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Sodium in PDB 3js4: Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum

Enzymatic activity of Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum

All present enzymatic activity of Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum, PDB code: 3js4 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 45.660, 66.600, 85.440, 102.09, 104.83, 88.58
R / Rfree (%) 16.7 / 20.6

Other elements in 3js4:

The structure of Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum (pdb code 3js4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum, PDB code: 3js4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3js4

Go back to Sodium Binding Sites List in 3js4
Sodium binding site 1 out of 4 in the Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum


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 Iron Superoxide Dismutase From Anaplasma Phagocytophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:30.5
occ:1.00
 O A:HOH407 2.3 13.5 1.0
O A:HOH235 2.3 20.5 1.0
O A:THR155 2.4 13.6 1.0
O A:PRO152 2.4 8.1 1.0
O A:GLN158 2.6 11.6 1.0
C A:PRO152 3.4 7.8 1.0
C A:THR155 3.5 12.7 1.0
C A:GLN158 3.5 11.9 1.0
N A:GLN158 3.8 12.5 1.0
CA A:GLN158 4.0 12.6 1.0
CB A:GLN158 4.0 13.1 1.0
N A:LEU153 4.2 8.2 1.0
N A:THR155 4.2 10.8 1.0
CA A:LEU153 4.2 8.4 1.0
CA A:PRO152 4.3 7.4 1.0
CA A:THR155 4.3 12.7 1.0
CB A:PRO152 4.4 7.2 1.0
C A:LEU153 4.4 8.7 1.0
N A:GLN156 4.5 13.5 1.0
N A:GLY157 4.5 13.4 1.0
CA A:GLN156 4.6 13.3 1.0
O A:LEU153 4.6 8.5 1.0
N A:LEU159 4.6 11.2 1.0
C A:GLN156 4.6 13.8 1.0
CB A:THR155 4.7 12.7 1.0
CD A:PRO160 4.8 9.6 1.0
O A:HOH590 4.9 20.9 1.0
C A:GLY157 5.0 13.0 1.0
CA A:LEU159 5.0 10.9 1.0

Sodium binding site 2 out of 4 in 3js4

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Sodium binding site 2 out of 4 in the Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum


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 Iron Superoxide Dismutase From Anaplasma Phagocytophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na208

b:35.3
occ:1.00
 O B:HOH222 2.2 23.6 1.0
O B:HOH408 2.3 20.2 1.0
O B:THR155 2.5 15.5 1.0
O B:PRO152 2.5 8.0 1.0
O B:GLN158 2.9 11.2 1.0
C B:PRO152 3.6 8.3 1.0
C B:THR155 3.6 13.8 1.0
C B:GLN158 3.9 11.9 1.0
N B:GLN158 4.1 12.8 1.0
OG1 B:THR155 4.2 16.6 1.0
CA B:LEU153 4.3 9.2 1.0
N B:LEU153 4.3 8.6 1.0
N B:THR155 4.4 11.9 1.0
C B:LEU153 4.4 9.3 1.0
O B:LEU153 4.4 9.3 1.0
CA B:GLN158 4.5 12.7 1.0
CA B:GLN156 4.5 13.6 1.0
N B:GLY157 4.5 13.6 1.0
N B:GLN156 4.5 13.6 1.0
CA B:PRO152 4.5 7.4 1.0
CA B:THR155 4.6 13.5 1.0
CB B:PRO152 4.6 7.5 1.0
C B:GLN156 4.7 13.5 1.0
N B:LEU159 4.9 11.4 1.0
CB B:GLN158 4.9 12.6 1.0
CD B:PRO160 4.9 9.8 1.0

Sodium binding site 3 out of 4 in 3js4

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Sodium binding site 3 out of 4 in the Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum


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 Iron Superoxide Dismutase From Anaplasma Phagocytophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na208

b:22.1
occ:1.00
 O C:HOH268 2.3 12.1 1.0
O C:THR155 2.3 13.8 1.0
O C:PRO152 2.4 8.2 1.0
O C:HOH274 2.5 8.5 1.0
O C:GLN158 2.5 10.9 1.0
C C:THR155 3.5 13.5 1.0
C C:PRO152 3.5 9.2 1.0
C C:GLN158 3.5 10.8 1.0
N C:GLN158 3.9 11.1 1.0
CA C:GLN158 4.1 11.5 1.0
N C:THR155 4.1 12.6 1.0
CB C:GLN158 4.1 12.2 1.0
CA C:LEU153 4.1 10.1 1.0
N C:LEU153 4.2 9.2 1.0
C C:LEU153 4.3 10.8 1.0
CA C:THR155 4.3 13.7 1.0
O C:LEU153 4.4 10.5 1.0
N C:GLN156 4.4 13.4 1.0
CA C:PRO152 4.5 8.3 1.0
CA C:GLN156 4.5 12.9 1.0
O C:HOH489 4.5 28.1 1.0
CB C:PRO152 4.6 8.0 1.0
N C:GLY157 4.6 12.1 1.0
N C:LEU159 4.6 10.5 1.0
C C:GLN156 4.6 12.3 1.0
CB C:THR155 4.8 14.1 1.0
N C:LEU154 4.9 10.6 1.0
CD C:PRO160 4.9 8.5 1.0
CA C:LEU159 5.0 9.8 1.0

Sodium binding site 4 out of 4 in 3js4

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Sodium binding site 4 out of 4 in the Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum


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 Iron Superoxide Dismutase From Anaplasma Phagocytophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na208

b:24.0
occ:1.00
 O D:HOH217 2.3 11.5 1.0
O D:HOH390 2.3 22.0 1.0
O D:THR155 2.4 14.2 1.0
O D:PRO152 2.5 9.4 1.0
O D:HOH268 2.5 13.6 1.0
O D:GLN158 2.5 11.1 1.0
C D:THR155 3.5 13.6 1.0
C D:GLN158 3.5 11.3 1.0
C D:PRO152 3.6 9.0 1.0
N D:GLN158 3.8 12.5 1.0
CA D:GLN158 4.0 11.9 1.0
CB D:GLN158 4.2 12.3 1.0
N D:THR155 4.2 12.3 1.0
CA D:LEU153 4.2 10.2 1.0
C D:LEU153 4.3 10.6 1.0
N D:LEU153 4.3 9.5 1.0
O D:LEU153 4.3 9.7 1.0
N D:GLN156 4.3 13.8 1.0
CA D:THR155 4.4 13.3 1.0
CA D:GLN156 4.4 13.7 1.0
N D:GLY157 4.5 13.6 1.0
CA D:PRO152 4.6 8.1 1.0
C D:GLN156 4.6 13.7 1.0
CB D:PRO152 4.6 7.6 1.0
N D:LEU159 4.6 10.8 1.0
CB D:THR155 4.9 13.6 1.0
N D:LEU154 4.9 10.7 1.0
CD D:PRO160 5.0 8.7 1.0
C D:GLY157 5.0 13.2 1.0

Reference:

T.E.Edwards, B.L.Staker, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of Iron Superoxide Dismutase From Anaplasma Phagocytophilum To Be Published.
Page generated: Mon Oct 7 11:05:58 2024

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