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Sodium in PDB 2g79: Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution

Protein crystallography data

The structure of Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution, PDB code: 2g79 was solved by S.Vaezeslami, J.H.Geiger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.493, 46.325, 73.597, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 21.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution (pdb code 2g79). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution, PDB code: 2g79:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 2g79

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Sodium binding site 1 out of 4 in the Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms 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 of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na300

b:54.2
occ:1.00
O A:HOH547 2.0 36.2 1.0
O A:HOH546 2.1 47.1 1.0
NZ A:LYS92 3.5 29.7 1.0
OG1 A:THR122 3.8 17.8 1.0
OG1 A:THR110 3.8 16.6 1.0
CG2 A:THR122 4.1 17.1 1.0
CE A:LYS92 4.1 26.3 1.0
O A:HOH433 4.2 31.2 1.0
CG2 A:THR110 4.4 14.4 1.0
CB A:THR122 4.4 15.6 1.0
O A:HOH467 4.5 52.9 1.0
CB A:THR110 4.7 12.9 1.0
O A:HOH403 4.9 20.2 1.0
O A:HOH422 5.0 25.6 1.0

Sodium binding site 2 out of 4 in 2g79

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Sodium binding site 2 out of 4 in the Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms 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 of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:46.8
occ:1.00
O A:HOH431 2.1 30.5 1.0
O A:HOH509 2.4 53.3 1.0
OE1 A:GLU73 2.6 28.2 1.0
O A:HOH416 3.2 27.5 1.0
NE1 A:TRP109 3.4 16.4 1.0
CD A:GLU73 3.5 25.4 1.0
CD1 A:ILE63 3.7 26.4 1.0
OE2 A:GLU73 3.8 25.3 1.0
NA A:NA302 3.9 32.9 0.5
CD1 A:TRP109 3.9 16.9 1.0
CE2 A:TRP109 4.0 17.1 1.0
O A:HOH530 4.2 39.5 1.0
O A:HOH485 4.3 45.3 1.0
O A:HOH543 4.5 45.1 1.0
O A:HOH435 4.5 35.0 1.0
CZ2 A:TRP109 4.5 16.8 1.0
NH1 A:ARG111 4.5 23.3 1.0
CG2 A:ILE63 4.6 25.4 1.0
CG1 A:ILE63 4.8 21.8 1.0
CG A:GLU73 4.8 26.4 1.0
O A:GLN74 4.8 21.0 1.0
CG A:TRP109 4.8 16.5 1.0
NE2 A:GLN97 4.8 23.0 1.0
CD2 A:TRP109 4.9 16.0 1.0
NH2 A:ARG111 5.0 24.2 1.0

Sodium binding site 3 out of 4 in 2g79

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Sodium binding site 3 out of 4 in the Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms 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 of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:33.8
occ:0.50
NA A:NA302 0.0 33.8 0.5
NA A:NA302 1.4 32.9 0.5
O A:HOH543 2.0 45.1 1.0
O A:HOH544 2.3 41.9 1.0
O A:HOH554 2.9 39.6 1.0
C14 A:RET200 3.3 36.2 0.7
O A:HOH439 3.6 34.6 1.0
C14 A:RET200 3.7 35.7 0.3
C12 A:RET200 3.7 36.9 1.0
O1 A:RET200 3.7 34.0 0.7
C13 A:RET200 3.9 38.0 0.7
C15 A:RET200 4.0 34.7 0.7
C13 A:RET200 4.0 36.8 0.3
O A:HOH509 4.0 53.3 1.0
OG1 A:THR61 4.1 23.0 1.0
CG2 A:THR61 4.2 23.0 1.0
CG2 A:VAL76 4.3 30.4 1.0
O A:HOH485 4.4 45.3 1.0
CA A:VAL76 4.6 26.4 1.0
C11 A:RET200 4.6 36.9 1.0
C15 A:RET200 4.6 33.4 0.3
O A:HOH461 4.6 38.5 1.0
CB A:THR61 4.7 21.2 1.0
O A:HOH530 4.8 39.5 1.0
CB A:VAL76 4.8 27.1 1.0
C10 A:RET200 4.9 35.5 1.0
NE A:ARG59 4.9 31.2 1.0
O A:VAL76 4.9 28.7 1.0
O A:HOH416 5.0 27.5 1.0

Sodium binding site 4 out of 4 in 2g79

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Sodium binding site 4 out of 4 in the Crystal Structure of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms 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 of the R132K:Y134F Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-Trans-Retinal at 1.69 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:32.9
occ:0.50
NA A:NA302 0.0 32.9 0.5
NA A:NA302 1.4 33.8 0.5
O A:HOH543 2.2 45.1 1.0
O A:HOH509 3.2 53.3 1.0
O A:HOH439 3.4 34.6 1.0
O A:HOH544 3.5 41.9 1.0
O A:HOH530 3.6 39.5 1.0
O1 A:RET200 3.7 34.0 0.7
O A:HOH416 3.8 27.5 1.0
NA A:NA301 3.9 46.8 1.0
O A:HOH554 3.9 39.6 1.0
C14 A:RET200 4.0 36.2 0.7
O A:HOH485 4.1 45.3 1.0
O A:HOH431 4.1 30.5 1.0
C14 A:RET200 4.3 35.7 0.3
C15 A:RET200 4.3 34.7 0.7
CA A:VAL76 4.5 26.4 1.0
OG1 A:THR61 4.5 23.0 1.0
CG2 A:VAL76 4.6 30.4 1.0
CB A:VAL76 4.7 27.1 1.0
C12 A:RET200 4.8 36.9 1.0
SD A:MET123 4.8 23.5 1.0
CG2 A:THR61 4.9 23.0 1.0
C13 A:RET200 4.9 38.0 0.7
C15 A:RET200 5.0 33.4 0.3
C13 A:RET200 5.0 36.8 0.3

Reference:

C.Vasileiou, S.Vaezeslami, R.M.Crist, M.Rabago-Smith, J.H.Geiger, B.Borhan. Protein Design: Reengineering Cellular Retinoic Acid Binding Protein II Into A Rhodopsin Protein Mimic. J.Am.Chem.Soc. V. 129 6140 2007.
ISSN: ISSN 0002-7863
PubMed: 17447762
DOI: 10.1021/JA067546R
Page generated: Tue Dec 15 05:49:24 2020

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