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Sodium in PDB 5oee: Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)

Protein crystallography data

The structure of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3), PDB code: 5oee was solved by R.G.Xu, H.T.Jenkins, S.J.Greive, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.69 / 2.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 100.757, 102.628, 103.114, 90.72, 117.39, 119.37
R / Rfree (%) 20.2 / 25.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) (pdb code 5oee). 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 Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3), PDB code: 5oee:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5oee

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Sodium binding site 1 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:62.7
occ:1.00
 O A:HOH605 2.2 67.5 1.0
O A:HOH604 2.2 62.9 1.0
O A:HOH607 2.2 60.2 1.0
O A:HOH629 2.2 58.5 1.0
OD2 A:ASP263 2.2 60.9 1.0
ND1 A:HIS402 2.3 57.9 1.0
CE1 A:HIS402 3.2 59.1 1.0
CG A:HIS402 3.4 56.5 1.0
CG A:ASP263 3.4 61.6 1.0
CB A:HIS402 3.7 54.9 1.0
OD1 A:ASP263 3.8 63.2 1.0
CA A:HIS402 3.9 54.4 1.0
NE2 A:HIS402 4.4 57.8 1.0
OD1 A:ASP401 4.4 67.8 1.0
O A:PRO269 4.4 69.0 1.0
CD2 A:HIS402 4.5 57.0 1.0
N A:HIS402 4.6 55.4 1.0
OD2 A:ASP405 4.6 70.7 1.0
CB A:ASP263 4.6 62.8 1.0
CB A:ASN268 4.7 81.7 1.0
ND2 A:ASN268 4.8 77.9 1.0
C A:ASP401 4.9 56.6 1.0
O A:ASP401 4.9 56.7 1.0

Sodium binding site 2 out of 6 in 5oee

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Sodium binding site 2 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:63.9
occ:1.00
 O B:HOH604 2.2 68.3 1.0
O B:HOH601 2.2 62.9 1.0
O B:HOH609 2.2 63.2 1.0
OD2 B:ASP263 2.2 59.3 1.0
ND1 B:HIS402 2.3 64.5 1.0
CE1 B:HIS402 3.2 65.4 1.0
CG B:HIS402 3.4 64.2 1.0
CG B:ASP263 3.4 59.6 1.0
O B:HOH630 3.4 64.1 1.0
CB B:HIS402 3.7 62.6 1.0
OD1 B:ASP263 3.9 61.8 1.0
CA B:HIS402 4.0 63.0 1.0
OD1 B:ASP401 4.2 74.0 1.0
NE2 B:HIS402 4.3 64.0 1.0
O B:PRO269 4.4 67.5 1.0
CD2 B:HIS402 4.5 64.5 1.0
N B:HIS402 4.6 63.8 1.0
CB B:ASP263 4.6 59.6 1.0
OD2 B:ASP405 4.8 71.0 1.0
ND2 B:ASN268 4.8 79.5 1.0
CB B:ASN268 4.9 81.9 1.0
C B:ASP401 4.9 65.0 1.0
O B:ASP401 5.0 63.6 1.0
O B:TYR264 5.0 70.7 1.0

Sodium binding site 3 out of 6 in 5oee

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Sodium binding site 3 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:62.9
occ:1.00
 O C:HOH606 2.2 60.7 1.0
O C:HOH612 2.2 63.9 1.0
O C:HOH622 2.2 64.4 1.0
O C:HOH632 2.2 61.0 1.0
OD2 C:ASP263 2.2 63.1 1.0
ND1 C:HIS402 2.3 61.4 1.0
CE1 C:HIS402 3.2 60.8 1.0
CG C:HIS402 3.4 60.6 1.0
CG C:ASP263 3.4 64.3 1.0
CB C:HIS402 3.7 59.2 1.0
OD1 C:ASP263 4.0 64.6 1.0
O C:PRO269 4.0 62.8 1.0
CA C:HIS402 4.0 59.0 1.0
NE2 C:HIS402 4.4 61.5 1.0
CB C:ASN268 4.4 77.4 1.0
CD2 C:HIS402 4.5 61.5 1.0
O C:TYR264 4.5 63.8 1.0
CB C:ASP263 4.6 64.3 1.0
N C:HIS402 4.8 60.8 1.0
OD1 C:ASP401 4.8 64.5 1.0
CG C:ASN268 4.9 78.0 1.0

Sodium binding site 4 out of 6 in 5oee

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Sodium binding site 4 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:66.9
occ:1.00
 O D:HOH609 2.2 67.6 1.0
O D:HOH615 2.2 70.8 1.0
O D:HOH619 2.2 65.8 1.0
O D:HOH645 2.2 65.4 1.0
OD2 D:ASP263 2.2 65.6 1.0
ND1 D:HIS402 2.3 60.2 1.0
CE1 D:HIS402 3.2 58.6 1.0
CG D:ASP263 3.3 66.4 1.0
CG D:HIS402 3.4 59.0 1.0
OD1 D:ASP263 3.7 68.8 1.0
CB D:HIS402 3.7 57.2 1.0
CA D:HIS402 3.9 55.8 1.0
O D:HOH654 4.1 56.6 1.0
NE2 D:HIS402 4.4 58.4 1.0
O D:PRO269 4.4 64.1 1.0
OD1 D:ASP401 4.4 59.3 1.0
OD2 D:ASP405 4.4 64.3 1.0
CD2 D:HIS402 4.5 59.0 1.0
N D:HIS402 4.6 57.4 1.0
CB D:ASP263 4.6 64.7 1.0
O D:ASP401 4.8 60.4 1.0
CB D:ASN268 4.8 88.2 1.0
C D:ASP401 4.8 59.6 1.0
CG D:ASN268 4.9 92.8 1.0

Sodium binding site 5 out of 6 in 5oee

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Sodium binding site 5 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:70.9
occ:1.00
 O E:HOH606 2.2 66.4 1.0
O E:HOH626 2.2 75.7 1.0
O E:HOH624 2.2 70.7 1.0
OD2 E:ASP263 2.2 71.5 1.0
O E:HOH643 2.2 69.1 1.0
ND1 E:HIS402 2.3 63.0 1.0
CE1 E:HIS402 3.2 61.6 1.0
CG E:ASP263 3.2 71.8 1.0
CG E:HIS402 3.4 60.5 1.0
OD1 E:ASP263 3.5 75.7 1.0
CB E:HIS402 3.8 57.7 1.0
CA E:HIS402 4.0 55.5 1.0
O E:PRO269 4.2 59.8 1.0
OD1 E:ASP401 4.3 56.9 1.0
NE2 E:HIS402 4.3 60.9 1.0
O E:HOH633 4.5 57.7 1.0
CD2 E:HIS402 4.5 60.9 1.0
CB E:ASN268 4.5 73.8 1.0
CB E:ASP263 4.6 69.6 1.0
N E:HIS402 4.7 55.8 1.0
OD2 E:ASP405 4.8 58.2 1.0
O E:TYR264 5.0 66.6 1.0

Sodium binding site 6 out of 6 in 5oee

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Sodium binding site 6 out of 6 in the Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Large Terminase From the Thermophilic Bacteriophage D6E (Crystal Form 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:67.5
occ:1.00
 O F:HOH605 2.2 68.9 1.0
O F:HOH604 2.2 66.2 1.0
O F:HOH643 2.2 73.6 1.0
O F:HOH612 2.2 69.2 1.0
OD2 F:ASP263 2.2 66.3 1.0
ND1 F:HIS402 2.3 58.2 1.0
CE1 F:HIS402 3.2 55.9 1.0
CG F:ASP263 3.3 63.7 1.0
CG F:HIS402 3.4 56.6 1.0
CB F:HIS402 3.7 55.1 1.0
OD1 F:ASP263 3.8 65.8 1.0
CA F:HIS402 3.9 54.7 1.0
NE2 F:HIS402 4.4 55.7 1.0
OD1 F:ASP401 4.4 56.6 1.0
O F:PRO269 4.5 62.8 1.0
CD2 F:HIS402 4.5 56.0 1.0
OD2 F:ASP405 4.5 58.4 1.0
N F:HIS402 4.6 55.0 1.0
CB F:ASP263 4.6 61.1 1.0
O F:TYR264 4.8 64.3 1.0
CB F:ASN268 4.8 75.6 1.0

Reference:

R.G.Xu, H.T.Jenkins, A.A.Antson, S.J.Greive. Structure of the Large Terminase From A Hyperthermophilic Virus Reveals A Unique Mechanism For Oligomerization and Atp Hydrolysis. Nucleic Acids Res. V. 45 13029 2017.
ISSN: ESSN 1362-4962
PubMed: 29069443
DOI: 10.1093/NAR/GKX947
Page generated: Mon Aug 18 01:31:03 2025

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