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Sodium in PDB 6obh: Structure of Hiv-1 Ca 1/2-Hexamer

Protein crystallography data

The structure of Structure of Hiv-1 Ca 1/2-Hexamer, PDB code: 6obh was solved by B.J.Summers, Y.Xiong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 77.770, 77.746, 77.758, 70.65, 70.70, 70.59
R / Rfree (%) 20.8 / 26.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Hiv-1 Ca 1/2-Hexamer (pdb code 6obh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Hiv-1 Ca 1/2-Hexamer, PDB code: 6obh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6obh

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Sodium binding site 1 out of 6 in the Structure of Hiv-1 Ca 1/2-Hexamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hiv-1 Ca 1/2-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:70.1
occ:1.00
OE1 F:GLU71 2.8 0.8 1.0
N A:GLU212 3.5 77.8 1.0
CB A:GLU212 3.5 94.7 1.0
CD F:GLU71 3.6 1.0 1.0
CB F:GLU71 3.7 86.4 1.0
CG F:MET68 3.9 83.6 1.0
CA F:MET68 3.9 75.2 1.0
O F:MET68 4.0 96.4 1.0
CG F:GLU71 4.0 96.9 1.0
CB F:MET68 4.0 79.9 1.0
CA A:GLU212 4.1 88.2 1.0
CB A:THR210 4.1 97.2 1.0
N A:LEU211 4.1 86.1 1.0
CB A:LEU211 4.3 84.7 1.0
OG1 A:THR210 4.4 0.9 1.0
C F:MET68 4.5 70.2 1.0
C A:LEU211 4.5 80.8 1.0
CE F:MET68 4.5 77.8 1.0
OE2 F:GLU71 4.5 0.6 1.0
CA A:LEU211 4.6 84.2 1.0
OE1 A:GLU212 4.6 0.0 1.0
SD F:MET68 4.7 83.9 1.0
CG2 A:THR210 4.8 93.1 1.0
CG A:GLU212 4.8 0.9 1.0
C A:THR210 5.0 92.4 1.0

Sodium binding site 2 out of 6 in 6obh

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Sodium binding site 2 out of 6 in the Structure of Hiv-1 Ca 1/2-Hexamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Hiv-1 Ca 1/2-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:80.5
occ:1.00
O B:GLU175 3.8 90.4 1.0
C B:GLU175 3.9 76.5 1.0
CD B:ARG143 4.1 0.0 1.0
O B:GLN176 4.2 0.9 1.0
N B:GLN176 4.3 76.4 1.0
CA B:GLU175 4.3 88.9 1.0
CB B:GLU175 4.4 97.8 1.0
C B:GLN176 4.9 0.3 1.0
NH1 B:ARG143 4.9 0.8 1.0
CG B:ARG143 5.0 0.1 1.0

Sodium binding site 3 out of 6 in 6obh

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Sodium binding site 3 out of 6 in the Structure of Hiv-1 Ca 1/2-Hexamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Hiv-1 Ca 1/2-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:68.4
occ:1.00
OE1 B:GLU71 3.3 0.1 1.0
N C:GLU212 3.4 81.0 1.0
CB C:GLU212 3.6 0.7 1.0
CD B:GLU71 3.6 0.5 1.0
CB B:GLU71 3.7 87.2 1.0
CA B:MET68 3.9 75.9 1.0
CG B:MET68 3.9 87.6 1.0
CG B:GLU71 3.9 94.8 1.0
O B:MET68 3.9 88.7 1.0
CB B:MET68 4.0 80.0 1.0
CA C:GLU212 4.1 89.8 1.0
N C:LEU211 4.1 78.4 1.0
CB C:THR210 4.1 94.7 1.0
OE2 B:GLU71 4.1 0.0 1.0
CB C:LEU211 4.3 85.8 1.0
OG1 C:THR210 4.4 98.6 1.0
C B:MET68 4.4 72.3 1.0
C C:LEU211 4.4 84.3 1.0
CE B:MET68 4.4 83.7 1.0
CA C:LEU211 4.5 83.2 1.0
OE1 C:GLU212 4.7 0.3 1.0
SD B:MET68 4.7 90.6 1.0
CG2 C:THR210 4.8 92.8 1.0
CG C:GLU212 4.8 0.5 1.0
C C:THR210 5.0 87.5 1.0

