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Sodium in PDB 6cl5: Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701

Protein crystallography data

The structure of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701, PDB code: 6cl5 was solved by S.A.Buth, M.M.Shneider, P.G.Leiman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.69 / 2.32
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 144.504, 155.031, 200.481, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.6

Other elements in 6cl5:

The structure of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 (pdb code 6cl5). 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 P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701, PDB code: 6cl5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6cl5

Go back to Sodium Binding Sites List in 6cl5
Sodium binding site 1 out of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:65.6
occ:1.00
O A:LEU688 2.3 77.4 1.0
O A:HIS627 2.3 83.1 1.0
OE1 A:GLN690 2.4 70.7 1.0
OD1 A:ASP626 2.5 81.5 1.0
OE1 A:GLU684 2.5 78.6 1.0
O A:HOH1136 3.0 66.9 1.0
H A:HIS627 3.0 80.6 1.0
HB3 A:HIS627 3.0 71.5 1.0
HE22 A:GLN690 3.1 92.4 1.0
CD A:GLN690 3.1 75.3 1.0
HA A:ALA689 3.3 0.7 1.0
C A:HIS627 3.4 87.8 1.0
NE2 A:GLN690 3.4 77.0 1.0
C A:LEU688 3.4 88.4 1.0
CD A:GLU684 3.4 76.7 1.0
H A:GLN690 3.5 84.6 1.0
CG A:ASP626 3.5 77.7 1.0
N A:HIS627 3.6 67.1 1.0
OE2 A:GLU684 3.7 79.8 1.0
CA A:HIS627 3.8 73.2 1.0
CB A:HIS627 3.8 59.9 1.0
O A:HOH1014 3.9 85.4 1.0
OD2 A:ASP626 3.9 91.5 1.0
CA A:ALA689 4.1 84.7 1.0
N A:GLN690 4.1 70.4 1.0
HE21 A:GLN690 4.1 92.4 1.0
N A:ALA689 4.1 83.4 1.0
H A:LEU688 4.2 0.9 1.0
HB2 A:HIS627 4.2 71.5 1.0
N A:LEU688 4.3 0.7 1.0
CG A:GLN690 4.3 63.7 1.0
HG3 A:GLN690 4.4 76.1 1.0
C A:ALA689 4.4 80.7 1.0
CA A:LEU688 4.4 89.2 1.0
H A:GLY629 4.5 0.7 1.0
HA A:PRO628 4.5 94.4 1.0
N A:PRO628 4.5 79.8 1.0
HA A:ASP626 4.6 92.3 1.0
HB2 A:GLN690 4.7 81.7 1.0
C A:ASP626 4.7 70.0 1.0
C A:GLY687 4.7 0.6 1.0
HA A:HIS627 4.7 88.0 1.0
HA2 A:GLY687 4.8 0.9 1.0
CG A:GLU684 4.8 75.2 1.0
HB3 A:GLU684 4.8 79.3 1.0
CB A:ASP626 4.8 81.1 1.0
HA A:LEU688 4.9 0.1 1.0
CA A:PRO628 4.9 78.6 1.0
CB A:GLN690 4.9 68.0 1.0
H A:ALA689 5.0 0.2 1.0
CG A:HIS627 5.0 63.1 1.0
N A:GLY629 5.0 85.5 1.0
CA A:ASP626 5.0 76.8 1.0

Sodium binding site 2 out of 6 in 6cl5

Go back to Sodium Binding Sites List in 6cl5
Sodium binding site 2 out of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na801

