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Sodium in PDB 3a07: Crystal Structure of Actinohivin; Potent Anti-Hiv Protein

Protein crystallography data

The structure of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein, PDB code: 3a07 was solved by M.Tsunoda, K.Suzuki, T.Sagara, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.30 / 1.19
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.346, 51.633, 175.296, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 16.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein (pdb code 3a07). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein, PDB code: 3a07:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3a07

Go back to Sodium Binding Sites List in 3a07
Sodium binding site 1 out of 6 in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1

b:12.7
occ:1.00
 O A:GLN155 2.7 6.5 1.0
O A:LEU136 2.8 5.2 1.0
N A:ILE127 2.9 5.0 1.0
CB A:VAL135 3.4 4.8 1.0
N A:LEU136 3.4 4.8 1.0
CA A:TYR126 3.5 5.5 1.0
O A:ILE127 3.5 6.3 1.0
CD1 A:TRP157 3.5 5.7 1.0
NE1 A:TRP157 3.6 5.8 1.0
C A:TYR126 3.6 5.4 1.0
C A:GLN155 3.7 5.5 1.0
C A:LEU136 3.8 4.6 1.0
CD2 A:TYR126 3.8 7.3 1.0
CG2 A:VAL135 3.8 6.3 1.0
CA A:ILE127 3.8 5.2 1.0
CA A:LEU136 4.0 5.5 1.0
CA A:GLN155 4.0 5.3 1.0
C A:VAL135 4.0 4.8 1.0
C A:ILE127 4.0 5.1 1.0
CB A:GLN155 4.0 6.3 1.0
CB A:TYR126 4.1 5.9 1.0
CB A:LEU136 4.1 5.5 1.0
CA A:VAL135 4.2 4.5 1.0
O A:GLY125 4.2 6.2 1.0
CB A:ILE127 4.2 5.7 1.0
CG A:TYR126 4.4 5.2 1.0
CG1 A:VAL135 4.4 5.5 1.0
N A:TYR126 4.6 5.7 1.0
CE2 A:TYR126 4.7 6.3 1.0
N A:LYS156 4.8 5.9 1.0
CG1 A:ILE127 4.8 6.5 1.0
O A:VAL135 4.8 5.2 1.0
CG A:TRP157 4.8 6.0 1.0
C A:GLY125 4.8 5.8 1.0
O A:TYR126 4.9 5.6 1.0
CE2 A:TRP157 4.9 5.6 1.0
CG A:GLN155 4.9 7.2 1.0

Sodium binding site 2 out of 6 in 3a07

Go back to Sodium Binding Sites List in 3a07
Sodium binding site 2 out of 6 in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2

b:12.9
occ:1.00
 O A:GLN79 2.7 6.9 1.0
O A:LEU60 2.8 5.2 1.0
N A:ILE51 2.8 5.0 1.0
O A:ILE51 3.3 5.7 1.0
N A:LEU60 3.5 5.2 1.0
CA A:THR50 3.5 6.5 1.0
CB A:LEU59 3.5 5.1 1.0
C A:GLN79 3.6 5.5 1.0
NE1 A:TRP81 3.6 5.7 1.0
C A:THR50 3.7 5.3 1.0
CD1 A:TRP81 3.7 6.2 1.0
CB A:THR50 3.7 7.0 1.0
C A:LEU60 3.8 4.9 1.0
CA A:ILE51 3.8 5.9 1.0
C A:ILE51 3.8 4.5 1.0
CD2 A:LEU59 3.9 19.0 1.0
C A:LEU59 4.0 4.4 1.0
CG A:LEU59 4.0 7.5 1.0
CA A:LEU60 4.0 5.7 1.0
CA A:GLN79 4.0 5.5 1.0
CA A:LEU59 4.0 5.1 1.0
CD1 A:LEU59 4.0 9.1 1.0
CB A:GLN79 4.0 5.6 1.0
CB A:LEU60 4.1 6.1 1.0
CB A:ILE51 4.2 5.6 1.0
CG2 A:THR50 4.3 8.3 1.0
N A:ARG80 4.6 6.2 1.0
O A:VAL49 4.7 7.1 1.0
O A:LEU59 4.8 4.9 1.0
CG A:GLN79 4.8 8.8 1.0
N A:THR50 4.8 6.0 1.0
CG1 A:ILE51 4.8 6.9 1.0
N A:ARG52 4.9 4.9 1.0
O A:THR50 4.9 6.0 1.0
CE2 A:TRP81 5.0 5.1 1.0
OG1 A:THR50 5.0 7.6 1.0

