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Sodium in PDB 1kj8: Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar

Protein crystallography data

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar, PDB code: 1kj8 was solved by J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.100, 179.300, 75.800, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1kj8:

The structure of Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar (pdb code 1kj8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar, PDB code: 1kj8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1kj8

Go back to Sodium Binding Sites List in 1kj8
Sodium binding site 1 out of 2 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar


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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na395

b:29.6
occ:1.00
ND2 A:ASN100 2.5 50.9 1.0
O A:PRO103 2.6 15.3 1.0
O A:VAL101 2.8 13.7 1.0
O A:HOH797 2.8 24.3 1.0
O A:HOH429 3.2 14.0 1.0
C A:PRO103 3.5 14.0 1.0
CG A:ASN100 3.6 42.1 1.0
O A:HOH475 3.7 27.6 1.0
C A:VAL101 3.8 14.6 1.0
OD1 A:ASN100 4.0 35.7 1.0
CA A:CYS104 4.1 15.1 1.0
N A:CYS104 4.1 14.8 1.0
N A:VAL101 4.2 17.7 1.0
O A:HOH554 4.2 22.0 1.0
O A:HOH626 4.3 39.7 1.0
CB A:CYS104 4.3 13.4 1.0
O A:HOH864 4.4 70.7 1.0
CA A:PRO103 4.5 13.4 1.0
CA A:VAL102 4.6 14.9 1.0
N A:VAL102 4.6 14.7 1.0
CA A:VAL101 4.7 14.6 1.0
CB A:ASN100 4.7 19.7 1.0
C A:ASN100 4.7 26.0 1.0
CA A:ASN100 4.8 14.3 1.0
OE1 A:GLU95 4.8 22.5 1.0
CA A:GLY260 5.0 12.8 1.0

Sodium binding site 2 out of 2 in 1kj8

Go back to Sodium Binding Sites List in 1kj8
Sodium binding site 2 out of 2 in the Crystal Structure of Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar


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 Purt-Encoded Glycinamide Ribonucleotide Transformylase in Complex with Mg-Atp and Gar within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na395

b:23.4
occ:1.00
O B:HOH540 2.5 33.9 1.0
OD1 B:ASN100 2.5 55.4 1.0
O B:PRO103 2.7 18.0 1.0
O B:VAL101 2.9 18.9 1.0
O B:HOH493 3.0 23.4 1.0
O B:HOH402 3.2 16.3 1.0
O B:HOH665 3.5 30.0 1.0
C B:PRO103 3.6 19.8 1.0
CG B:ASN100 3.7 38.6 1.0
C B:VAL101 3.9 17.9 1.0
O B:HOH471 4.1 27.4 1.0
N B:VAL101 4.3 20.5 1.0
O B:HOH537 4.3 53.1 1.0
CA B:CYS104 4.3 14.0 1.0
N B:CYS104 4.3 16.2 1.0
ND2 B:ASN100 4.3 47.0 1.0
O B:HOH587 4.5 47.3 1.0
CB B:CYS104 4.5 14.8 1.0
CA B:PRO103 4.6 17.2 1.0
CA B:VAL102 4.7 18.7 1.0
N B:VAL102 4.7 16.6 1.0
O B:HOH705 4.7 60.1 1.0
CA B:VAL101 4.8 17.8 1.0
O B:HOH735 4.8 73.9 1.0
CB B:ASN100 4.8 26.3 1.0
C B:ASN100 4.9 25.9 1.0
OE1 B:GLU95 4.9 24.9 1.0
CA B:ASN100 4.9 24.9 1.0

Reference:

J.B.Thoden, S.M.Firestine, S.J.Benkovic, H.M.Holden. Purt-Encoded Glycinamide Ribonucleotide Transformylase. Accommodation of Adenosine Nucleotide Analogs Within the Active Site. J.Biol.Chem. V. 277 23898 2002.
ISSN: ISSN 0021-9258
PubMed: 11953435
DOI: 10.1074/JBC.M202251200
Page generated: Tue Dec 15 05:28:29 2020

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