b:75.8
occ:1.00
O B:HIS627 2.2 76.8 1.0
O B:LEU688 2.4 88.3 1.0
OE1 B:GLU684 2.4 91.4 1.0
OE1 B:GLN690 2.5 73.1 1.0
OD1 B:ASP626 2.5 0.1 1.0
O B:HOH924 3.0 72.5 1.0
O B:HOH919 3.1 68.8 1.0
HB3 B:HIS627 3.1 90.1 1.0
HE22 B:GLN690 3.2 86.0 1.0
CD B:GLU684 3.2 94.1 1.0
H B:HIS627 3.2 94.7 1.0
HA B:ALA689 3.2 0.2 1.0
OE2 B:GLU684 3.2 85.4 1.0
C B:HIS627 3.3 77.9 1.0
CD B:GLN690 3.3 71.8 1.0
C B:LEU688 3.5 97.4 1.0
NE2 B:GLN690 3.5 71.6 1.0
CG B:ASP626 3.6 0.1 1.0
N B:HIS627 3.7 79.2 1.0
CA B:HIS627 3.8 80.1 1.0
CB B:HIS627 3.9 75.3 1.0
OD2 B:ASP626 3.9 0.1 1.0
CA B:ALA689 4.0 95.1 1.0
H B:GLN690 4.0 0.7 1.0
N B:ALA689 4.2 87.9 1.0
HA B:PRO628 4.3 96.9 1.0
HE21 B:GLN690 4.3 86.0 1.0
N B:GLN690 4.4 94.7 1.0
N B:PRO628 4.4 83.0 1.0
N B:LEU688 4.4 96.9 1.0
HB2 B:HIS627 4.4 90.1 1.0
H B:LEU688 4.4 0.3 1.0
C B:ALA689 4.5 99.7 1.0
CA B:LEU688 4.6 98.4 1.0
CG B:GLN690 4.6 76.6 1.0
O B:TYR686 4.6 0.9 1.0
CG B:GLU684 4.6 88.0 1.0
CA B:PRO628 4.6 80.7 1.0
HB2 B:GLN690 4.7 98.1 1.0
C B:PRO628 4.7 88.9 1.0
C B:ASP626 4.7 82.2 1.0
HA2 B:GLY687 4.7 0.7 1.0
C B:GLY687 4.7 97.5 1.0
HA B:HIS627 4.8 96.2 1.0
HG3 B:GLN690 4.8 92.0 1.0
HA B:ASP626 4.8 0.5 1.0
HB3 B:GLU684 4.8 92.9 1.0
CB B:ASP626 4.9 0.4 1.0
O B:PRO628 4.9 90.7 1.0
CG B:HIS627 4.9 79.3 1.0
HG2 B:GLU684 5.0 0.7 1.0
HA B:LEU688 5.0 0.1 1.0
ND1 B:HIS627 5.0 73.2 1.0

Sodium binding site 3 out of 6 in 6cl5

Go back to Sodium Binding Sites List in 6cl5
Sodium binding site 3 out of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na801

b:77.9
occ:1.00
O C:LEU688 2.4 0.4 1.0
O C:HOH963 2.4 59.2 1.0
OE1 C:GLN690 2.4 96.1 1.0
OE1 C:GLU684 2.5 0.5 1.0
O C:HIS627 2.5 0.2 1.0
OD1 C:ASP626 2.5 0.7 1.0
HE22 C:GLN690 3.1 90.6 1.0
CD C:GLN690 3.2 85.5 1.0
CD C:GLU684 3.3 0.1 1.0
H C:HIS627 3.4 0.5 1.0
OE2 C:GLU684 3.5 94.0 1.0
NE2 C:GLN690 3.5 75.5 1.0
C C:LEU688 3.5 0.4 1.0
CG C:ASP626 3.5 99.0 1.0
HB3 C:HIS627 3.6 0.3 1.0
C C:HIS627 3.6 99.1 1.0
HA C:ALA689 3.7 0.4 1.0
HA2 C:GLY687 3.7 0.5 1.0
H C:GLN690 3.8 0.5 1.0
OD2 C:ASP626 3.8 0.0 1.0
O C:TYR686 3.8 0.7 1.0
N C:HIS627 4.0 88.7 1.0
C C:GLY687 4.0 0.4 1.0
N C:LEU688 4.0 94.8 1.0
CA C:HIS627 4.2 95.4 1.0
H C:LEU688 4.2 0.4 1.0
O C:GLY687 4.2 1.0 1.0
HE21 C:GLN690 4.3 90.6 1.0
CB C:HIS627 4.3 96.1 1.0
CA C:LEU688 4.3 99.5 1.0
CA C:GLY687 4.4 0.7 1.0
N C:ALA689 4.4 0.1 1.0
CA C:ALA689 4.4 0.8 1.0
HA C:PRO628 4.4 0.2 1.0
N C:GLN690 4.5 0.4 1.0
CG C:GLN690 4.5 86.3 1.0
HG3 C:GLN690 4.6 0.6 1.0
HA C:LEU688 4.7 0.4 1.0
N C:PRO628 4.7 0.6 1.0
CG C:GLU684 4.8 93.2 1.0
HB2 C:HIS627 4.8 0.3 1.0
C C:TYR686 4.8 0.8 1.0
HA C:ASP626 4.9 0.7 1.0
CA C:PRO628 4.9 0.7 1.0
CB C:ASP626 4.9 98.3 1.0
C C:ALA689 4.9 0.1 1.0
HB2 C:GLU684 4.9 0.1 1.0
C C:ASP626 5.0 95.2 1.0
HB3 C:GLU684 5.0 0.1 1.0

