Sodium in PDB 1kji: Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp, PDB code: 1kji 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 (°)	62.200, 179.200, 76.200, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp (pdb code 1kji). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp, PDB code: 1kji:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na395 b:47.1 occ:1.00 O B:HOH651 2.4 23.4 1.0 O A:HOH521 2.4 25.3 1.0 O B:HOH456 2.5 31.4 1.0 O A:ALA53 2.7 14.8 1.0 O B:HOH745 2.9 63.9 1.0 O B:ALA53 3.0 17.4 1.0 O A:HOH453 3.0 23.3 1.0 C A:ALA53 3.9 19.9 1.0 O B:HOH428 4.1 22.0 1.0 O B:HIS51 4.1 15.3 1.0 O A:HOH431 4.2 18.2 1.0 C B:ALA53 4.2 17.4 1.0 O B:HIS54 4.3 19.9 1.0 O A:HIS54 4.3 17.5 1.0 O A:HIS51 4.4 16.1 1.0 N A:ALA53 4.4 14.8 1.0 CA A:HIS54 4.5 11.5 1.0 C A:HIS54 4.6 15.1 1.0 O B:MET50 4.6 15.8 1.0 C B:HIS54 4.6 21.8 1.0 N A:HIS54 4.7 14.8 1.0 CA B:HIS54 4.8 15.9 1.0 O A:MET50 4.8 13.2 1.0 CA A:ALA53 4.8 12.8 1.0 C B:HIS51 4.8 14.5 1.0 N B:ALA53 4.9 14.2 1.0 C A:VAL52 4.9 18.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na396 b:30.4 occ:1.00 O A:HOH637 2.6 25.2 1.0 O A:HOH567 2.6 37.5 1.0 OE1 A:GLU95 2.7 21.5 1.0 N A:VAL101 3.1 17.6 1.0 O A:VAL101 3.3 17.9 1.0 ND2 A:ASN100 3.3 64.1 1.0 CD A:GLU95 3.4 38.5 1.0 CA A:ASN100 3.6 20.0 1.0 CG A:GLU95 3.6 22.9 1.0 O A:HOH744 3.8 48.2 1.0 C A:ASN100 3.8 24.1 1.0 O A:LEU99 3.8 39.6 1.0 CA A:VAL101 3.9 15.0 1.0 C A:VAL101 4.0 20.2 1.0 CG A:ASN100 4.0 53.4 1.0 CB A:VAL101 4.2 18.4 1.0 CA A:CYS104 4.2 13.4 1.0 O A:HOH627 4.3 33.4 1.0 CB A:ASN100 4.4 21.5 1.0 CB A:CYS104 4.4 16.2 1.0 O A:HOH743 4.4 65.4 1.0 O A:PRO103 4.4 18.9 1.0 OE2 A:GLU95 4.5 27.8 1.0 N A:ASN100 4.6 24.3 1.0 CB A:GLU95 4.6 21.2 1.0 C A:LEU99 4.6 31.7 1.0 O A:HOH745 4.7 56.3 1.0 CG2 A:VAL101 4.7 20.4 1.0 OD1 A:ASN100 4.8 32.7 1.0 N A:ALA105 4.9 24.4 1.0 O A:ASN100 5.0 22.8 1.0 O A:HOH746 5.0 46.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp


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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na395 b:51.0 occ:1.00 O B:HOH690 2.5 36.9 1.0 ND2 B:ASN100 2.5 43.7 1.0 O B:VAL101 2.5 17.9 1.0 O B:PRO103 2.5 25.0 1.0 O B:HOH461 2.9 24.8 1.0 O B:HOH406 3.2 18.6 1.0 C B:PRO103 3.2 19.9 1.0 C B:VAL101 3.5 16.6 1.0 CG B:ASN100 3.8 38.4 1.0 O B:HOH623 3.8 29.6 1.0 N B:CYS104 3.8 20.0 1.0 CA B:CYS104 3.8 20.0 1.0 N B:VAL101 4.0 23.3 1.0 CB B:CYS104 4.2 20.9 1.0 CA B:PRO103 4.3 14.8 1.0 O B:HOH722 4.3 79.9 1.0 O B:HOH483 4.3 25.9 1.0 CA B:VAL102 4.3 19.8 1.0 N B:VAL102 4.3 17.3 1.0 OD1 B:ASN100 4.3 54.5 1.0 CA B:VAL101 4.4 22.4 1.0 OE1 B:GLU95 4.5 34.6 1.0 C B:ASN100 4.6 27.1 1.0 O B:HOH599 4.7 36.8 1.0 CA B:ASN100 4.7 18.0 1.0 CB B:ASN100 4.8 19.8 1.0 O B:HOH691 5.0 43.0 1.0

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