.3 39.3 1.0
N B:PHE20 4.3 13.4 1.0
OG1 B:THR19 4.4 22.4 1.0
CA B:ALA4 4.4 13.9 1.0
N B:VAL5 4.4 12.8 1.0
C B:LYS3 4.5 16.4 1.0
CA B:VAL5 4.6 15.3 1.0
OE2 B:GLU21 4.6 29.9 1.0
CA B:LYS3 4.7 17.3 1.0
C B:THR19 4.7 16.2 1.0
CG B:GLU21 4.8 22.7 1.0
CG2 B:VAL5 4.9 15.1 1.0
CG1 B:VAL5 4.9 17.1 1.0
C B:PHE20 5.0 14.8 1.0

Sodium binding site 6 out of 15 in 6zs1

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Sodium binding site 6 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:38.7
occ:1.00
 O B:HOH685 2.7 21.0 1.0
O B:HOH636 2.8 27.7 1.0
O B:HOH911 2.8 45.0 1.0
O E:HOH816 2.9 41.2 1.0
O B:HOH734 3.0 31.1 1.0
O G:HOH831 3.1 33.0 1.0
O B:HOH909 3.9 29.4 1.0
CG2 B:VAL2 4.0 18.3 1.0
CG2 B:ILE108 4.1 14.4 1.0
CG1 B:ILE108 4.1 15.3 1.0
O B:HOH627 4.1 24.2 1.0
O E:HOH789 4.1 38.7 1.0
O G:HOH714 4.4 29.7 1.0
CB B:ILE108 4.4 11.8 1.0
CA B:ILE108 4.4 12.2 1.0
O B:HOH828 4.6 40.5 1.0
O G:HOH689 4.6 22.1 1.0
O B:LEU107 4.7 18.2 1.0
O B:HOH765 4.8 33.0 1.0
OH B:TYR-2 4.8 23.0 1.0
OE2 B:GLU0 4.9 27.7 1.0
O E:HOH696 4.9 38.1 1.0
CD1 B:ILE108 5.0 15.0 1.0

Sodium binding site 7 out of 15 in 6zs1

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Sodium binding site 7 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:38.5
occ:1.00
 O C:HOH660 2.2 37.2 1.0
O C:GLY10 2.7 20.6 1.0
O C:HOH812 3.1 26.1 1.0
O C:HOH765 3.4 42.1 1.0
NH2 C:ARG9 3.5 40.9 1.0
O C:SER12 3.6 23.7 1.0
C C:GLY10 3.8 16.1 1.0
O C:HOH643 3.8 20.4 1.0
O C:HOH745 4.1 55.2 1.0
O C:HOH811 4.3 39.5 1.0
N C:SER12 4.3 24.4 1.0
CZ C:ARG9 4.3 31.0 1.0
N C:GLY10 4.6 18.3 1.0
C C:SER12 4.7 20.2 1.0
N C:ASP11 4.7 19.9 1.0
CA C:ASP11 4.7 27.5 1.0
CA C:GLY10 4.7 19.9 1.0
NE C:ARG9 4.8 28.0 1.0
O C:HOH754 4.8 44.7 1.0
O C:HOH796 4.9 42.2 1.0

Sodium binding site 8 out of 15 in 6zs1

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Sodium binding site 8 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na504

b:47.2
occ:1.00
 O D:HOH823 2.5 30.9 1.0
O D:THR101 2.6 14.7 1.0
O A:HOH910 2.7 30.9 1.0
O D:HOH715 2.9 19.6 1.0
O D:HOH744 3.6 18.6 1.0
C D:THR101 3.8 13.9 1.0
CD2 D:HIS103 4.0 24.9 1.0
O A:HOH825 4.0 31.3 1.0
CA D:ASP102 4.1 13.2 1.0
O D:HOH833 4.3 28.6 1.0
CB D:PRO75 4.4 20.3 1.0
N D:ASP102 4.4 15.1 1.0
CE D:MET100 4.5 32.5 1.0
NE2 D:HIS103 4.5 20.9 1.0
O D:HOH665 4.7 21.0 1.0
O D:PRO75 4.7 19.8 1.0
O A:HOH698 4.7 24.8 1.0
O D:HOH759 4.7 34.5 1.0
O D:HOH861 4.8 21.9 1.0
N D:HIS103 4.8 17.2 1.0
C D:PRO75 4.9 21.3 1.0
N D:THR101 4.9 13.4 1.0
CA D:THR101 4.9 14.8 1.0
O A:HOH884 4.9 27.3 1.0
OD2 D:ASP102 4.9 23.5 1.0
CB D:ASP102 5.0 12.9 1.0
C D:ASP102 5.0 16.6 1.0

