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Sodium in PDB 8ubs: Crystal Structure of Nrdj-1 Split Intein Fusion

Protein crystallography data

The structure of Crystal Structure of Nrdj-1 Split Intein Fusion, PDB code: 8ubs was solved by C.Kofoed, X.Ye, P.D.Jeffrey, T.W.Muir, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.12 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.793, 84.383, 174.709, 90, 90, 90
R / Rfree (%) 18 / 22.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Nrdj-1 Split Intein Fusion (pdb code 8ubs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Nrdj-1 Split Intein Fusion, PDB code: 8ubs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 8ubs

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Sodium binding site 1 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


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 Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:32.5
occ:1.00
 O A:HOH302 2.2 29.9 1.0
O A:GLY3 2.3 27.5 1.0
O A:HOH314 2.3 28.0 1.0
OD2 A:ASP131 2.5 44.4 1.0
O A:HOH310 2.6 28.5 1.0
O A:HOH395 2.6 33.9 1.0
CB A:ASP131 3.2 24.3 1.0
CG A:ASP131 3.2 39.5 1.0
C A:GLY3 3.5 27.8 1.0
O A:HOH315 3.8 52.4 1.0
O A:HOH326 3.9 37.5 1.0
N A:GLY3 3.9 41.2 1.0
N A:SER149 4.0 24.7 1.0
C A:GLY2 4.2 45.9 1.0
CA A:GLY3 4.2 30.6 1.0
N A:GLY2 4.3 48.3 1.0
OD1 A:ASP131 4.3 46.5 1.0
CB A:SER149 4.5 30.0 1.0
O A:GLY2 4.5 45.5 1.0
N A:ALA4 4.5 22.5 1.0
O A:SER149 4.5 31.7 1.0
O2 A:FMT201 4.6 38.3 1.0
CA A:ASP131 4.6 27.6 1.0
NE2 A:HIS83 4.7 23.4 1.0
CA A:SER149 4.7 26.0 1.0
CA A:ALA148 4.7 20.8 1.0
CA A:ALA4 4.7 21.6 1.0
CA A:GLY2 4.7 52.2 1.0
O A:HIS147 4.7 21.2 1.0
O A:ILE132 4.8 21.6 1.0
C A:ALA148 4.8 23.1 1.0

Sodium binding site 2 out of 10 in 8ubs

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Sodium binding site 2 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


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 Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:26.4
occ:1.00
 O A:HOH377 2.1 29.2 1.0
O B:ASP101 2.3 22.6 1.0
O A:ARG90 2.4 24.3 1.0
O B:HOH336 2.4 32.1 1.0
C B:ASP101 3.4 22.6 1.0
C A:ARG90 3.5 22.2 1.0
CB A:ARG90 3.7 21.9 1.0
CB B:ASP101 3.8 21.7 1.0
CA B:ASP101 3.9 20.7 1.0
NZ B:LYS117 3.9 45.0 1.0
CA A:ARG90 4.0 24.2 1.0
OD1 B:ASP101 4.3 32.2 1.0
CG A:ARG90 4.3 21.6 1.0
CG B:ASP101 4.4 30.7 1.0
N A:GLY91 4.5 21.8 1.0
CD A:ARG90 4.6 30.1 1.0
N B:ASP102 4.6 20.3 1.0
O A:TYR92 4.6 20.3 1.0
O B:HOH374 4.6 30.4 1.0
ND2 B:ASN89 4.7 24.3 1.0
CG B:GLU103 4.8 24.1 1.0
CA A:GLY91 4.8 21.1 1.0
CA B:ASP102 4.9 20.8 1.0

Sodium binding site 3 out of 10 in 8ubs

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Sodium binding site 3 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


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 Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:56.1
occ:1.00
 O A:HOH401 2.2 58.7 1.0
O A:ARG121 2.4 21.6 1.0
O A:HOH411 2.6 53.1 1.0
O A:HOH378 2.7 42.7 1.0
O A:HOH419 2.8 41.7 1.0
C A:ARG121 3.6 21.5 1.0
O A:HOH422 4.3 56.1 1.0
N A:ARG121 4.3 23.3 1.0
CA A:ARG121 4.5 26.2 1.0
N A:LYS122 4.5 18.9 1.0
CA A:LYS122 4.5 24.2 1.0
O A:HOH385 4.7 31.3 1.0
O A:HOH423 4.7 42.1 1.0
CB A:LYS122 4.8 22.8 1.0
CB A:ARG121 5.0 22.4 1.0

