Atomistry » Sodium » PDB 1k7e-1l0i » 1kjj
Atomistry »
  Sodium »
    PDB 1k7e-1l0i »
      1kjj »

Sodium in PDB 1kjj: Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S

Protein crystallography data

The structure of Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S, PDB code: 1kjj 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 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.900, 179.300, 76.100, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1kjj:

The structure of Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S (pdb code 1kjj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S, PDB code: 1kjj:

Sodium binding site 1 out of 1 in 1kjj

Go back to Sodium Binding Sites List in 1kjj
Sodium binding site 1 out of 1 in the Crystal Structure of Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S


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 Glycniamide Ribonucleotide Transformylase in Complex with Mg-Atp-Gamma-S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na395

b:35.8
occ:1.00
O A:PRO103 2.5 21.5 1.0
O A:HOH432 2.5 24.7 1.0
O A:VAL101 2.7 20.8 1.0
ND2 A:ASN100 2.8 65.7 1.0
O A:HOH443 3.2 25.3 1.0
C A:PRO103 3.4 19.8 1.0
O A:HOH415 3.5 23.1 1.0
CG A:ASN100 3.7 74.5 1.0
C A:VAL101 3.8 22.9 1.0
CA A:CYS104 4.0 16.6 1.0
OD1 A:ASN100 4.0 54.0 1.0
N A:CYS104 4.0 17.2 1.0
N A:VAL101 4.1 22.5 1.0
CB A:CYS104 4.2 20.2 1.0
O A:HOH695 4.2 49.1 1.0
O A:HOH558 4.3 28.3 1.0
O A:HOH717 4.3 46.4 1.0
CA A:PRO103 4.5 17.4 1.0
CA A:VAL102 4.6 17.2 1.0
OE1 A:GLU95 4.6 26.1 1.0
CA A:VAL101 4.6 20.1 1.0
N A:VAL102 4.6 20.1 1.0
C A:ASN100 4.6 29.0 1.0
CA A:ASN100 4.7 27.7 1.0
CB A:ASN100 4.7 31.5 1.0
CA A:GLY260 4.8 20.1 1.0
O A:HOH718 4.9 65.2 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 05:28:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy