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Sodium in PDB 4jd0: Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.

Protein crystallography data

The structure of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima., PDB code: 4jd0 was solved by B.Stec, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 115.47 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.090, 133.090, 43.365, 90.00, 90.00, 120.00
R / Rfree (%) 11.1 / 16.6

Other elements in 4jd0:

The structure of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. also contains other interesting chemical elements:

Arsenic (As) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. (pdb code 4jd0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima., PDB code: 4jd0:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4jd0

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Sodium binding site 1 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:18.3
occ:0.40
 O2P A:1KH301 0.2 40.0 0.6
AS A:1KH301 1.5 44.2 0.6
OD2 A:ASP166 2.4 19.3 1.0
C1P A:1KH301 2.6 24.2 0.6
O4P A:1KH301 2.7 20.9 0.6
O3P A:1KH301 2.7 25.8 0.6
CL A:CL302 3.0 34.9 0.4
CG A:ASP166 3.3 15.5 1.0
N A:TYR192 3.3 17.2 1.0
OD1 A:ASP166 3.4 16.4 1.0
CZ A:PHE170 3.5 16.4 1.0
CB A:TYR192 3.6 18.1 1.0
CB A:LEU191 3.7 26.0 1.0
CA A:TYR192 3.7 17.7 1.0
C A:LEU191 3.8 16.9 1.0
C1 A:1KH301 4.0 29.1 0.6
CE1 A:PHE170 4.0 16.3 1.0
OG A:SER143 4.1 19.6 0.6
CA A:LEU191 4.3 19.6 1.0
CD1 A:TYR192 4.5 22.4 1.0
O A:LEU191 4.5 18.2 1.0
CE2 A:PHE170 4.6 15.5 1.0
OG A:SER143 4.6 10.6 0.2
CG A:TYR192 4.6 17.8 1.0
CB A:ASP166 4.6 16.0 1.0
O1 A:1KH301 4.7 23.8 0.6
O A:HOH420 4.7 27.4 1.0
N A:LEU191 4.7 19.4 1.0
O A:HOH455 4.8 36.4 1.0
CD1 A:LEU191 4.8 19.1 1.0
O5 A:1KH301 4.8 38.4 0.6
CG A:LEU191 4.9 26.4 1.0
CB A:SER143 4.9 17.2 0.2
CB A:SER143 4.9 13.3 0.2
C2 A:1KH301 5.0 27.7 0.6
C4 A:1KH301 5.0 27.0 0.6

Sodium binding site 2 out of 8 in 4jd0

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Sodium binding site 2 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:27.4
occ:0.40
 O4 A:PO4305 1.2 30.7 0.6
P A:PO4305 2.2 32.1 0.6
OD2 A:ASP200 2.3 27.3 1.0
O3 A:PO4305 2.4 27.8 0.6
O1 A:PO4305 3.2 26.5 0.6
CG A:ASP200 3.2 21.5 1.0
CB A:ASP200 3.3 21.2 1.0
O2 A:PO4305 3.4 35.8 0.6
CA A:LYS197 3.6 19.4 1.0
NZ A:LYS197 3.7 53.8 1.0
CD A:LYS197 3.7 27.2 1.0
N A:LYS197 4.1 16.3 1.0
CE A:LYS197 4.1 38.6 1.0
CB A:LYS197 4.2 19.9 1.0
O A:GLN196 4.2 19.0 1.0
C A:GLN196 4.4 17.6 1.0
OD1 A:ASP200 4.4 21.8 1.0
CG A:LYS197 4.6 25.5 1.0
C A:LYS197 4.6 18.8 1.0
O A:LYS197 4.7 20.8 1.0
CG A:GLN196 4.8 15.3 1.0
CA A:ASP200 4.8 23.0 1.0
O A:HOH481 4.8 40.1 1.0