Sodium binding site 4 out of 10 in 8ubs

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Sodium binding site 4 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


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 Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:57.4
occ:1.00
 O A:ASN30 2.5 36.5 1.0
O A:HOH416 2.6 59.8 1.0
O C:HOH382 2.6 55.6 1.0
O C:HOH373 2.6 40.0 1.0
C A:ASN30 3.6 32.1 1.0
CA A:ASN30 4.0 32.0 1.0
NE2 C:HIS42 4.1 31.2 1.0
CE1 C:HIS42 4.3 36.6 1.0
O C:HOH338 4.3 31.2 1.0
NE2 C:HIS137 4.4 51.0 1.0
CB A:ASN30 4.6 48.8 1.0
CD2 C:HIS137 4.7 49.8 1.0
N A:ASP31 4.7 32.2 1.0

Sodium binding site 5 out of 10 in 8ubs

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Sodium binding site 5 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


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 Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:36.4
occ:1.00
 O A:TYR16 2.3 24.7 1.0
O A:HOH410 2.4 38.8 1.0
OG1 A:THR19 2.4 26.1 1.0
O A:HOH398 2.5 39.8 1.0
O A:HOH405 2.6 37.0 1.0
O A:LYS18 2.7 31.2 1.0
O A:HOH307 3.3 46.3 1.0
CB A:THR19 3.4 26.7 1.0
C A:TYR16 3.5 28.1 1.0
C A:LYS18 3.5 30.7 1.0
CA A:THR19 3.8 26.4 1.0
CG2 A:THR19 3.8 32.5 1.0
O A:GLY17 4.0 20.2 1.0
C A:GLY17 4.0 25.1 1.0
N A:THR19 4.0 25.3 1.0
CB A:TYR16 4.1 20.8 1.0
N A:LYS18 4.3 25.8 1.0
CA A:TYR16 4.4 26.5 1.0
N A:GLY17 4.4 25.3 1.0
CA A:GLY17 4.4 23.9 1.0
CA A:LYS18 4.6 32.1 1.0

Sodium binding site 6 out of 10 in 8ubs

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Sodium binding site 6 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


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 Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:63.8
occ:1.00
 O A:LYS88 2.3 24.5 1.0
O A:HOH414 2.4 48.1 1.0
O B:HOH327 2.5 36.5 1.0
O A:HOH350 2.6 29.9 1.0
C A:LYS88 3.4 28.6 1.0
CA A:LYS88 4.0 27.8 1.0
O B:HOH305 4.3 33.2 1.0
OD2 B:ASP101 4.4 33.9 1.0
N A:ASN89 4.4 23.0 1.0
OH A:TYR86 4.5 42.6 1.0
CB A:LYS88 4.6 29.2 1.0
CA A:ASN89 4.7 24.8 1.0
C A:ASN89 4.7 26.4 1.0
O A:THR87 4.8 22.5 1.0
O A:ASN89 4.9 27.7 1.0

Sodium binding site 7 out of 10 in 8ubs

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Sodium binding site 7 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:35.5
occ:1.00
 O D:HOH356 2.3 27.7 1.0
O C:ASP101 2.3 23.8 1.0
O C:HOH365 2.3 38.5 1.0
O D:ARG90 2.4 27.7 1.0
O C:HOH392 2.4 43.0 1.0
C C:ASP101 3.4 27.1 1.0
C D:ARG90 3.5 31.8 1.0
CB D:ARG90 3.7 23.0 1.0
CB C:ASP101 3.8 26.1 1.0
CA C:ASP101 3.9 29.3 1.0
CA D:ARG90 4.0 30.2 1.0
CG D:ARG90 4.3 22.6 1.0
NZ C:LYS117 4.4 52.6 1.0
OD1 C:ASP101 4.5 36.8 1.0
N C:ASP102 4.5 22.2 1.0
O D:HOH382 4.5 61.1 1.0
CG C:GLU103 4.5 49.9 1.0
N D:GLY91 4.6 25.2 1.0
CG C:ASP101 4.6 39.4 1.0
ND2 C:ASN89 4.7 21.6 1.0
CD D:ARG90 4.7 26.7 1.0
O D:TYR92 4.8 25.3 1.0
O C:HOH370 4.8 35.4 1.0
CA C:ASP102 4.9 26.5 1.0
CA D:GLY91 4.9 27.4 1.0
CG C:ASN89 5.0 19.6 1.0

Sodium binding site 8 out of 10 in 8ubs

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Sodium binding site 8 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:75.6
occ:1.00
 O C:HOH378 2.5 50.8 1.0
O C:ARG121 2.5 27.9 1.0
O C:HOH390 2.5 42.5 1.0
O C:HOH379 2.7 36.0 1.0
C C:ARG121 3.7 28.8 1.0
N C:ARG121 4.3 25.5 1.0
O C:HOH403 4.3 56.0 1.0
CA C:ARG121 4.5 25.5 1.0
N C:LYS122 4.6 19.2 1.0
CA C:LYS122 4.7 21.8 1.0
CB C:ARG121 4.9 23.7 1.0

Sodium binding site 9 out of 10 in 8ubs

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Sodium binding site 9 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:38.1
occ:1.00
 O D:HOH304 2.3 45.4 1.0
OD2 D:ASP131 2.4 56.0 1.0
O D:HOH315 2.5 34.6 1.0
O D:GLY3 2.5 32.7 1.0
O D:HOH364 2.5 32.8 1.0
O D:HOH347 2.5 42.2 1.0
CG D:ASP131 3.2 50.7 1.0
CB D:ASP131 3.2 34.1 1.0
C D:GLY3 3.7 29.9 1.0
N D:SER149 4.0 25.3 1.0
O D:HOH312 4.1 49.1 1.0
N D:GLY3 4.1 38.8 1.0
C D:GLY2 4.3 54.6 1.0
OD1 D:ASP131 4.4 60.6 1.0
CA D:GLY3 4.4 25.8 1.0
O D:SER149 4.5 39.4 1.0
O D:HOH329 4.5 26.4 1.0
CB D:SER149 4.5 42.5 1.0
N D:GLY2 4.5 58.2 1.0
NE2 D:HIS83 4.6 29.7 1.0
O D:GLY2 4.6 65.2 1.0
O D:HIS147 4.6 25.9 1.0
CA D:ALA148 4.7 28.4 1.0
N D:ALA4 4.7 26.5 1.0
CA D:ASP131 4.7 33.6 1.0
O D:ILE132 4.7 30.5 1.0
CA D:SER149 4.7 34.9 1.0
CA D:GLY2 4.7 60.7 1.0
C D:ALA148 4.8 29.1 1.0
CA D:ALA4 4.8 21.9 1.0

Sodium binding site 10 out of 10 in 8ubs

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Sodium binding site 10 out of 10 in the Crystal Structure of Nrdj-1 Split Intein Fusion


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Nrdj-1 Split Intein Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:60.6
occ:1.00
 O D:HOH367 2.1 56.3 1.0
O D:HOH355 2.3 55.9 1.0
O D:LYS88 2.4 27.4 1.0
O C:HOH376 2.5 43.7 1.0
O D:HOH331 2.5 33.8 1.0
C D:LYS88 3.5 27.5 1.0
O C:HOH301 3.9 49.7 1.0
CA D:LYS88 4.1 27.8 1.0
OD2 C:ASP101 4.2 40.0 1.0
O D:HOH330 4.3 44.7 1.0
OH D:TYR86 4.3 44.7 1.0
N D:ASN89 4.5 23.2 1.0
O D:THR87 4.7 23.9 1.0
C D:ASN89 4.8 27.7 1.0
CB D:LYS88 4.8 26.4 1.0
CA D:ASN89 4.8 28.3 1.0
O D:ASN89 4.9 28.7 1.0
O D:HOH362 5.0 45.9 1.0

Reference:

T.W.Muir, C.Kofoed, X.Ye, P.Jeffrey. Cell Surface Sculpting Using Logic-Gated Protein Actuators To Be Published.
Page generated: Thu Oct 31 22:59:19 2024

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