Atomistry » Magnesium » PDB 2vu9-2wb1 » 2w35
Atomistry »
  Magnesium »
    PDB 2vu9-2wb1 »
      2w35 »

Magnesium in PDB 2w35: Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair

Enzymatic activity of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair

All present enzymatic activity of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair:
3.1.21.7;

Protein crystallography data

The structure of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair, PDB code: 2w35 was solved by B.Dalhus, A.S.Arvai, I.Rosnes, O.E.Olsen, P.H.Backe, I.Alseth, H.Gao, W.Cao, J.A.Tainer, M.Bjoras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 55.064, 134.292, 194.450, 90.00, 90.00, 90.00
R / Rfree (%) 25.9 / 28.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair (pdb code 2w35). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair, PDB code: 2w35:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2w35

Go back to Magnesium Binding Sites List in 2w35
Magnesium binding site 1 out of 2 in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1224

b:33.5
occ:1.00
OD1 A:ASP43 1.9 40.3 1.0
O3' C:DG9 2.0 39.5 1.0
O C:HOH2009 2.0 39.4 1.0
O C:HOH2007 2.2 33.2 1.0
OD1 A:ASP110 2.2 42.2 1.0
O A:HOH2024 2.2 33.4 1.0
CG A:ASP43 3.0 41.5 1.0
CG A:ASP110 3.3 41.7 1.0
C3' C:DG9 3.3 34.1 1.0
OD2 A:ASP43 3.4 41.5 1.0
CB A:ASP110 3.7 38.7 1.0
O A:LEU44 3.9 37.5 1.0
C5' D:DA10 4.0 56.5 1.0
C4' C:DG9 4.1 36.2 1.0
N A:LEU44 4.1 36.7 1.0
OP2 D:DA10 4.2 55.5 1.0
CB A:ASP43 4.3 41.3 1.0
OD2 A:ASP110 4.3 47.2 1.0
C2' C:DG9 4.4 35.0 1.0
O A:ASP110 4.5 39.8 1.0
OE2 A:GLU89 4.5 45.5 1.0
CA A:ASP43 4.5 38.7 1.0
OE1 A:GLU89 4.6 46.3 1.0
O A:HOH2119 4.7 43.7 1.0
C A:LEU44 4.9 36.2 1.0
C A:ASP43 4.9 37.8 1.0
C5' C:DG9 4.9 30.9 1.0
NZ A:LYS139 5.0 39.4 1.0

Magnesium binding site 2 out of 2 in 2w35

Go back to Magnesium Binding Sites List in 2w35
Magnesium binding site 2 out of 2 in the Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1224

b:38.6
occ:1.00
O B:HOH2041 1.9 34.6 1.0
OD1 B:ASP43 1.9 46.1 1.0
O3' F:DG9 1.9 40.2 1.0
O F:HOH2004 2.2 35.4 1.0
OD2 B:ASP110 2.2 42.5 1.0
O F:HOH2005 2.4 35.4 1.0
CG B:ASP43 3.0 45.0 1.0
C3' F:DG9 3.3 34.9 1.0
CG B:ASP110 3.3 42.0 1.0
OD2 B:ASP43 3.4 46.7 1.0
CB B:ASP110 3.8 37.9 1.0
O B:LEU44 3.8 41.9 1.0
C5' G:DA10 4.0 51.1 1.0
N B:LEU44 4.0 41.4 1.0
C4' F:DG9 4.2 35.6 1.0
CB B:ASP43 4.2 44.4 1.0
C2' F:DG9 4.3 37.8 1.0
OP2 G:DA10 4.4 54.1 1.0
OD1 B:ASP110 4.4 45.5 1.0
OE2 B:GLU89 4.4 45.2 1.0
CA B:ASP43 4.5 41.3 1.0
OE1 B:GLU89 4.5 47.2 1.0
O B:ASP110 4.5 35.0 1.0
C B:LEU44 4.8 41.0 1.0
C B:ASP43 4.8 41.0 1.0
CD B:GLU89 4.9 44.6 1.0
CA B:LEU44 4.9 40.6 1.0
C4' G:DA10 5.0 48.4 1.0

Reference:

B.Dalhus, A.S.Arvai, I.Rosnes, O.E.Olsen, P.H.Backe, I.Alseth, H.Gao, W.Cao, J.A.Tainer, M.Bjoras. Structures of Endonuclease V with Dna Reveal Initiation of Deaminated Adenine Repair. Nat.Struct.Mol.Biol. V. 16 138 2009.
ISSN: ISSN 1545-9993
PubMed: 19136958
DOI: 10.1038/NSMB.1538
Page generated: Mon Dec 14 07:43:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy