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Sodium in PDB 4zg3: In-Vacuum Long-Wavelength Crystallography

Protein crystallography data

The structure of In-Vacuum Long-Wavelength Crystallography, PDB code: 4zg3 was solved by A.Wagner, R.Duman, K.Henderson, V.Mykhaylyk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.99 / 1.20
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.842, 57.842, 150.370, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 16.8

Sodium Binding Sites:

The binding sites of Sodium atom in the In-Vacuum Long-Wavelength Crystallography (pdb code 4zg3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the In-Vacuum Long-Wavelength Crystallography, PDB code: 4zg3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4zg3

Go back to Sodium Binding Sites List in 4zg3
Sodium binding site 1 out of 6 in the In-Vacuum Long-Wavelength Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of In-Vacuum Long-Wavelength Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:29.8
occ:1.00
 OD1 A:ASP70 2.5 10.7 0.3
O A:LEU74 2.9 17.0 1.0
NH1 A:ARG53 2.9 13.2 1.0
OD1 A:ASP70 3.0 15.4 0.7
N A:CYS71 3.0 14.5 1.0
SG A:CYS71 3.5 15.8 1.0
CG A:ASP70 3.5 11.1 0.3
CA A:ASP70 3.5 12.7 0.3
CA A:ASP70 3.5 13.3 0.7
CG A:ASP70 3.6 14.8 0.7
N A:LEU74 3.6 17.3 1.0
C A:ASP70 3.7 13.2 1.0
C A:LEU74 3.8 17.1 1.0
SG A:CYS66 3.8 12.9 1.0
CZ A:PHE58 3.8 16.2 1.0
CD A:ARG53 3.9 12.2 1.0
CA A:CYS71 4.0 15.5 1.0
CE1 A:PHE58 4.0 17.6 1.0
CB A:ASP70 4.1 12.0 0.3
C A:GLY73 4.1 18.5 1.0
CZ A:ARG53 4.1 11.8 1.0
CB A:ASP70 4.1 14.2 0.7
N A:GLY73 4.2 17.6 1.0
CA A:GLY73 4.2 18.1 1.0
C A:CYS71 4.2 16.4 1.0
O A:CYS71 4.3 17.1 1.0
CB A:CYS71 4.3 15.9 1.0
CA A:LEU74 4.3 18.4 1.0
OD2 A:ASP70 4.4 15.9 0.7
NE A:ARG53 4.4 11.2 1.0
OD2 A:ASP70 4.4 11.2 0.3
SG A:CYS77 4.6 14.7 1.0
O A:GLY69 4.7 12.9 1.0
CB A:CYS66 4.7 12.4 1.0
N A:ASP70 4.7 13.3 1.0
N A:LEU75 4.8 17.1 1.0
O A:GLY73 4.8 21.1 1.0
N A:CYS66 4.9 12.9 1.0
N A:GLY72 5.0 17.5 1.0
O A:ASP70 5.0 13.4 1.0

Sodium binding site 2 out of 6 in 4zg3

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Sodium binding site 2 out of 6 in the In-Vacuum Long-Wavelength Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of In-Vacuum Long-Wavelength Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:29.8
occ:1.00
 O A:HOH544 3.0 17.3 1.0
O A:HOH500 3.3 17.4 1.0
CA A:PRO135 4.3 13.0 1.0
O A:GLN133 4.4 11.4 1.0
O A:CYS134 4.8 11.8 1.0
N A:PRO135 4.8 11.0 1.0
O A:HOH528 4.9 16.8 1.0
N A:ALA136 5.0 12.8 1.0

Sodium binding site 3 out of 6 in 4zg3

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Sodium binding site 3 out of 6 in the In-Vacuum Long-Wavelength Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of In-Vacuum Long-Wavelength Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:29.9
occ:1.00
 O A:HOH591 2.7 28.5 1.0
OG1 A:THR206 2.8 27.4 1.0
N A:THR206 3.1 15.3 1.0
C A:CYS204 3.3 10.1 1.0
CA A:CYS204 3.3 10.1 1.0
N A:PRO205 3.3 10.1 1.0
CD A:PRO205 3.4 10.3 1.0
CG A:PRO111 3.6 10.9 1.0
CB A:PRO111 3.7 10.0 1.0
CB A:THR206 3.7 24.5 1.0
CA A:THR206 3.8 20.8 1.0
CB A:ALA127 3.9 16.6 1.0
O A:CYS204 3.9 11.3 1.0
CG A:PRO205 4.0 11.9 1.0
N A:ALA207 4.0 30.9 1.0
CB A:CYS204 4.1 10.6 1.0
C A:THR206 4.1 27.4 1.0
O A:ALA127 4.1 16.1 1.0
C A:PRO205 4.1 13.6 1.0
CA A:PRO205 4.2 11.4 1.0
CG2 A:THR206 4.3 25.4 1.0
N A:CYS204 4.4 9.8 1.0
CA A:ALA127 4.5 13.4 1.0
C A:ALA127 4.8 13.7 1.0
CB A:PRO205 4.8 12.3 1.0
O A:THR206 4.8 29.4 1.0
SG A:CYS204 4.9 11.2 1.0
CA A:ALA207 4.9 33.0 1.0

