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Sodium in PDB 3nv0: Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution

Protein crystallography data

The structure of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution, PDB code: 3nv0 was solved by D.E.Kerkow, A.B.Carmel, J.R.Williamson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.01 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.004, 49.547, 148.680, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.1

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution (pdb code 3nv0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution, PDB code: 3nv0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in 3nv0

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Sodium binding site 1 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na450

b:40.6
occ:1.00
CG2 A:THR235 2.5 16.7 0.2
OG1 A:THR235 2.5 15.9 0.8
O A:ASP228 2.8 15.8 1.0
O A:HOH555 3.1 34.6 1.0
CG2 A:THR235 3.3 15.0 0.8
CB A:THR235 3.3 17.6 0.2
CB A:THR235 3.3 17.5 0.8
OG1 A:THR235 3.7 15.9 0.2
O A:ILE226 3.8 14.4 1.0
C A:ASP228 3.9 14.9 1.0
N A:GLY232 4.0 14.5 1.0
CA A:GLY232 4.1 21.2 1.0
C A:ASP231 4.2 15.8 1.0
O A:LYS225 4.3 14.3 1.0
O A:ASP231 4.4 15.7 1.0
O A:HOH578 4.4 36.8 1.0
C A:ILE226 4.5 16.3 1.0
CA A:GLY229 4.5 14.4 1.0
N A:GLY229 4.6 13.0 1.0
CB A:ASP231 4.7 23.8 1.0
CA A:THR235 4.7 18.9 0.2
CA A:THR235 4.7 19.3 0.8
CA A:ASP231 4.8 17.0 1.0
O A:HOH602 4.8 34.3 1.0
N A:ASP228 4.8 12.4 1.0
N A:ASP231 4.8 19.5 1.0
C A:GLY229 4.9 19.3 1.0
CA A:ILE226 4.9 14.3 1.0
O A:GLY229 4.9 14.7 1.0
CA A:ASP228 5.0 11.7 1.0

Sodium binding site 2 out of 19 in 3nv0

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Sodium binding site 2 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na451

b:30.4
occ:1.00
OG A:SER386 2.7 18.3 1.0
OD1 A:ASP259 2.7 16.4 1.0
NE A:ARG388 2.8 28.3 1.0
O A:HOH507 2.8 14.5 1.0
OD2 A:ASP259 3.0 15.5 1.0
CG A:ASP259 3.2 19.9 1.0
CB A:SER386 3.3 16.9 1.0
NH2 A:ARG388 3.5 21.9 1.0
CZ A:ARG388 3.6 28.2 1.0
CG1 A:ILE261 3.6 20.9 1.0
CB A:ILE261 3.7 20.9 1.0
CD A:ARG388 3.7 32.5 1.0
CB A:ARG388 3.7 21.3 1.0
O A:HOH505 4.2 17.3 1.0
CG A:ARG388 4.3 25.6 1.0
CE A:LYS262 4.5 24.5 1.0
N A:ARG389 4.5 16.1 1.0
CG A:LYS262 4.6 25.5 1.0
CG2 A:ILE261 4.6 18.9 1.0
CB A:ASP259 4.6 16.8 1.0
N A:ILE261 4.7 17.4 1.0
CG2 A:VAL264 4.7 13.7 1.0
CA A:ILE261 4.7 20.8 1.0
CA A:SER386 4.7 12.2 1.0
CA A:ARG388 4.8 21.6 1.0
O A:HOH618 4.8 13.0 1.0
NH1 A:ARG388 4.9 28.9 1.0
N A:ARG388 4.9 19.3 1.0

Sodium binding site 3 out of 19 in 3nv0

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Sodium binding site 3 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na452

b:30.2
occ:1.00
OH A:TYR358 2.6 12.9 1.0
O A:HOH564 2.6 27.1 1.0
O B:TYR135 3.0 11.0 1.0
CE1 A:TYR393 3.3 41.8 1.0
CZ A:TYR358 3.4 13.9 1.0
CE1 A:TYR358 3.5 12.0 1.0
O B:VAL136 3.6 28.3 1.0
O B:HOH563 3.7 20.6 0.5
CA B:VAL136 3.7 10.0 1.0
CD B:ARG134 3.9 9.5 1.0
O B:HOH610 3.9 13.9 1.0
CG B:ARG134 4.0 8.5 1.0
C B:TYR135 4.0 14.8 1.0
C B:VAL136 4.0 21.6 1.0
O B:HOH564 4.0 15.6 0.5
CD1 A:TYR393 4.0 32.0 1.0
CB A:HIS337 4.2 5.8 1.0
N B:VAL136 4.3 10.2 1.0
CZ A:TYR393 4.3 36.0 1.0
OH A:TYR393 4.4 23.5 1.0
CG A:HIS337 4.6 7.5 1.0
CD2 A:HIS337 4.6 7.6 1.0
CE2 A:TYR358 4.7 9.5 1.0
CB B:VAL136 4.8 12.7 1.0
CD1 A:TYR358 4.8 12.6 1.0
CB B:ARG134 4.9 7.3 1.0

Sodium binding site 4 out of 19 in 3nv0

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Sodium binding site 4 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na453

b:37.2
occ:1.00
OE1 A:GLN238 2.6 22.5 1.0
CD A:GLN238 3.4 28.9 1.0
CB A:GLN238 3.5 14.1 1.0
CG A:GLN238 3.9 24.5 1.0
CD1 A:ILE226 3.9 33.6 1.0
CG1 A:ILE226 4.0 28.0 1.0
NE2 A:GLN238 4.5 21.4 1.0
CA A:GLN238 4.9 15.9 1.0
CG2 A:ILE226 4.9 17.8 1.0

Sodium binding site 5 out of 19 in 3nv0

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Sodium binding site 5 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na454

b:44.9
occ:1.00
O A:SER294 2.6 32.5 1.0
O A:HOH552 2.7 30.8 1.0
O A:HOH654 3.0 45.6 1.0
CA A:ARG295 3.5 17.6 1.0
C A:SER294 3.6 26.3 1.0
CD A:ARG295 3.8 18.9 1.0
N A:ARG295 4.0 19.0 1.0
CG2 A:THR278 4.2 33.2 1.0
C A:ARG295 4.4 20.0 1.0
CB A:THR278 4.4 24.7 1.0
CB A:ARG295 4.4 13.2 1.0
NE A:ARG295 4.5 25.3 1.0
CG A:ARG295 4.5 17.1 1.0
O A:HOH536 4.6 25.6 1.0
O A:ALA293 4.6 26.8 1.0
CA A:THR278 4.7 17.5 1.0
O A:THR278 4.7 14.8 1.0
C A:ALA293 4.8 33.9 1.0
CB A:ALA293 4.8 33.8 1.0
CA A:SER294 4.9 28.8 1.0
N A:ILE296 4.9 13.3 1.0
NA A:NA456 4.9 55.8 1.0
N A:SER294 4.9 25.8 1.0
O A:ARG295 4.9 18.9 1.0

Sodium binding site 6 out of 19 in 3nv0

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Sodium binding site 6 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na455

b:46.8
occ:1.00
OD2 A:ASP228 2.4 12.7 1.0
O A:HOH634 2.7 53.5 1.0
O A:HOH633 3.0 47.6 1.0
O A:HIS315 3.2 16.6 1.0
CG A:ASP228 3.4 13.3 1.0
CB A:ASP228 3.7 14.0 1.0
N A:HIS315 4.0 12.8 1.0
CG1 A:ILE314 4.3 18.9 1.0
C A:HIS315 4.3 19.8 1.0
O A:TYR224 4.3 14.4 1.0
O A:HOH544 4.3 30.4 1.0
CG A:MET317 4.4 30.1 0.5
CG A:MET317 4.4 30.5 0.6
CB A:TYR224 4.5 11.3 1.0
OD1 A:ASP228 4.6 13.0 1.0
CA A:HIS315 4.6 11.6 1.0
SD A:MET317 4.7 74.5 0.6
SD A:MET317 4.8 71.7 0.5
CB A:HIS315 4.8 8.4 1.0
C A:TYR224 4.9 16.1 1.0
C A:ILE314 4.9 15.2 1.0
CE A:MET317 4.9 67.8 0.6
CA A:ILE314 4.9 10.1 1.0

Sodium binding site 7 out of 19 in 3nv0

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Sodium binding site 7 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na456

b:55.8
occ:1.00
O A:ALA293 2.5 26.8 1.0
NE A:ARG295 2.9 25.3 1.0
NH1 A:ARG292 3.3 33.7 1.0
CG A:ARG292 3.4 41.9 1.0
CB A:ARG292 3.4 40.1 1.0
C A:ALA293 3.4 33.9 1.0
N A:ALA293 3.5 25.8 1.0
NH2 A:ARG295 3.5 25.8 1.0
CZ A:ARG295 3.6 28.4 1.0
CD A:ARG292 3.7 40.6 1.0
CA A:ALA293 3.8 28.6 1.0
CD A:ARG295 3.8 18.9 1.0
C A:ARG292 3.9 30.7 1.0
CB A:ALA293 4.1 33.8 1.0
CG A:ARG295 4.2 17.1 1.0
CA A:ARG292 4.3 34.6 1.0
CZ A:ARG292 4.3 37.9 1.0
O A:ARG292 4.4 32.3 1.0
NE A:ARG292 4.5 33.9 1.0
N A:SER294 4.6 25.8 1.0
O A:SER294 4.8 32.5 1.0
C A:SER294 4.8 26.3 1.0
NH1 A:ARG295 4.9 21.2 1.0
NA A:NA454 4.9 44.9 1.0

