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Sodium in PDB 1hx6: P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.

Protein crystallography data

The structure of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1., PDB code: 1hx6 was solved by S.D.Benson, J.K.H.Bamford, D.H.Bamford, R.M.Burnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.45 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.960, 121.300, 126.390, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20.8

Other elements in 1hx6:

The structure of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. (pdb code 1hx6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1., PDB code: 1hx6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 1hx6

Go back to Sodium Binding Sites List in 1hx6
Sodium binding site 1 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:27.1
occ:1.00
 O A:ASN262 2.3 22.3 1.0
O A:HOH1194 2.3 24.0 1.0
O A:HOH1184 2.4 33.4 1.0
O A:HOH1183 2.5 37.2 1.0
OD1 A:ASN262 2.8 22.9 1.0
C A:ASN262 3.3 21.9 1.0
CG A:ASN262 3.8 22.2 1.0
N A:ASN262 3.8 19.5 1.0
O A:HOH1192 4.0 23.2 1.0
CA A:ASN262 4.0 20.6 1.0
N A:SER263 4.3 22.5 0.5
N A:SER263 4.3 21.9 0.5
O A:GLU111 4.4 14.5 1.0
O A:HOH1185 4.4 37.0 1.0
CA A:SER263 4.5 23.4 0.5
CB A:ASN262 4.5 20.2 1.0
CA A:SER263 4.5 22.2 0.5
OE1 A:GLU261 4.5 22.0 1.0
ND2 A:ASN262 4.6 21.5 1.0
O A:HOH1182 4.7 30.1 1.0
O A:HOH1768 4.9 41.4 1.0
CG A:GLU111 4.9 18.4 1.0
C A:GLU261 4.9 19.0 1.0

Sodium binding site 2 out of 7 in 1hx6

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Sodium binding site 2 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:39.3
occ:1.00
 O A:HOH1585 2.2 38.8 1.0
O A:HOH1583 2.3 30.9 1.0
O A:HOH1590 2.4 39.3 1.0
O A:HOH1584 2.5 44.9 1.0
O A:HOH1581 2.5 46.8 1.0
O A:ASN199 2.6 22.2 1.0
C A:ASN199 3.7 22.1 1.0
O A:HOH1582 4.0 38.3 1.0
O A:HOH1586 4.0 43.9 1.0
ND2 A:ASN200 4.1 29.5 1.0
O A:HOH1580 4.4 46.1 1.0
O A:HOH1759 4.4 50.9 1.0
CA A:ASN200 4.4 24.3 1.0
O A:ALA221 4.5 27.8 1.0
N A:ASN200 4.5 22.6 1.0
CB A:ASN199 4.5 22.7 1.0
CA A:ASN199 4.6 21.6 1.0
O A:CYS223 4.7 22.3 1.0
CD2 A:PHE203 4.8 21.0 1.0
O A:ALA220 4.9 24.2 1.0

Sodium binding site 3 out of 7 in 1hx6

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Sodium binding site 3 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na705

b:27.7
occ:1.00
 OD2 A:ASP143 2.3 19.5 1.0
OD1 A:ASP149 2.4 24.8 1.0
OD1 A:ASN146 2.4 22.6 1.0
O B:HOH1125 2.4 25.6 1.0
O B:HOH1564 2.5 17.6 1.0
O A:HOH1124 2.5 30.2 1.0
CG A:ASP149 3.2 23.7 1.0
CG A:ASP143 3.3 18.5 1.0
O A:HOH1126 3.5 24.1 1.0
CG A:ASN146 3.5 22.5 1.0
CB A:ASP149 3.6 19.6 1.0
OD1 A:ASP143 3.6 15.9 1.0
OD2 A:ASP149 4.1 27.3 1.0
O A:HOH1123 4.1 24.9 1.0
CB A:ASN146 4.2 20.4 1.0
CA A:ASN146 4.3 18.2 1.0
OD2 B:ASP136 4.3 16.4 1.0
CA A:ASP149 4.3 16.6 1.0
O A:HOH1154 4.3 37.6 1.0
O A:ILE148 4.4 15.9 1.0
CB A:ASP143 4.6 16.7 1.0
ND2 A:ASN146 4.6 24.0 1.0
O B:ASP136 4.7 14.6 1.0
CB B:ASP136 4.9 15.6 1.0
CG B:ASP136 4.9 15.7 1.0

Sodium binding site 4 out of 7 in 1hx6

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Sodium binding site 4 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:32.0
occ:1.00
 OD1 B:ASP149 2.3 17.5 0.5
OD2 B:ASP143 2.3 21.9 1.0
O B:HOH1345 2.4 26.4 1.0
OD1 B:ASN146 2.5 23.0 1.0
O C:HOH1486 2.5 23.0 1.0
O C:HOH1139 2.6 25.8 1.0
CG B:ASP149 3.0 14.2 0.5
CB B:ASP149 3.2 18.6 0.5
CG B:ASP143 3.3 18.6 1.0
O B:HOH1140 3.5 24.8 1.0
CB B:ASP149 3.5 13.8 0.5
CG B:ASN146 3.6 21.5 1.0
OD1 B:ASP143 3.7 19.1 1.0
OD2 B:ASP149 3.9 19.3 0.5
O B:HOH1138 4.1 23.9 1.0
CA B:ASP149 4.2 12.6 0.5
OD2 C:ASP136 4.2 18.1 1.0
CA B:ASP149 4.2 14.7 0.5
CB B:ASN146 4.3 18.3 1.0
CG B:ASP149 4.3 21.4 0.5
O B:HOH1639 4.4 39.0 1.0
O B:ILE148 4.4 14.2 1.0
OD2 B:ASP149 4.4 24.0 0.5
CA B:ASN146 4.4 17.6 1.0
CB B:ASP143 4.6 16.2 1.0
O B:HOH1346 4.6 41.8 1.0
O C:ASP136 4.7 13.8 1.0
ND2 B:ASN146 4.7 21.3 1.0
CB C:ASP136 4.8 14.6 1.0
CG C:ASP136 4.9 15.6 1.0

Sodium binding site 5 out of 7 in 1hx6

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Sodium binding site 5 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:28.1
occ:1.00
 O B:HOH1008 2.3 21.1 1.0
O B:HOH1518 2.4 38.7 1.0
O B:HOH1010 2.4 30.6 1.0
O B:HOH1519 2.5 31.4 1.0
O B:ASN199 2.5 19.3 1.0
O B:HOH1007 2.6 30.9 1.0
C B:ASN199 3.6 19.1 1.0
O B:HOH1517 3.7 35.1 1.0
O B:HOH1009 4.3 27.5 1.0
ND2 B:ASN200 4.3 22.6 1.0
O B:HOH1663 4.4 44.4 1.0
CB B:ASN199 4.4 18.5 1.0
N B:ASN200 4.4 19.6 1.0
CA B:ASN200 4.5 21.6 1.0
CA B:ASN199 4.5 18.2 1.0
O B:ALA221 4.6 17.3 1.0
CD2 B:PHE203 4.6 15.5 1.0
O B:HOH1011 4.7 35.4 1.0
O B:CYS223 4.7 15.9 1.0
O B:ALA220 4.7 16.3 1.0
CB B:PHE203 4.9 16.5 1.0

Sodium binding site 6 out of 7 in 1hx6

Go back to Sodium Binding Sites List in 1hx6
Sodium binding site 6 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na706

b:40.4
occ:1.00
 O B:HOH1436 2.3 30.2 1.0
O B:HOH1433 2.3 42.5 1.0
OE1 B:GLU261 2.3 24.4 1.0
O B:HOH1435 2.4 25.3 1.0
OE1 B:GLU111 2.7 24.9 1.0
O B:HOH1434 2.7 35.0 1.0
CD B:GLU261 3.5 25.1 1.0
CD B:GLU111 3.5 23.3 1.0
OE2 B:GLU111 3.7 25.4 1.0
NH2 B:ARG108 4.0 24.4 1.0
CG B:GLU261 4.1 22.4 1.0
O B:ASN262 4.1 23.5 1.0
CM B:MPD511 4.2 50.7 1.0
CB B:GLU261 4.3 20.3 1.0
OE2 B:GLU261 4.5 26.2 1.0
CZ B:ARG108 4.6 23.4 1.0
O B:HOH1696 4.6 44.4 1.0
O B:GLU111 4.6 14.5 1.0
O B:HOH1437 4.7 42.0 1.0
CG B:GLU111 4.7 20.7 1.0
C1 B:MPD511 4.8 50.4 1.0
NH1 B:ARG108 4.9 23.7 1.0
CB B:GLU111 4.9 18.3 1.0
O B:HOH1731 5.0 44.0 1.0
N B:ASN262 5.0 20.7 1.0
O B:HOH1429 5.0 41.4 1.0

Sodium binding site 7 out of 7 in 1hx6

Go back to Sodium Binding Sites List in 1hx6
Sodium binding site 7 out of 7 in the P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na707

b:30.9
occ:1.00
 O C:ASN51 2.4 20.8 1.0
O C:HOH1059 2.5 47.5 1.0
C C:ASN51 3.5 20.8 1.0
CA C:ASN51 4.1 18.7 1.0
N C:ARG52 4.7 20.8 1.0
O C:ALA50 4.8 20.1 1.0
CA C:ARG52 4.9 22.0 1.0
CB C:ASN51 5.0 18.0 1.0

Reference:

S.D.Benson, J.K.Bamford, D.H.Bamford, R.M.Burnett. The X-Ray Crystal Structure of P3, the Major Coat Protein of the Lipid-Containing Bacteriophage PRD1, at 1.65 A Resolution. Acta Crystallogr.,Sect.D V. 58 39 2002.
ISSN: ISSN 0907-4449
PubMed: 11752778
DOI: 10.1107/S0907444901017279
Page generated: Sun Oct 6 18:50:02 2024

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