Sodium binding site 3 out of 8 in 4jd0

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Sodium binding site 3 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:26.1
occ:1.00
 O A:ALA213 2.6 19.3 1.0
OG A:SER131 2.7 14.7 1.0
O A:GLY211 2.7 21.9 1.0
CB A:PHE210 3.2 13.2 1.0
N A:ALA213 3.4 17.4 1.0
CB A:SER131 3.5 14.5 1.0
C A:GLY211 3.6 19.2 1.0
C A:ALA213 3.6 16.8 1.0
CB A:ARG133 3.7 15.2 1.0
CD1 A:TRP215 3.7 16.5 1.0
C A:PHE210 3.8 18.6 1.0
CA A:ALA213 3.9 17.2 1.0
C A:ASN212 3.9 17.4 1.0
O A:PHE210 3.9 20.6 1.0
CD2 A:PHE210 4.1 14.2 1.0
N A:GLY211 4.1 20.5 1.0
CB A:ALA213 4.1 15.4 1.0
CG A:PHE210 4.2 13.3 1.0
O A:HOH406 4.2 24.8 1.0
CA A:PHE210 4.2 15.9 1.0
N A:ASN212 4.2 19.3 1.0
NE1 A:TRP215 4.2 17.9 1.0
CA A:ASN212 4.2 19.2 0.2
CA A:ASN212 4.3 21.4 0.8
CA A:SER131 4.4 15.1 1.0
CD A:ARG133 4.5 19.0 1.0
CA A:GLY211 4.5 23.7 1.0
N A:ARG133 4.6 16.0 1.0
O A:ASN212 4.6 21.4 1.0
CG A:ARG133 4.6 20.1 1.0
CG A:TRP215 4.7 16.0 1.0
CA A:ARG133 4.7 15.6 1.0
N A:LEU214 4.8 15.2 1.0

Sodium binding site 4 out of 8 in 4jd0

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Sodium binding site 4 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:44.0
occ:1.00
 O A:HOH421 2.2 41.0 1.0
OE2 A:GLU99 2.5 43.5 1.0
O A:HOH529 2.9 61.2 1.0
N A:LYS175 3.1 24.6 1.0
CD A:GLU99 3.4 33.3 1.0
OE1 A:GLU99 3.5 34.7 1.0
CB A:LYS175 3.7 31.7 1.0
N A:LYS174 3.8 22.1 1.0
CA A:LYS175 3.8 23.7 1.0
C A:LYS174 3.9 22.2 1.0
CB A:LYS174 4.0 23.9 1.0
CA A:LYS174 4.1 19.0 1.0
OG1 A:THR173 4.1 23.2 1.0
CB A:THR173 4.1 19.6 1.0
C A:THR173 4.5 20.4 1.0
CG A:GLU99 4.8 31.8 1.0
CG A:LYS175 4.9 31.4 1.0
CA A:THR173 4.9 19.0 1.0
O A:LYS174 5.0 21.8 1.0

Sodium binding site 5 out of 8 in 4jd0

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Sodium binding site 5 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:85.6
occ:1.00
 O A:HOH418 2.2 32.8 1.0
O A:HOH468 2.5 47.3 1.0
O A:HOH482 2.5 59.4 1.0
ND2 A:ASN163 3.3 21.2 1.0
O A:HOH600 3.7 52.2 1.0
O A:VAL147 3.8 18.7 1.0
O A:HOH430 4.4 30.4 1.0
N A:GLU149 4.5 16.7 1.0
O A:HOH598 4.5 65.5 1.0
CG A:ASN163 4.6 20.1 1.0
CE1 A:TYR164 4.6 23.1 1.0
C A:VAL147 4.7 16.0 1.0
CA A:ASN148 4.8 17.6 1.0
OH A:TYR164 4.9 28.9 1.0