Sodium binding site 4 out of 6 in 4zg3

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Sodium binding site 4 out of 6 in the In-Vacuum Long-Wavelength Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of In-Vacuum Long-Wavelength Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:29.9
occ:1.00
 O A:HOH592 2.5 30.9 1.0
OE2 A:GLU89 2.7 11.9 1.0
OG A:SER103 2.7 10.3 1.0
CB A:SER103 3.3 10.0 1.0
CD A:GLU89 3.4 10.5 1.0
OE1 A:GLU89 3.5 11.0 1.0
CB A:ILE105 3.7 9.9 1.0
CD1 A:ILE105 3.7 13.0 1.0
O1 A:GOL303 3.9 34.9 1.0
CD1 A:LEU87 4.1 12.0 1.0
C1 A:GOL303 4.1 34.2 1.0
CG1 A:ILE105 4.1 11.2 1.0
CG2 A:ILE105 4.2 11.5 1.0
NZ A:LYS49 4.6 15.7 1.0
CA A:SER103 4.8 9.7 1.0
CA A:ILE105 4.8 9.0 1.0
N A:ILE105 4.8 8.8 1.0
CG A:GLU89 4.8 10.7 1.0
O A:HOH593 4.9 30.0 1.0

Sodium binding site 5 out of 6 in 4zg3

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Sodium binding site 5 out of 6 in the In-Vacuum Long-Wavelength Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of In-Vacuum Long-Wavelength Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:29.9
occ:1.00
 O A:THR86 2.7 10.2 1.0
N A:ALA52 2.8 9.0 1.0
OD1 A:ASN109 2.9 9.1 1.0
N A:THR86 3.6 9.1 1.0
O A:ALA52 3.6 10.6 1.0
CB A:TRP51 3.6 9.9 1.0
C A:THR86 3.6 9.0 1.0
CA A:TRP51 3.7 9.1 1.0
CB A:ALA52 3.7 10.7 1.0
CA A:ALA52 3.7 9.2 1.0
CB A:THR86 3.7 9.3 1.0
C A:TRP51 3.7 8.8 1.0
CG A:ASN109 3.8 9.4 1.0
CA A:THR86 3.8 9.0 1.0
CE A:MET112 4.0 12.1 1.0
ND2 A:ASN109 4.0 10.8 1.0
C A:ALA52 4.1 9.5 1.0
OG1 A:THR86 4.1 9.2 1.0
C A:THR85 4.4 9.9 1.0
CB A:VAL110 4.4 10.1 1.0
CE1 A:PHE203 4.4 11.8 1.0
O A:VAL110 4.4 9.4 1.0
N A:VAL110 4.6 8.9 1.0
CA A:THR85 4.6 9.2 1.0
CG A:TRP51 4.7 9.9 1.0
N A:LEU87 4.9 9.1 1.0
CB A:THR85 4.9 10.3 1.0
CD1 A:PHE203 4.9 11.4 1.0
CG2 A:VAL110 4.9 10.9 1.0
O A:TRP51 4.9 9.5 1.0
CD1 A:TRP51 5.0 10.0 1.0
CG2 A:THR86 5.0 10.6 1.0
CA A:VAL110 5.0 9.6 1.0

Sodium binding site 6 out of 6 in 4zg3

Go back to Sodium Binding Sites List in 4zg3
Sodium binding site 6 out of 6 in the In-Vacuum Long-Wavelength Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of In-Vacuum Long-Wavelength Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:30.0
occ:1.00
 O A:HOH501 2.7 29.9 0.9
O A:HOH490 2.8 14.5 1.0
N A:ALA148 2.9 8.9 1.0
O A:HOH518 3.5 29.9 1.0
CB A:ALA148 3.6 10.2 1.0
CE2 A:PHE173 3.6 10.2 1.0
CA A:ASP147 3.6 9.9 1.0
C A:ASP147 3.7 8.8 1.0
CB A:ASP147 3.8 10.4 1.0
CD2 A:PHE173 3.8 10.2 1.0
CA A:ALA148 3.8 9.3 1.0
CB A:TYR169 4.0 10.3 1.0
O A:HOH548 4.1 29.8 1.0
N A:SER170 4.1 9.6 1.0
C A:TYR169 4.1 9.9 1.0
CA A:SER170 4.3 9.2 1.0
O A:SER182 4.3 10.7 1.0
O A:TYR169 4.3 10.0 1.0
O A:HOH455 4.6 11.8 1.0
CZ A:PHE173 4.7 10.6 1.0
CA A:TYR169 4.7 9.6 1.0
CB A:SER170 4.8 10.0 1.0
N A:CYS149 4.9 9.7 1.0
CD1 A:LEU138 4.9 11.8 1.0
C A:ALA148 4.9 9.3 1.0
O A:ASP147 5.0 10.1 1.0
N A:ASP147 5.0 9.9 1.0

Reference:

A.Wagner, R.Duman, K.Henderson, V.Mykhaylyk. In-Vacuum Long-Wavelength Macromolecular Crystallography. Acta Crystallogr D Struct V. 72 430 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 26960130
DOI: 10.1107/S2059798316001078
Page generated: Sun Aug 17 22:44:36 2025

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