Sodium binding site 8 out of 19 in 3nv0

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Sodium binding site 8 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na457

b:48.9
occ:1.00
OH A:TYR206 2.4 32.8 1.0
ND2 B:ASN56 2.7 29.0 1.0
O A:HOH646 3.2 56.0 1.0
CZ A:TYR206 3.5 22.9 1.0
CB B:PRO54 3.7 10.5 1.0
CG B:ASN56 3.8 30.5 1.0
CG B:PRO54 3.8 12.3 1.0
CE1 A:TYR206 4.0 19.1 1.0
OD1 B:ASN56 4.1 26.8 1.0
O A:HOH583 4.3 45.6 1.0
O A:HOH660 4.5 17.6 0.6
CE2 A:TYR206 4.7 17.1 1.0
O B:HOH587 4.7 35.5 1.0

Sodium binding site 9 out of 19 in 3nv0

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Sodium binding site 9 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na458

b:36.1
occ:1.00
O A:HOH669 2.4 37.3 1.0
O A:GLN238 2.8 17.2 1.0
N A:ASP241 2.8 16.2 1.0
OD2 A:ASP241 3.2 56.4 1.0
N A:LEU240 3.4 15.3 1.0
CB A:ASP241 3.4 25.3 1.0
CB A:LEU240 3.5 22.7 1.0
CG A:ASP241 3.6 57.2 1.0
C A:GLN238 3.6 15.1 1.0
CA A:ASP241 3.7 16.8 1.0
CA A:LEU240 3.7 13.2 1.0
C A:LEU240 3.7 18.3 1.0
O A:HOH591 3.7 38.8 1.0
C A:LEU239 4.1 13.9 1.0
CA A:GLN238 4.3 15.9 1.0
N A:LEU239 4.4 14.2 1.0
OD1 A:ASP241 4.5 54.5 1.0
O A:LYS237 4.5 16.0 1.0
CG A:LEU240 4.6 22.8 1.0
CA A:LEU239 4.6 12.3 1.0
C A:ASP241 4.7 19.4 1.0
O A:LEU239 4.7 14.1 1.0
N A:ALA242 4.8 14.7 1.0
CD2 A:LEU240 4.9 23.9 1.0
O A:LEU240 4.9 17.7 1.0

Sodium binding site 10 out of 19 in 3nv0

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Sodium binding site 10 out of 19 in the Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure and Mutational Analysis of the NXF2/NXT1 Heterodimeric Complex From Caenorhabditis Elegans at 1.84 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na459

b:47.5
occ:1.00
OE2 A:GLU270 2.3 90.1 1.0
CD A:GLU270 2.6 80.5 1.0
NH2 A:ARG273 2.8 81.5 1.0
NH2 A:ARG277 3.0 51.6 1.0
OE1 A:GLU270 3.1 90.6 1.0
CZ A:ARG273 3.1 80.6 1.0
CG A:MET274 3.1 18.1 0.5
O A:GLU270 3.1 19.3 1.0
NH1 A:ARG273 3.4 81.5 1.0
CG A:GLU270 3.4 55.5 1.0
NH1 A:ARG277 3.4 52.7 1.0
CZ A:ARG277 3.6 54.7 1.0
CE A:MET274 3.9 28.4 0.5
C A:GLU270 3.9 19.8 1.0
N A:MET274 3.9 19.6 1.0
NE A:ARG273 3.9 75.8 1.0
CB A:ARG273 4.0 21.8 1.0
SD A:MET274 4.1 25.4 0.5
CA A:GLU270 4.2 20.3 1.0
CB A:MET274 4.2 15.0 0.5
CB A:MET274 4.3 14.0 0.5
CA A:MET274 4.3 18.4 0.5
CB A:GLU270 4.4 35.5 1.0
CA A:MET274 4.4 17.2 0.5
C A:ARG273 4.5 18.1 1.0
SD A:MET274 4.7 39.3 0.5
CA A:ARG273 4.8 19.6 1.0
NE A:ARG277 4.9 54.8 1.0
CD A:ARG273 5.0 61.3 1.0
CG A:MET274 5.0 19.9 0.5

Reference:

D.E.Kerkow, A.B.Carmel, E.Menichelli, G.Ambrus, R.D.Hills, L.Gerace, J.R.Williamson. The Structure of the NXF2/NXT1 Heterodimeric Complex Reveals the Combined Specificity and Versatility of the NTF2-Like Fold. J.Mol.Biol. V. 415 649 2012.
ISSN: ISSN 0022-2836
PubMed: 22123199
DOI: 10.1016/J.JMB.2011.11.027
Page generated: Tue Dec 15 06:19:24 2020

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