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Sodium in PDB 7y44: Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

Enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

All present enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44 was solved by T.Tsukihara, K.Hirata, H.Ago, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.31 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.6, 204.51, 178.29, 90, 90, 90
R / Rfree (%) 18.5 / 22.7

Other elements in 7y44:

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution also contains other interesting chemical elements:

Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 4 atoms
Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution (pdb code 7y44). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 7y44

Go back to Sodium Binding Sites List in 7y44
Sodium binding site 1 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:20.7
occ:1.00
 O A:HOH856 2.2 18.6 1.0
O A:GLY45 2.3 25.1 1.0
OE1 A:GLU40 2.3 22.2 1.0
O A:SER441 2.3 21.9 1.0
O A:GLU40 2.4 20.0 1.0
CD A:GLU40 3.3 27.8 1.0
C A:GLU40 3.4 20.2 1.0
C A:GLY45 3.5 27.9 1.0
O A:HOH735 3.5 29.0 1.0
C A:SER441 3.5 25.3 1.0
CG A:GLU40 3.6 19.6 1.0
OD2 A:ASP442 3.9 21.1 1.0
O A:GLN43 4.0 20.5 1.0
CA A:ASP442 4.0 21.5 1.0
CA A:THR46 4.1 29.9 1.0
CB A:ASP442 4.1 15.9 1.0
CG A:ASP442 4.1 29.1 1.0
N A:ASP442 4.2 19.6 1.0
N A:THR46 4.2 23.9 1.0
CA A:GLU40 4.2 24.9 1.0
N A:LEU41 4.3 23.1 1.0
N A:LEU47 4.4 28.1 1.0
CA A:LEU41 4.4 13.7 1.0
N A:GLY45 4.4 23.7 1.0
CB A:GLU40 4.4 20.5 1.0
OE2 A:GLU40 4.5 20.2 1.0
CD2 A:LEU41 4.6 20.1 1.0
CA A:GLY45 4.6 29.7 1.0
C A:THR46 4.7 31.9 1.0
CA A:SER441 4.7 23.3 1.0
OD1 A:ASP442 4.8 24.8 1.0
CB A:SER441 4.9 16.1 1.0

Sodium binding site 2 out of 4 in 7y44

Go back to Sodium Binding Sites List in 7y44
Sodium binding site 2 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:58.6
occ:1.00
 O C:HOH432 1.9 28.6 1.0
NE2 C:HIS148 2.3 29.2 1.0
NE2 C:HIS232 2.3 22.8 1.0
CD2 C:HIS232 2.6 22.5 1.0
CG C:GLU236 2.8 39.1 1.0
CD C:GLU236 2.9 45.1 1.0
CD2 C:HIS148 3.1 36.6 1.0
OE1 C:GLU236 3.3 42.7 1.0
CE1 C:HIS148 3.3 40.8 1.0
CE1 C:HIS232 3.6 25.1 1.0
OE2 C:GLU236 3.6 41.5 1.0
CG C:HIS232 3.9 26.4 1.0
CG C:HIS148 4.2 29.1 1.0
CB C:GLU236 4.3 19.6 1.0
ND1 C:HIS148 4.3 30.8 1.0
ND1 C:HIS232 4.4 23.7 1.0
O C:HOH501 4.5 54.0 1.0
CG C:MET152 4.6 30.4 1.0
SD C:MET152 4.7 34.0 1.0
O C:HIS232 4.7 17.4 1.0
CD2 C:PHE235 4.8 25.2 1.0
O C:HOH477 4.8 45.9 1.0
CA C:GLU236 4.9 23.1 1.0
N C:GLU236 5.0 18.5 1.0

Sodium binding site 3 out of 4 in 7y44

Go back to Sodium Binding Sites List in 7y44
Sodium binding site 3 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na605

b:25.5
occ:1.00
 O N:HOH870 2.3 27.5 1.0
OE1 N:GLU40 2.3 25.3 1.0
O N:SER441 2.3 26.0 1.0
O N:GLU40 2.3 24.7 1.0
O N:GLY45 2.3 31.3 1.0
CD N:GLU40 3.2 47.5 1.0
O N:HOH708 3.3 35.8 1.0
C N:GLU40 3.3 33.1 1.0
CG N:GLU40 3.5 24.8 1.0
C N:GLY45 3.5 33.5 1.0
C N:SER441 3.5 21.4 1.0
O N:GLN43 4.0 27.8 1.0
CA N:ASP442 4.0 22.9 1.0
CB N:ASP442 4.1 25.4 1.0
CA N:THR46 4.2 31.9 1.0
OD2 N:ASP442 4.2 30.2 1.0
N N:LEU41 4.2 29.8 1.0
CA N:GLU40 4.2 29.4 1.0
N N:ASP442 4.2 24.1 1.0
N N:THR46 4.2 30.6 1.0
CG N:ASP442 4.3 34.7 1.0
CA N:LEU41 4.3 23.8 1.0
OE2 N:GLU40 4.3 24.1 1.0
CB N:GLU40 4.4 22.7 1.0
CD2 N:LEU41 4.5 23.5 1.0
N N:LEU47 4.5 39.1 1.0
N N:GLY45 4.6 29.6 1.0
CA N:SER441 4.6 28.6 1.0
CA N:GLY45 4.6 26.2 1.0
C N:THR46 4.8 46.7 1.0
CB N:SER441 4.9 32.1 1.0

Sodium binding site 4 out of 4 in 7y44

Go back to Sodium Binding Sites List in 7y44
Sodium binding site 4 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na303

b:42.1
occ:1.00
 NE2 P:HIS148 2.5 32.2 1.0
NE2 P:HIS232 2.6 19.8 1.0
CE1 P:HIS148 3.3 34.2 1.0
CD2 P:HIS232 3.4 27.6 1.0
CD P:GLU236 3.4 103.4 1.0
CE1 P:HIS232 3.6 27.2 1.0
CD2 P:HIS148 3.6 26.5 1.0
CG P:GLU236 3.7 39.5 1.0
OE2 P:GLU236 3.7 43.0 1.0
OE1 P:GLU236 3.7 37.8 1.0
O P:HOH507 3.9 59.4 1.0
SD P:MET152 4.0 33.8 1.0
CG P:MET152 4.1 30.5 1.0
O P:HOH528 4.4 57.8 1.0
ND1 P:HIS148 4.5 43.1 1.0
CG P:HIS232 4.6 22.7 1.0
ND1 P:HIS232 4.7 21.2 1.0
CG P:HIS148 4.7 30.4 1.0
O P:HOH471 4.8 53.7 1.0
O P:HOH442 4.9 24.8 1.0

Reference:

K.Hirata, T.Tsukihara, H.Ago. Determination of Damage-Free Crystal Structure of An X-Ray-Sensitive Protein Using An Xfel Nature Methods V. 11 734 2014.
DOI: 10.1038/NMETH.2962
Page generated: Wed Oct 9 09:51:40 2024

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