Atomistry » Magnesium » PDB 3s99-3si8 » 3saf
Atomistry »
  Magnesium »
    PDB 3s99-3si8 »
      3saf »

Magnesium in PDB 3saf: Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site

Protein crystallography data

The structure of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site, PDB code: 3saf was solved by K.Januszyk, Q.Liu, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.74 / 2.50
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 138.900, 138.900, 58.400, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24

Other elements in 3saf:

The structure of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site also contains other interesting chemical elements:

Yttrium (Y) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site (pdb code 3saf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site, PDB code: 3saf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3saf

Go back to Magnesium Binding Sites List in 3saf
Magnesium binding site 1 out of 2 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:59.5
occ:1.00
O A:HOH38 2.5 54.6 1.0
O A:HOH31 2.6 54.9 1.0
O A:HOH74 2.6 63.8 1.0
OD1 A:ASN313 2.6 40.9 1.0
CG A:ASN313 3.7 41.4 1.0
OD2 A:ASP371 3.7 59.1 1.0
O A:HIS366 3.9 51.1 1.0
ND2 A:ASN313 4.2 41.4 1.0
O A:GLY367 4.2 51.0 1.0
OD1 A:ASP371 4.5 62.4 1.0
O A:HOH5 4.5 35.7 1.0
CG A:ASP371 4.6 58.8 1.0
O A:HOH36 4.6 45.5 1.0
O A:LEU314 4.9 43.0 1.0
CB A:ASN313 5.0 39.8 1.0

Magnesium binding site 2 out of 2 in 3saf

Go back to Magnesium Binding Sites List in 3saf
Magnesium binding site 2 out of 2 in the Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Human RRP6 Catalytic Domain with D313N Mutation in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:74.0
occ:1.00
O B:HOH647 2.0 87.1 1.0
O B:HOH648 2.0 46.5 1.0
O B:HOH165 2.4 59.6 1.0
OD1 B:ASN313 2.8 35.9 1.0
O B:HIS366 3.5 40.1 1.0
OD1 B:ASP371 3.7 57.2 1.0
O B:HOH168 3.7 54.9 1.0
O B:GLY367 3.7 42.2 1.0
CG B:ASN313 4.0 35.1 1.0
OD2 B:ASP371 4.1 54.2 1.0
O B:HOH46 4.2 33.4 1.0
CG B:ASP371 4.3 52.1 1.0
O B:HOH9 4.6 42.1 1.0
C B:HIS366 4.6 40.9 1.0
ND2 B:ASN313 4.6 36.5 1.0
C B:GLY367 4.7 42.0 1.0
O B:LEU314 4.8 39.9 1.0

Reference:

K.Januszyk, Q.Liu, C.D.Lima. Activities of Human RRP6 and Structure of the Human RRP6 Catalytic Domain. Rna V. 17 1566 2011.
ISSN: ISSN 1355-8382
PubMed: 21705430
DOI: 10.1261/RNA.2763111
Page generated: Thu Aug 15 10:49:35 2024

Last articles

Cl in 3MC5
Cl in 3MC3
Cl in 3MC1
Cl in 3MBH
Cl in 3MBY
Cl in 3MB4
Cl in 3MBJ
Cl in 3M9F
Cl in 3MBD
Cl in 3MAA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy