Atomistry » Magnesium » PDB 3nkv-3o0n » 3ntu
Atomistry »
  Magnesium »
    PDB 3nkv-3o0n »
      3ntu »

Magnesium in PDB 3ntu: Rada Recombinase D302K Mutant in Complex with Amp-Pnp

Protein crystallography data

The structure of Rada Recombinase D302K Mutant in Complex with Amp-Pnp, PDB code: 3ntu was solved by Y.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 84.970, 84.970, 104.320, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 21.4

Other elements in 3ntu:

The structure of Rada Recombinase D302K Mutant in Complex with Amp-Pnp also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp (pdb code 3ntu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp, PDB code: 3ntu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3ntu

Go back to Magnesium Binding Sites List in 3ntu
Magnesium binding site 1 out of 2 in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rada Recombinase D302K Mutant in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:25.9
occ:1.00
O2G A:ANP401 2.0 29.9 1.0
O1B A:ANP401 2.0 21.2 1.0
O A:HOH603 2.1 29.5 1.0
O A:HOH601 2.1 24.4 1.0
O A:HOH602 2.1 24.8 1.0
OG1 A:THR112 2.2 24.5 1.0
PG A:ANP401 3.1 29.2 1.0
CB A:THR112 3.2 21.9 1.0
PB A:ANP401 3.2 25.7 1.0
N3B A:ANP401 3.4 25.6 1.0
O A:HOH609 3.8 27.3 1.0
N A:THR112 3.9 22.5 1.0
OD1 A:ASP211 4.0 28.1 1.0
O1G A:ANP401 4.0 26.0 1.0
O2A A:ANP401 4.1 25.4 1.0
CA A:THR112 4.1 23.4 1.0
O2B A:ANP401 4.1 22.8 1.0
O3G A:ANP401 4.2 31.0 1.0
CG2 A:THR112 4.3 24.5 1.0
O3A A:ANP401 4.3 25.6 1.0
OD2 A:ASP211 4.4 26.0 1.0
OE1 A:GLU151 4.4 36.6 1.0
OG1 A:THR153 4.4 31.0 1.0
PA A:ANP401 4.6 27.2 1.0
CE A:LYS111 4.6 28.4 1.0
CG A:ASP211 4.7 26.5 1.0
O1A A:ANP401 4.7 27.1 1.0
CB A:LYS111 4.7 21.4 1.0
C A:LYS111 4.9 25.4 1.0
O A:HOH623 5.0 33.4 1.0

Magnesium binding site 2 out of 2 in 3ntu

Go back to Magnesium Binding Sites List in 3ntu
Magnesium binding site 2 out of 2 in the Rada Recombinase D302K Mutant in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rada Recombinase D302K Mutant in Complex with Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:27.3
occ:1.00
O A:HOH607 1.9 27.3 1.0
O A:GLN98 2.0 24.8 1.0
O A:HOH604 2.1 25.2 1.0
O A:HOH606 2.1 26.8 1.0
OD1 A:ASP246 2.1 28.2 1.0
O A:HOH605 2.2 28.8 1.0
CG A:ASP246 3.1 37.4 1.0
C A:GLN98 3.1 25.1 1.0
OD2 A:ASP246 3.4 34.5 1.0
CA A:SER99 3.9 24.0 1.0
N A:SER99 4.0 23.8 1.0
CA A:GLN98 4.1 24.2 1.0
O A:HOH689 4.1 40.1 1.0
OG A:SER99 4.2 31.1 1.0
CB A:GLN98 4.2 21.4 1.0
O A:HOH630 4.3 35.9 1.0
O A:ASN242 4.3 25.2 1.0
OD1 A:ASN242 4.3 28.2 1.0
O A:HOH651 4.4 49.5 1.0
CB A:ASP246 4.5 31.3 1.0
CB A:SER99 4.7 27.0 1.0
N A:ASP246 4.7 26.5 1.0
CA A:ASP246 4.8 30.1 1.0
CB A:ALA245 4.9 24.3 1.0

Reference:

R.Amunugama, Y.He, S.Willcox, R.A.Forties, K.S.Shim, R.Bundschuh, Y.Luo, J.Griffith, R.Fishel. RAD51 Protein Atp Cap Regulates Nucleoprotein Filament Stability. J.Biol.Chem. V. 287 8724 2012.
ISSN: ISSN 0021-9258
PubMed: 22275364
DOI: 10.1074/JBC.M111.239426
Page generated: Mon Dec 14 08:30:07 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