Sodium binding site 4 out of 6 in 6obh

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Sodium binding site 4 out of 6 in the Structure of Hiv-1 Ca 1/2-Hexamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Hiv-1 Ca 1/2-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:81.2
occ:1.00
O D:GLU175 3.9 0.3 1.0
C D:GLU175 3.9 84.4 1.0
CD D:ARG143 4.1 0.9 1.0
CA D:GLU175 4.3 99.3 1.0
O D:GLN176 4.3 0.1 1.0
N D:GLN176 4.3 83.6 1.0
CB D:GLU175 4.3 0.4 1.0
C D:GLN176 4.9 0.9 1.0
CG D:ARG143 5.0 0.6 1.0
NH1 D:ARG143 5.0 0.0 1.0

Sodium binding site 5 out of 6 in 6obh

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Sodium binding site 5 out of 6 in the Structure of Hiv-1 Ca 1/2-Hexamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Hiv-1 Ca 1/2-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:75.2
occ:1.00
N E:GLU212 3.3 88.0 1.0
OE1 D:GLU71 3.3 0.1 1.0
CB E:GLU212 3.5 0.3 1.0
CD D:GLU71 3.6 0.1 1.0
CB D:GLU71 3.8 91.4 1.0
CG D:MET68 3.8 87.2 1.0
CA D:MET68 3.9 73.7 1.0
N E:LEU211 3.9 78.4 1.0
CB E:THR210 4.0 91.6 1.0
CA E:GLU212 4.0 96.9 1.0
CG D:GLU71 4.0 99.3 1.0
CB D:MET68 4.1 79.2 1.0
O D:MET68 4.1 87.8 1.0
CB E:LEU211 4.1 82.6 1.0
OE2 D:GLU71 4.2 0.1 1.0
OG1 E:THR210 4.2 97.9 1.0
C E:LEU211 4.3 84.3 1.0
CA E:LEU211 4.4 85.4 1.0
CE D:MET68 4.5 79.9 1.0
C D:MET68 4.5 70.5 1.0
SD D:MET68 4.6 89.5 1.0
CG2 E:THR210 4.7 85.3 1.0
OE1 E:GLU212 4.8 0.7 1.0
CG E:GLU212 4.8 0.4 1.0
C E:THR210 4.8 84.3 1.0
CA E:THR210 4.9 91.9 1.0

Sodium binding site 6 out of 6 in 6obh

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Sodium binding site 6 out of 6 in the Structure of Hiv-1 Ca 1/2-Hexamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Hiv-1 Ca 1/2-Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:84.2
occ:1.00
O F:GLU175 4.0 0.6 1.0
C F:GLU175 4.1 84.6 1.0
CD F:ARG143 4.1 0.7 1.0
O F:GLN176 4.2 0.8 1.0
N F:GLN176 4.4 81.2 1.0
CA F:GLU175 4.5 97.3 1.0
CB F:GLU175 4.6 0.7 1.0
C F:GLN176 4.9 0.7 1.0
NH1 F:ARG143 5.0 0.9 1.0

Reference:

B.J.Summers, K.M.Digianantonio, S.S.Smaga, P.T.Huang, K.Zhou, E.E.Gerber, W.Wang, Y.Xiong. Modular Hiv-1 Capsid Assemblies Reveal Diverse Host-Capsid Recognition Mechanisms. Cell Host Microbe V. 26 203 2019.
ISSN: ESSN 1934-6069
PubMed: 31415753
DOI: 10.1016/J.CHOM.2019.07.007
Page generated: Tue Dec 15 12:41:16 2020

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