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Magnesium in PDB 3fyh: Recombinase in Complex with Adp and Metatungstate

Protein crystallography data

The structure of Recombinase in Complex with Adp and Metatungstate, PDB code: 3fyh was solved by Y.Li, Y.He, Y.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 83.160, 83.160, 106.850, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 22.7

Other elements in 3fyh:

The structure of Recombinase in Complex with Adp and Metatungstate also contains other interesting chemical elements:

Tungsten (W) 24 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Recombinase in Complex with Adp and Metatungstate (pdb code 3fyh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Recombinase in Complex with Adp and Metatungstate, PDB code: 3fyh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3fyh

Go back to Magnesium Binding Sites List in 3fyh
Magnesium binding site 1 out of 2 in the Recombinase in Complex with Adp and Metatungstate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Recombinase in Complex with Adp and Metatungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:24.9
occ:1.00
O A:HOH603 2.1 22.6 1.0
O1B A:ADP401 2.1 20.2 1.0
OG1 A:THR112 2.1 23.2 1.0
O A:HOH602 2.2 25.2 1.0
O A:HOH601 2.2 18.9 1.0
O A:HOH608 2.2 23.3 1.0
CB A:THR112 3.2 21.7 1.0
PB A:ADP401 3.3 23.6 1.0
O3B A:ADP401 3.5 22.2 1.0
O A:HOH651 4.0 38.7 1.0
N A:THR112 4.0 19.9 1.0
O2A A:ADP401 4.1 24.1 1.0
CA A:THR112 4.2 21.2 1.0
CG2 A:THR112 4.2 21.8 1.0
OG1 A:THR153 4.3 24.8 1.0
OD2 A:ASP211 4.3 27.4 1.0
OD1 A:ASP211 4.3 29.0 1.0
O2B A:ADP401 4.3 22.6 1.0
O3A A:ADP401 4.3 23.8 1.0
O A:HOH618 4.4 34.5 1.0
PA A:ADP401 4.6 25.2 1.0
O1A A:ADP401 4.6 24.9 1.0
CG A:ASP211 4.7 26.4 1.0
CB A:LYS111 5.0 20.6 1.0

Magnesium binding site 2 out of 2 in 3fyh

Go back to Magnesium Binding Sites List in 3fyh
Magnesium binding site 2 out of 2 in the Recombinase in Complex with Adp and Metatungstate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Recombinase in Complex with Adp and Metatungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:30.0
occ:1.00
O A:HOH606 2.0 30.4 1.0
O A:HOH604 2.1 29.8 1.0
O A:GLN98 2.1 24.3 1.0
OD1 A:ASP246 2.1 25.9 1.0
O A:HOH607 2.1 28.9 1.0
O A:HOH605 2.1 30.6 1.0
CG A:ASP246 3.1 26.7 1.0
C A:GLN98 3.2 24.9 1.0
OD2 A:ASP246 3.4 30.3 1.0
N A:SER99 4.0 24.4 1.0
CA A:SER99 4.0 26.8 1.0
CA A:GLN98 4.2 23.1 1.0
OG A:SER99 4.2 33.7 1.0
ND2 A:ASN242 4.3 25.0 1.0
O A:ASN242 4.3 25.8 1.0
CB A:GLN98 4.4 25.5 1.0
CB A:ASP246 4.5 25.9 1.0
CB A:SER99 4.8 28.8 1.0
CA A:ASP246 4.8 29.1 1.0
N A:ASP246 4.8 27.6 1.0

Reference:

Y.Li, Y.He, Y.Luo. Crystal Structure of An Archaeal RAD51 Homologue in Complex with A Metatungstate Inhibitor. Biochemistry V. 48 6805 2009.
ISSN: ISSN 0006-2960
PubMed: 19555119
DOI: 10.1021/BI900832T
Page generated: Mon Dec 14 08:09:32 2020

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