Sodium binding site 3 out of 6 in 3a07

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Sodium binding site 3 out of 6 in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3

b:13.2
occ:1.00
 O A:GLN117 2.7 6.2 1.0
O A:LEU98 2.8 5.3 1.0
N A:VAL89 2.9 5.9 1.0
N A:LEU98 3.3 5.2 1.0
CB A:CYS97 3.4 5.6 1.0
CA A:THR88 3.4 5.5 1.0
O A:VAL89 3.4 5.9 1.0
CB A:THR88 3.5 5.9 1.0
C A:GLN117 3.6 6.2 1.0
C A:THR88 3.6 5.4 1.0
SG A:CYS97 3.7 7.9 1.0
C A:LEU98 3.7 4.6 1.0
C A:CYS97 3.8 5.7 1.0
NE1 A:TRP119 3.8 6.2 1.0
CD1 A:TRP119 3.8 6.3 1.0
CA A:CYS97 3.8 5.0 1.0
CB A:GLN117 3.9 5.8 1.0
CA A:VAL89 3.9 5.8 1.0
C A:VAL89 3.9 5.5 1.0
CA A:LEU98 3.9 5.4 1.0
CA A:GLN117 4.0 5.6 1.0
CG2 A:THR88 4.0 7.9 1.0
CB A:LEU98 4.1 5.9 1.0
CB A:VAL89 4.2 6.2 1.0
CG A:GLN117 4.6 6.8 1.0
O A:CYS97 4.6 6.2 1.0
OG1 A:THR88 4.7 6.9 1.0
N A:THR88 4.7 6.0 1.0
O A:GLY87 4.7 7.2 1.0
N A:LYS118 4.8 6.1 1.0
CG2 A:VAL89 4.8 7.5 1.0
O A:THR88 4.9 5.8 1.0
N A:ARG90 4.9 5.1 1.0
N A:ASP99 5.0 4.9 1.0

Sodium binding site 4 out of 6 in 3a07

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Sodium binding site 4 out of 6 in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4

b:12.0
occ:1.00
 O B:GLN117 2.7 6.1 1.0
O B:LEU98 2.8 5.5 1.0
N B:VAL89 2.9 5.5 1.0
N B:LEU98 3.3 5.6 1.0
CB B:CYS97 3.4 6.0 1.0
CA B:THR88 3.4 5.2 1.0
O B:VAL89 3.4 6.5 1.0
CB B:THR88 3.5 6.1 1.0
C B:THR88 3.6 5.6 1.0
C B:GLN117 3.6 5.4 1.0
SG B:CYS97 3.7 8.5 1.0
C B:LEU98 3.7 5.3 1.0
C B:CYS97 3.7 4.8 1.0
CA B:CYS97 3.8 6.0 1.0
CD1 B:TRP119 3.8 5.4 1.0
NE1 B:TRP119 3.8 6.1 1.0
CB B:GLN117 3.8 6.5 1.0
CA B:VAL89 3.8 5.8 1.0
CA B:LEU98 3.9 4.9 1.0
C B:VAL89 3.9 5.2 1.0
CA B:GLN117 4.0 5.5 1.0
CG2 B:THR88 4.0 7.4 1.0
CB B:LEU98 4.1 5.9 1.0
CB B:VAL89 4.2 5.8 1.0
CG B:GLN117 4.5 6.4 1.0
O B:CYS97 4.6 5.8 1.0
N B:THR88 4.7 5.0 1.0
OG1 B:THR88 4.7 6.6 1.0
O B:GLY87 4.8 6.9 1.0
CG2 B:VAL89 4.8 7.0 1.0
N B:LYS118 4.8 5.5 1.0
O B:THR88 4.9 6.3 1.0
N B:ARG90 4.9 5.2 1.0
N B:ASP99 5.0 5.3 1.0

Sodium binding site 5 out of 6 in 3a07

Go back to Sodium Binding Sites List in 3a07
Sodium binding site 5 out of 6 in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na5

b:11.3
occ:1.00
 O B:GLN155 2.7 6.3 1.0
O B:LEU136 2.8 4.7 1.0
N B:ILE127 2.9 4.5 1.0
N B:LEU136 3.5 4.4 1.0
O B:ILE127 3.5 5.4 1.0
CB B:VAL135 3.5 4.5 1.0
CA B:TYR126 3.5 5.5 1.0
CD1 B:TRP157 3.5 5.1 1.0
C B:GLN155 3.6 5.0 1.0
NE1 B:TRP157 3.6 5.0 1.0
C B:TYR126 3.6 5.1 1.0
CD1 B:TYR126 3.7 6.0 1.0
C B:LEU136 3.8 4.6 1.0
CA B:ILE127 3.8 5.3 1.0
CG2 B:VAL135 3.8 6.0 1.0
CA B:GLN155 4.0 4.5 1.0
C B:ILE127 4.0 4.9 1.0
CA B:LEU136 4.0 4.5 1.0
C B:VAL135 4.0 4.3 1.0
CB B:GLN155 4.0 5.7 1.0
CB B:TYR126 4.1 5.4 1.0
CB B:LEU136 4.1 5.3 1.0
CB B:ILE127 4.2 5.8 1.0
O B:GLY125 4.2 4.8 1.0
CA B:VAL135 4.2 4.6 1.0
CG B:TYR126 4.4 4.8 1.0
CG1 B:VAL135 4.4 7.2 1.0
N B:TYR126 4.6 5.0 1.0
N B:LYS156 4.7 5.1 1.0
CE1 B:TYR126 4.7 5.5 1.0
CG1 B:ILE127 4.7 5.5 1.0
CG B:TRP157 4.8 5.3 1.0
O B:VAL135 4.8 4.7 1.0
CG B:GLN155 4.9 6.2 1.0
O B:TYR126 4.9 5.0 1.0
C B:GLY125 4.9 4.0 1.0
CE2 B:TRP157 4.9 4.9 1.0

Sodium binding site 6 out of 6 in 3a07

Go back to Sodium Binding Sites List in 3a07
Sodium binding site 6 out of 6 in the Crystal Structure of Actinohivin; Potent Anti-Hiv Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Actinohivin; Potent Anti-Hiv Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:12.4
occ:1.00
 O B:GLN79 2.7 6.5 1.0
O B:LEU60 2.8 5.1 1.0
N B:ILE51 2.8 4.8 1.0
O B:ILE51 3.4 5.4 1.0
N B:LEU60 3.4 4.8 1.0
CA B:THR50 3.5 5.8 1.0
CB B:LEU59 3.5 4.6 1.0
C B:GLN79 3.6 5.0 1.0
NE1 B:TRP81 3.6 6.2 1.0
C B:THR50 3.6 4.6 1.0
CB B:THR50 3.7 6.3 1.0
CD1 B:TRP81 3.7 5.7 1.0
C B:LEU60 3.8 5.2 1.0
CA B:ILE51 3.8 5.2 1.0
C B:ILE51 3.9 4.1 1.0
CG B:LEU59 3.9 7.5 1.0
C B:LEU59 3.9 4.7 1.0
CA B:LEU60 4.0 4.8 1.0
CA B:GLN79 4.0 5.5 1.0
CB B:GLN79 4.0 5.7 1.0
CA B:LEU59 4.0 4.4 1.0
CD2 B:LEU59 4.1 7.4 1.0
CB B:LEU60 4.1 6.1 1.0
CB B:ILE51 4.2 5.0 1.0
CG2 B:THR50 4.2 8.3 1.0
O B:VAL49 4.7 6.9 1.0
CG B:GLN79 4.8 7.1 1.0
N B:ARG80 4.8 5.8 1.0
O B:LEU59 4.8 5.3 1.0
N B:THR50 4.8 5.0 1.0
CG1 B:ILE51 4.8 6.2 1.0
O B:THR50 4.9 5.8 1.0
OG1 B:THR50 4.9 8.2 1.0
N B:ARG52 4.9 4.7 1.0
CE2 B:TRP81 5.0 5.7 1.0

Reference:

H.Tanaka, H.Chiba, J.Inokoshi, A.Kuno, T.Sugai, A.Takahashi, Y.Ito, M.Tsunoda, K.Suzuki, A.Takenaka, T.Sekiguchi, H.Umeyama, J.Hirabayashi, S.Omura. Mechanism By Which the Lectin Actinohivin Blocks Hiv Infection of Target Cells Proc.Natl.Acad.Sci.Usa V. 106 15633 2009.
ISSN: ISSN 0027-8424
PubMed: 19717426
DOI: 10.1073/PNAS.0907572106
Page generated: Mon Oct 7 05:44:25 2024

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