Sodium binding site 6 out of 8 in 4jd0

Go back to Sodium Binding Sites List in 4jd0
Sodium binding site 6 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na311

b:61.1
occ:1.00
 O A:HOH498 2.4 54.2 1.0
O3 A:1KH301 2.6 35.5 0.6
O2 A:1KH301 2.7 48.7 0.6
OG A:SER190 3.0 33.4 0.4
C2 A:1KH301 3.2 27.7 0.6
C3 A:1KH301 3.4 28.7 0.6
CE1 A:TYR192 3.9 26.0 1.0
CB A:SER190 3.9 21.5 0.4
O A:HOH546 4.1 62.4 1.0
CE A:LYS157 4.2 59.2 1.0
CB A:SER190 4.2 25.8 0.6
NZ A:LYS157 4.4 71.5 1.0
O5 A:1KH301 4.4 38.4 0.6
C4 A:1KH301 4.5 27.0 0.6
OH A:TYR192 4.5 37.2 1.0
CZ A:TYR192 4.7 31.8 1.0
C1 A:1KH301 4.7 29.1 0.6
CD A:LYS157 4.7 50.2 1.0
O A:HOH576 4.7 49.2 1.0
O1 A:1KH301 4.7 23.8 0.6
O A:HOH428 4.8 33.8 1.0
CD1 A:TYR192 4.8 22.4 1.0

Sodium binding site 7 out of 8 in 4jd0

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Sodium binding site 7 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:63.0
occ:1.00
 O A:HOH419 2.1 35.0 1.0
O A:HOH546 2.2 62.4 1.0
O A:HOH631 2.7 54.0 1.0
OG A:SER190 2.8 25.3 0.6
OH A:TYR192 3.2 37.2 1.0
CZ A:TYR192 3.4 31.8 1.0
CE2 A:TYR192 3.7 28.9 1.0
CB A:SER190 3.7 25.8 0.6
CB A:HIS193 3.8 21.6 1.0
ND1 A:HIS193 3.9 32.2 1.0
N A:SER190 4.0 22.5 1.0
CB A:SER190 4.2 21.5 0.4
CE1 A:TYR192 4.2 26.0 1.0
CG A:HIS193 4.2 29.0 1.0
O A:HOH498 4.3 54.2 1.0
OG A:SER190 4.4 33.4 0.4
CA A:SER190 4.5 23.5 0.6
CD2 A:TYR192 4.6 18.7 1.0
CA A:SER190 4.6 23.2 0.4
O A:HOH553 4.6 43.0 1.0
O A:ASP188 4.8 42.3 1.0
CA A:HIS193 4.9 17.6 1.0
OD1 A:ASP188 4.9 78.6 1.0
CE1 A:HIS193 5.0 35.0 1.0
N A:HIS193 5.0 16.4 1.0
C A:ILE189 5.0 25.2 1.0

Sodium binding site 8 out of 8 in 4jd0

Go back to Sodium Binding Sites List in 4jd0
Sodium binding site 8 out of 8 in the Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Inositol-1-Phosphate Ctp Transferase From T. Maritima. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:42.7
occ:1.00
 O A:HOH475 2.0 59.9 1.0
O A:HOH523 2.5 57.1 1.0
OD2 A:ASP107 2.5 28.7 1.0
O A:HOH550 2.5 46.9 1.0
OD1 A:ASP219 3.3 35.6 1.0
CG A:ASP107 3.3 23.2 1.0
OD1 A:ASP107 3.3 21.8 1.0
O A:HOH522 3.8 25.6 1.0
O A:HOH576 4.0 49.2 1.0
CG A:ASP219 4.1 34.2 1.0
OD2 A:ASP219 4.1 41.6 1.0
O A:HOH455 4.2 36.4 1.0
NZ A:LYS24 4.4 22.1 1.0
O4 A:1KH301 4.4 28.2 0.6
OE2 A:GLU217 4.7 35.3 1.0
O A:HOH462 4.7 52.0 1.0
O1 A:GOL314 4.7 49.6 0.7
CB A:ASP107 4.7 18.6 1.0
C3 A:1KH301 4.8 28.7 0.6
C1 A:GOL314 4.8 32.3 0.7
C2 A:GOL314 5.0 58.3 0.7

Reference:

O.V.Kurnasov, H.J.Luk, M.F.Roberts, B.Stec. Structure of the Inositol-1-Phosphate Cytidylyltransferase From Thermotoga Maritima. Acta Crystallogr.,Sect.D V. 69 1808 2013.
ISSN: ISSN 0907-4449
PubMed: 23999304
DOI: 10.1107/S0907444913015278
Page generated: Mon Oct 7 16:14:53 2024

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