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Sodium in PDB 4izm: Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury

Protein crystallography data

The structure of Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury, PDB code: 4izm was solved by N.Reyes, O.Boudker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 4.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 119.708, 119.708, 333.720, 90.00, 90.00, 120.00
R / Rfree (%) 25 / 29.9

Other elements in 4izm:

The structure of Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury also contains other interesting chemical elements:

Mercury (Hg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury (pdb code 4izm). 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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury, PDB code: 4izm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4izm

Go back to Sodium Binding Sites List in 4izm
Sodium binding site 1 out of 6 in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury


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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:0.3
occ:1.00
O A:THR352 2.5 0.5 1.0
O A:THR308 2.6 0.4 1.0
SD A:MET311 2.6 0.5 1.0
O A:SER349 2.7 0.4 1.0
C A:THR308 3.1 0.8 1.0
C A:THR352 3.5 0.1 1.0
O A:ILE350 3.6 0.9 1.0
CA A:THR308 3.7 0.1 1.0
N A:THR352 3.7 0.4 1.0
C A:ILE350 3.8 0.1 1.0
C A:SER349 3.8 0.3 1.0
CA A:THR352 3.9 0.9 1.0
N A:ILE309 3.9 0.1 1.0
CG A:MET311 4.0 0.2 1.0
CE A:MET311 4.0 0.0 1.0
CA A:ILE350 4.0 0.5 1.0
CB A:THR352 4.1 0.0 1.0
CB A:MET311 4.1 0.6 1.0
C A:GLY351 4.2 0.5 1.0
CA A:ILE309 4.3 0.5 1.0
O A:ILE309 4.4 0.8 1.0
C A:ILE309 4.4 0.8 1.0
N A:ILE350 4.4 0.8 1.0
N A:GLY351 4.5 0.6 1.0
O A:ALA353 4.5 0.2 1.0
O A:GLY351 4.5 1.0 1.0
OG1 A:THR352 4.6 0.7 1.0
N A:ALA353 4.7 0.3 1.0
N A:THR308 4.7 0.3 1.0
CB A:THR308 4.7 0.8 1.0

Sodium binding site 2 out of 6 in 4izm

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Sodium binding site 2 out of 6 in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury


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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:0.1
occ:1.00
O A:ASN310 2.1 0.7 1.0
O A:GLY306 2.8 1.0 1.0
O A:ASN401 2.8 0.4 1.0
C A:ASN310 3.3 0.8 1.0
OD2 A:ASP405 3.4 0.1 1.0
OD1 A:ASP405 3.4 0.9 1.0
C A:ASN401 3.7 0.7 1.0
CG A:ASP405 3.8 0.8 1.0
C A:GLY306 3.9 0.2 1.0
CA A:ALA307 3.9 0.1 1.0
C A:ALA307 4.1 0.4 1.0
CB A:ASN401 4.1 0.1 1.0
N A:MET311 4.2 0.4 1.0
CA A:ASN310 4.2 0.4 1.0
CE A:MET311 4.2 0.0 1.0
CA A:MET311 4.3 0.5 1.0
CA A:ASN401 4.3 0.5 1.0
N A:ALA307 4.4 0.8 1.0
N A:ASN310 4.4 1.0 1.0
OG A:SER278 4.4 0.7 1.0
N A:THR308 4.4 0.3 1.0
CB A:ASN310 4.5 0.2 1.0
O A:ALA307 4.5 1.0 1.0
SD A:MET311 4.5 0.5 1.0
CG A:MET311 4.6 0.2 1.0
CG A:ASN401 4.6 0.8 1.0
N A:VAL402 4.8 0.8 1.0
CB A:MET311 4.8 0.6 1.0
CB A:SER278 5.0 0.6 1.0

Sodium binding site 3 out of 6 in 4izm

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Sodium binding site 3 out of 6 in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury


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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:0.0
occ:1.00
O B:THR352 2.4 0.1 1.0
O B:SER349 2.6 0.2 1.0
O B:THR308 2.6 0.0 1.0
SD B:MET311 3.1 0.6 1.0
C B:THR308 3.4 0.1 1.0
C B:THR352 3.4 1.0 1.0
O B:ILE350 3.5 0.9 1.0
N B:THR352 3.6 1.0 1.0
C B:SER349 3.7 1.0 1.0
C B:ILE350 3.8 0.8 1.0
CA B:THR352 3.9 0.9 1.0
CG B:MET311 3.9 0.5 1.0
CA B:ILE350 4.0 0.5 1.0
CB B:MET311 4.1 0.1 1.0
CB B:THR352 4.1 0.1 1.0
CA B:THR308 4.1 0.5 1.0
CE B:MET311 4.2 0.8 1.0
C B:GLY351 4.2 0.4 1.0
N B:ILE309 4.2 0.9 1.0
N B:ILE350 4.4 0.8 1.0
N B:GLY351 4.4 0.2 1.0
CA B:ILE309 4.5 0.9 1.0
N B:ALA353 4.6 0.7 1.0
C B:ILE309 4.8 0.3 1.0
O B:GLY351 4.8 0.5 1.0
CA B:GLY351 4.9 0.3 1.0
O B:ILE309 4.9 0.6 1.0
O B:ALA353 4.9 0.8 1.0
CA B:SER349 5.0 0.7 1.0
CB B:THR308 5.0 0.6 1.0

Sodium binding site 4 out of 6 in 4izm

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Sodium binding site 4 out of 6 in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury


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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:0.1
occ:1.00
O B:ASN310 2.1 0.4 1.0
O B:GLY306 2.8 0.1 1.0
O B:ASN401 3.0 0.7 1.0
C B:ASN310 3.1 0.4 1.0
OD1 B:ASP405 3.3 0.2 1.0
OD2 B:ASP405 3.5 0.8 1.0
C B:ASN401 3.7 0.3 1.0
CG B:ASP405 3.9 1.0 1.0
SD B:MET311 3.9 0.6 1.0
C B:GLY306 3.9 1.0 1.0
CA B:ALA307 3.9 0.6 1.0
N B:MET311 4.0 0.4 1.0
CA B:ASN310 4.1 0.3 1.0
CA B:MET311 4.1 0.2 1.0
C B:ALA307 4.1 0.6 1.0
CB B:ASN401 4.2 0.1 1.0
N B:ASN310 4.2 0.9 1.0
CA B:ASN401 4.3 0.2 1.0
N B:ALA307 4.4 0.1 1.0
CB B:ASN310 4.4 1.0 1.0
N B:THR308 4.4 0.8 1.0
O B:ALA307 4.5 0.9 1.0
CG B:ASN401 4.6 0.3 1.0
N B:VAL402 4.6 0.7 1.0
CG B:MET311 4.7 0.5 1.0
OD1 B:ASN401 4.8 0.3 1.0
CB B:MET311 4.8 0.1 1.0
OG B:SER278 4.8 0.0 1.0
CA B:VAL402 4.9 0.2 1.0
CE B:MET311 4.9 0.8 1.0

Sodium binding site 5 out of 6 in 4izm

Go back to Sodium Binding Sites List in 4izm
Sodium binding site 5 out of 6 in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury


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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:0.7
occ:1.00
O C:THR352 1.9 0.1 1.0
O C:THR308 2.7 0.9 1.0
SD C:MET311 2.7 0.9 1.0
O C:SER349 2.8 0.5 1.0
C C:THR352 3.0 0.0 1.0
C C:THR308 3.4 0.9 1.0
O C:ILE350 3.5 0.4 1.0
N C:THR352 3.5 0.3 1.0
CA C:THR352 3.6 0.1 1.0
C C:ILE350 3.8 0.6 1.0
C C:GLY351 3.9 0.5 1.0
CB C:THR352 3.9 1.0 1.0
C C:SER349 4.0 0.5 1.0
CE C:MET311 4.0 0.9 1.0
CA C:THR308 4.0 0.9 1.0
O C:GLY351 4.1 0.2 1.0
N C:ALA353 4.2 0.5 1.0
CA C:ILE350 4.2 0.2 1.0
CG C:MET311 4.2 0.5 1.0
N C:ILE309 4.3 0.6 1.0
N C:GLY351 4.5 0.0 1.0
CB C:MET311 4.5 0.7 1.0
N C:ILE350 4.5 0.2 1.0
CA C:ILE309 4.6 0.9 1.0
CA C:ALA353 4.6 0.8 1.0
O C:ALA353 4.7 0.8 1.0
CA C:GLY351 4.8 0.1 1.0
C C:ALA353 4.8 0.5 1.0
CG2 C:THR352 4.9 0.9 1.0
CB C:THR308 4.9 0.1 1.0
OG1 C:THR352 4.9 0.4 1.0
C C:ILE309 5.0 0.4 1.0

Sodium binding site 6 out of 6 in 4izm

Go back to Sodium Binding Sites List in 4izm
Sodium binding site 6 out of 6 in the Crystal Structure of Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury


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 Gltph L66C-S300C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:0.7
occ:1.00
O C:ASN401 2.2 0.0 1.0
O C:ASN310 2.2 0.3 1.0
C C:ASN401 3.1 0.0 1.0
C C:ASN310 3.4 0.4 1.0
O C:GLY306 3.4 0.3 1.0
OD1 C:ASP405 3.5 0.1 1.0
OD2 C:ASP405 3.5 0.7 1.0
CA C:ASN401 3.8 0.1 1.0
CB C:ASN401 3.8 0.2 1.0
CG C:ASP405 3.9 0.9 1.0
CA C:ALA307 3.9 0.0 1.0
N C:VAL402 4.2 0.6 1.0
N C:MET311 4.2 0.3 1.0
C C:ALA307 4.2 0.7 1.0
CA C:MET311 4.3 0.5 1.0
C C:GLY306 4.3 0.0 1.0
CG C:ASN401 4.3 0.7 1.0
OD1 C:ASN310 4.4 0.9 1.0
CA C:ASN310 4.4 0.9 1.0
OG C:SER278 4.5 0.7 1.0
CB C:ASN310 4.5 0.0 1.0
O C:ALA307 4.5 0.1 1.0
CA C:VAL402 4.5 0.6 1.0
N C:ALA307 4.6 0.6 1.0
OD1 C:ASN401 4.6 0.0 1.0
N C:ASN310 4.7 0.6 1.0
CE C:MET311 4.7 0.9 1.0
CG C:MET311 4.8 0.5 1.0
SD C:MET311 4.8 0.9 1.0
N C:THR308 4.8 0.7 1.0
CB C:ALA307 4.9 0.3 1.0
CG C:ASN310 4.9 0.0 1.0

Reference:

N.Reyes, S.Oh, O.Boudker. Binding Thermodynamics of A Glutamate Transporter Homolog. Nat.Struct.Mol.Biol. V. 20 634 2013.
ISSN: ISSN 1545-9993
PubMed: 23563139
DOI: 10.1038/NSMB.2548
Page generated: Tue Dec 15 06:45:22 2020

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