Sodium binding site 4 out of 6 in 6cl5

Go back to Sodium Binding Sites List in 6cl5
Sodium binding site 4 out of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na803

b:84.6
occ:1.00
O D:LEU688 2.2 63.6 1.0
O D:HIS627 2.4 60.0 1.0
OE1 D:GLN690 2.5 58.3 1.0
OD1 D:ASP626 2.5 78.2 1.0
OE1 D:GLU684 2.5 78.9 1.0
H D:HIS627 3.0 67.2 1.0
HE22 D:GLN690 3.1 76.3 1.0
CD D:GLN690 3.1 67.1 1.0
HB3 D:HIS627 3.1 68.3 1.0
O D:HOH1114 3.1 61.5 1.0
NE2 D:GLN690 3.3 63.5 1.0
HA D:ALA689 3.3 79.5 1.0
C D:LEU688 3.3 61.7 1.0
O D:HOH1060 3.4 73.8 1.0
C D:HIS627 3.4 63.4 1.0
CD D:GLU684 3.4 80.6 1.0
H D:GLN690 3.5 59.9 1.0
CG D:ASP626 3.6 66.9 1.0
N D:HIS627 3.6 56.3 1.0
OE2 D:GLU684 3.7 80.1 1.0
CB D:HIS627 3.8 57.2 1.0
CA D:HIS627 3.8 56.8 1.0
OD2 D:ASP626 4.0 70.0 1.0
CA D:ALA689 4.0 66.2 1.0
HE21 D:GLN690 4.0 76.3 1.0
N D:GLN690 4.0 50.2 1.0
H D:LEU688 4.1 91.9 1.0
N D:ALA689 4.1 54.0 1.0
N D:LEU688 4.2 76.5 1.0
HB2 D:HIS627 4.2 68.3 1.0
HG3 D:GLN690 4.2 73.7 1.0
CG D:GLN690 4.2 61.4 1.0
C D:ALA689 4.4 64.7 1.0
CA D:LEU688 4.4 62.2 1.0
HA D:PRO628 4.6 81.4 1.0
N D:PRO628 4.6 67.3 1.0
H D:GLY629 4.6 95.4 1.0
HB2 D:GLN690 4.6 71.2 1.0
HA D:ASP626 4.7 81.5 1.0
C D:ASP626 4.7 59.8 1.0
C D:GLY687 4.7 86.0 1.0
HA2 D:GLY687 4.7 96.3 1.0
HA D:HIS627 4.8 68.2 1.0
HB3 D:GLU684 4.8 89.3 1.0
CG D:GLU684 4.8 75.0 1.0
HA D:LEU688 4.8 74.7 1.0
CB D:GLN690 4.9 59.3 1.0
CB D:ASP626 4.9 72.3 1.0
H D:ALA689 4.9 64.9 1.0
HB2 D:GLU684 5.0 89.3 1.0
HG2 D:GLN690 5.0 73.7 1.0

Sodium binding site 5 out of 6 in 6cl5

Go back to Sodium Binding Sites List in 6cl5
Sodium binding site 5 out of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na801

b:0.4
occ:1.00
O E:LEU688 2.1 0.3 1.0
O E:HIS627 2.2 82.6 1.0
OE1 E:GLU684 2.5 0.2 1.0
OD1 E:ASP626 2.5 0.6 1.0
OE1 E:GLN690 2.5 82.3 1.0
HB3 E:HIS627 2.8 95.2 1.0
H E:HIS627 3.0 97.1 1.0
HA E:ALA689 3.0 0.5 1.0
C E:HIS627 3.2 98.8 1.0
C E:LEU688 3.2 0.0 1.0
HE22 E:GLN690 3.3 97.3 1.0
CD E:GLN690 3.3 88.8 1.0
CD E:GLU684 3.3 0.8 1.0
N E:HIS627 3.5 81.2 1.0
OE2 E:GLU684 3.5 1.0 1.0
CB E:HIS627 3.6 79.7 1.0
CG E:ASP626 3.6 0.0 1.0
CA E:HIS627 3.6 89.4 1.0
NE2 E:GLN690 3.6 81.3 1.0
CA E:ALA689 3.8 0.2 1.0
H E:GLN690 3.9 0.2 1.0
N E:ALA689 3.9 0.7 1.0
OD2 E:ASP626 4.0 0.9 1.0
HB2 E:HIS627 4.1 95.2 1.0
N E:GLN690 4.2 0.8 1.0
C E:ALA689 4.3 0.3 1.0
N E:LEU688 4.3 0.1 1.0
H E:LEU688 4.3 1.0 1.0
CA E:LEU688 4.4 0.7 1.0
N E:PRO628 4.4 84.9 1.0
HE21 E:GLN690 4.4 97.3 1.0
HA E:PRO628 4.5 1.0 1.0
HA E:HIS627 4.6 0.3 1.0
C E:ASP626 4.6 91.8 1.0
CG E:GLN690 4.6 81.8 1.0
HB2 E:GLN690 4.6 98.1 1.0
HA E:ASP626 4.6 0.8 1.0
CG E:HIS627 4.6 81.2 1.0
CG E:GLU684 4.7 0.9 1.0
HB3 E:GLU684 4.7 0.9 1.0
C E:GLY687 4.7 0.3 1.0
ND1 E:HIS627 4.7 89.5 1.0
O E:TYR686 4.7 0.3 1.0
HG3 E:GLN690 4.8 97.8 1.0
CA E:PRO628 4.8 85.2 1.0
H E:ALA689 4.8 0.2 1.0
C E:PRO628 4.8 89.8 1.0
HA E:LEU688 4.8 0.5 1.0
CB E:ASP626 4.8 0.3 1.0
HA2 E:GLY687 4.8 0.1 1.0
CA E:ASP626 4.9 0.3 1.0
HG2 E:GLU684 5.0 0.7 1.0

Sodium binding site 6 out of 6 in 6cl5

Go back to Sodium Binding Sites List in 6cl5
Sodium binding site 6 out of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na801

b:75.5
occ:1.00
OE1 F:GLN690 2.3 98.1 1.0
O F:HIS627 2.3 0.5 1.0
O F:LEU688 2.4 84.3 1.0
OD1 F:ASP626 2.5 95.7 1.0
O F:HOH1025 2.6 60.4 1.0
OE1 F:GLU684 2.9 92.3 1.0
O F:HOH1117 3.1 66.2 1.0
H F:HIS627 3.2 0.8 1.0
HA F:ALA689 3.2 0.9 1.0
H F:GLN690 3.3 0.6 1.0
CD F:GLN690 3.3 98.2 1.0
HB3 F:HIS627 3.3 0.1 1.0
C F:HIS627 3.4 1.0 1.0
C F:LEU688 3.5 87.7 1.0
CG F:ASP626 3.5 0.1 1.0
HE22 F:GLN690 3.5 0.6 1.0
N F:HIS627 3.7 93.9 1.0
NE2 F:GLN690 3.8 87.9 1.0
CD F:GLU684 3.8 87.4 1.0
OD2 F:ASP626 3.8 0.7 1.0
OE2 F:GLU684 3.9 96.3 1.0
CA F:HIS627 4.0 0.8 1.0
CA F:ALA689 4.0 0.0 1.0
N F:GLN690 4.1 0.1 1.0
CB F:HIS627 4.1 85.0 1.0
N F:ALA689 4.2 0.2 1.0
HA F:PRO628 4.4 0.6 1.0
N F:LEU688 4.4 89.1 1.0
HA2 F:GLY687 4.4 0.1 1.0
C F:GLY687 4.4 84.8 1.0
CA F:LEU688 4.5 96.3 1.0
CG F:GLN690 4.5 94.0 1.0
O F:TYR686 4.5 0.9 1.0
N F:PRO628 4.5 0.1 1.0
C F:ALA689 4.5 0.6 1.0
O F:GLY687 4.5 98.2 1.0
HB2 F:HIS627 4.6 0.1 1.0
HG3 F:GLN690 4.6 0.9 1.0
HE21 F:GLN690 4.6 0.6 1.0
H F:LEU688 4.7 1.0 1.0
HA F:ASP626 4.7 1.0 1.0
HB2 F:GLN690 4.7 0.7 1.0
C F:ASP626 4.8 94.9 1.0
CA F:PRO628 4.8 0.1 1.0
HA F:LEU688 4.8 0.6 1.0
CB F:ASP626 4.8 0.8 1.0
C F:PRO628 4.9 0.1 1.0
HA F:HIS627 4.9 1.0 1.0
H F:ALA689 5.0 0.4 1.0
CA F:GLY687 5.0 84.5 1.0

Reference:

S.A.Buth, M.M.Shneider, D.Scholl, P.G.Leiman. Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers. Viruses V. 10 2018.
ISSN: ISSN 1999-4915
PubMed: 30110933
DOI: 10.3390/V10080427
Page generated: Tue Oct 8 06:35:45 2024

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