Sodium binding site 9 out of 15 in 6zs1

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Sodium binding site 9 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na503

b:25.6
occ:1.00
 O E:ILE108 2.7 22.6 1.0
N E:GLU111 2.8 17.4 1.0
C E:GLY109 3.2 22.9 1.0
OE2 E:GLU25 3.2 45.6 1.0
N E:PRO110 3.2 21.1 1.0
CA E:GLY109 3.4 23.6 1.0
CD E:LYS106 3.5 34.1 1.0
CA E:GLU111 3.5 16.9 1.0
CD E:PRO110 3.6 26.9 1.0
CB E:GLU111 3.6 18.1 1.0
O E:GLY109 3.6 18.6 1.0
OE1 E:GLU111 3.6 32.8 1.0
C E:ILE108 3.7 24.4 1.0
N E:SER112 3.7 17.3 1.0
C E:GLU111 3.7 13.6 1.0
CB E:LYS106 3.8 17.0 1.0
C E:PRO110 3.8 17.2 1.0
CD E:GLU25 3.9 47.4 1.0
N E:GLY109 4.0 22.4 1.0
CA E:PRO110 4.1 17.9 1.0
CD E:GLU111 4.1 35.6 1.0
O E:HOH602 4.2 30.3 1.0
CG E:LYS106 4.2 18.9 1.0
CG E:GLU25 4.3 31.8 1.0
O E:HOH658 4.4 34.6 1.0
O E:GLU111 4.5 16.8 1.0
CG E:GLU111 4.5 23.8 1.0
CA E:SER112 4.7 15.0 1.0
OE1 E:GLU25 4.7 42.8 1.0
CB E:PRO110 4.7 21.9 1.0
CE E:LYS106 4.7 31.1 1.0
CG E:PRO110 4.8 26.2 1.0
OE2 E:GLU111 4.9 35.5 1.0
O E:PRO110 5.0 21.7 1.0

Sodium binding site 10 out of 15 in 6zs1

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Sodium binding site 10 out of 15 in the Chaetomium Thermophilum Cuzn-Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Chaetomium Thermophilum Cuzn-Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na504

b:44.8
occ:1.00
 O E:THR101 2.5 17.6 1.0
O E:HOH802 2.5 32.5 1.0
O E:HOH716 2.7 20.6 1.0
C E:THR101 3.6 17.0 1.0
CD2 E:HIS103 3.7 21.5 1.0
O E:HOH722 3.9 16.5 1.0
CA E:ASP102 3.9 15.0 1.0
O E:HOH642 4.0 27.8 1.0
NE2 E:HIS103 4.2 19.0 1.0
N E:ASP102 4.2 13.0 1.0
O E:HOH767 4.4 35.5 1.0
N E:HIS103 4.4 17.3 1.0
O E:HOH689 4.5 20.2 1.0
C E:ASP102 4.7 14.2 1.0
CG E:HIS103 4.8 18.6 1.0
O E:PRO75 4.8 20.6 1.0
OD2 E:ASP102 4.8 22.5 1.0
CB E:PRO75 4.8 19.2 1.0
CA E:THR101 4.8 11.4 1.0
CB E:ASP102 4.8 14.8 1.0
N E:THR101 4.9 14.3 1.0
O E:HOH862 5.0 29.2 1.0
CG E:ASP102 5.0 18.3 1.0

Reference:

I.Mohsin, L.Q.Zhang, D.C.Li, A.C.Papageorgiou. Crystal Structure of A Cu,Zn Superoxide Dismutase From the Thermophilic Fungus Chaetomium Thermophilum. Protein Pept.Lett. 2021.
ISSN: ISSN 0929-8665
PubMed: 33726638
DOI: 10.2174/0929866528666210316104919
Page generated: Sat Apr 17 17:06:57 2021

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