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Sodium in PDB 1kjq: Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp

Protein crystallography data

The structure of Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp, PDB code: 1kjq 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 / 1.05
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 62.350, 179.340, 75.620, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1kjq:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp (pdb code 1kjq). 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 Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp, PDB code: 1kjq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1kjq

Go back to Sodium Binding Sites List in 1kjq
Sodium binding site 1 out of 2 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na394

b:14.6
occ:1.00
ND2 A:ASN100 2.4 13.6 1.0
O A:VAL101 2.4 10.1 1.0
O A:PRO103 2.4 11.0 1.0
O A:HOH821 2.4 32.4 1.0
O A:HOH445 2.6 16.5 1.0
O A:HOH432 3.1 11.0 1.0
C A:PRO103 3.3 10.3 1.0
C A:VAL101 3.4 8.3 1.0
CG A:ASN100 3.5 20.3 1.0
N A:VAL101 3.8 9.7 1.0
O A:HOH565 3.8 19.9 1.0
CA A:CYS104 3.9 9.3 1.0
N A:CYS104 3.9 9.5 1.0
OD1 A:ASN100 4.0 21.7 1.0
N A:VAL102 4.2 8.9 1.0
CA A:VAL101 4.2 8.4 1.0
CB A:CYS104 4.2 9.5 1.0
C A:ASN100 4.3 13.4 1.0
CA A:VAL102 4.3 8.4 1.0
CA A:PRO103 4.3 9.3 1.0
O A:HOH491 4.3 16.4 1.0
O A:HOH870 4.4 33.6 1.0
O A:HOH822 4.4 36.2 1.0
CA A:ASN100 4.5 11.8 1.0
CB A:ASN100 4.6 13.8 1.0
OE1 A:GLU95 4.6 15.5 1.0
O A:HOH767 4.9 44.3 1.0

Sodium binding site 2 out of 2 in 1kjq

Go back to Sodium Binding Sites List in 1kjq
Sodium binding site 2 out of 2 in the Crystal Structure of Glycinamide Ribonucleotide Transformylase in Complex with Mg-Adp


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-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na394

b:20.3
occ:1.00
O A:HOH811 2.4 34.9 1.0
O A:HOH920 2.5 61.3 1.0
O B:HIS51 2.6 9.3 1.0
O B:HOH555 2.8 24.8 1.0
O A:HOH586 2.8 48.5 1.0
O A:HOH505 2.9 18.1 1.0
O A:ALA53 3.2 11.2 1.0
O B:MET50 3.2 10.4 1.0
C B:HIS51 3.3 8.1 1.0
CA A:HIS54 3.7 8.9 1.0
CA B:HIS51 3.8 9.5 1.0
O B:HOH438 3.8 15.2 1.0
O B:ALA53 3.9 11.9 1.0
C A:ALA53 3.9 9.1 1.0
O B:HOH744 4.0 36.2 1.0
O A:HIS54 4.1 10.8 1.0
N A:HIS54 4.2 8.0 1.0
O A:HOH500 4.2 17.4 1.0
O A:HOH543 4.2 25.2 1.0
C B:MET50 4.3 8.9 1.0
N B:VAL52 4.3 8.1 1.0
C A:HIS54 4.3 9.2 1.0
O A:HOH495 4.3 16.5 1.0
CD2 A:HIS54 4.4 8.8 1.0
N B:HIS51 4.6 7.8 1.0
N B:ALA53 4.6 10.1 1.0
O A:HOH859 4.7 35.4 1.0
CG A:HIS54 4.7 8.1 1.0
CB A:HIS54 4.7 8.0 1.0
CA B:VAL52 4.8 8.1 1.0
O B:HOH592 4.8 33.5 1.0
NE2 A:GLN32 4.9 8.4 1.0
O B:HOH458 5.0 17.5 1.0
CB B:HIS51 5.0 8.2 1.0
C B:ALA53 5.0 10.2 1.0
C B:VAL52 5.0 9.6 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 05:28:34 2020

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