Magnesium in PDB 5f3w: Structure of the Atprs-MRE11/RAD50-Dna Complex

Protein crystallography data

The structure of Structure of the Atprs-MRE11/RAD50-Dna Complex, PDB code: 5f3w was solved by Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.87 / 3.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.303, 130.111, 166.656, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Atprs-MRE11/RAD50-Dna Complex (pdb code 5f3w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Atprs-MRE11/RAD50-Dna Complex, PDB code: 5f3w:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5f3w

Go back to Magnesium Binding Sites List in 5f3w
Magnesium binding site 1 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:95.7
occ:1.00
OD2 A:ASP8 1.9 0.0 1.0
NE2 A:HIS188 2.2 90.1 1.0
NE2 A:HIS10 2.3 66.5 1.0
OD2 A:ASP49 2.7 0.2 1.0
MG A:MG402 2.9 80.3 1.0
CE1 A:HIS10 3.0 85.5 1.0
CE1 A:HIS188 3.1 0.5 1.0
O A:HOH501 3.1 70.7 1.0
CD2 A:HIS188 3.2 86.3 1.0
CG A:ASP8 3.2 1.0 1.0
CD2 A:HIS10 3.5 71.4 1.0
CG A:ASP49 3.7 1.0 1.0
ND1 A:HIS186 3.9 1.0 1.0
OD1 A:ASP8 4.0 93.1 1.0
CB A:ASP49 4.1 86.4 1.0
O A:HIS186 4.1 0.1 1.0
CB A:ASP8 4.1 85.8 1.0
CA A:HIS186 4.2 0.4 1.0
ND1 A:HIS188 4.2 0.9 1.0
ND1 A:HIS10 4.2 89.2 1.0
CG A:HIS188 4.3 0.6 1.0
C A:HIS186 4.3 0.6 1.0
CG A:HIS10 4.5 67.0 1.0
CE1 A:HIS186 4.6 0.5 1.0
OD1 A:ASP49 4.7 99.7 1.0
CD2 A:HIS85 4.7 98.8 1.0
CA A:ASP8 4.8 68.2 1.0
CE1 A:HIS158 4.9 86.5 1.0
CG A:HIS186 4.9 0.1 1.0
N A:HIS186 4.9 84.3 1.0
NE2 A:HIS85 5.0 1.0 1.0
ND2 A:ASN84 5.0 0.0 1.0

Magnesium binding site 2 out of 4 in 5f3w

Go back to Magnesium Binding Sites List in 5f3w
Magnesium binding site 2 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:80.3
occ:1.00
OD2 A:ASP49 1.9 0.2 1.0
ND1 A:HIS186 2.1 1.0 1.0
ND2 A:ASN84 2.3 0.0 1.0
CE1 A:HIS186 2.6 0.5 1.0
CG A:HIS186 2.8 0.1 1.0
MG A:MG401 2.9 95.7 1.0
NE2 A:HIS158 3.0 58.4 1.0
CG A:ASP49 3.1 1.0 1.0
O A:HOH501 3.4 70.7 1.0
NE2 A:HIS186 3.4 1.0 1.0
CA A:HIS186 3.4 0.4 1.0
CB A:HIS186 3.4 0.9 1.0
CG A:ASN84 3.4 0.5 1.0
CD2 A:HIS186 3.5 0.5 1.0
CE1 A:HIS158 3.6 86.5 1.0
OD1 A:ASP49 3.7 99.7 1.0
OD1 A:ASN84 3.8 0.8 1.0
O A:HIS186 3.9 0.1 1.0
OD2 A:ASP8 3.9 0.0 1.0
CD2 A:HIS85 4.1 98.8 1.0
C A:HIS186 4.1 0.6 1.0
CD2 A:HIS158 4.2 61.7 1.0
CB A:ASP49 4.3 86.4 1.0
N A:HIS186 4.5 84.3 1.0
NE2 A:HIS85 4.5 1.0 1.0
NE2 A:HIS10 4.5 66.5 1.0
NE2 A:HIS188 4.6 90.1 1.0
CB A:ASN84 4.7 83.1 1.0
CE1 A:HIS10 4.8 85.5 1.0
ND1 A:HIS158 4.8 84.2 1.0
CG A:ASP8 4.9 1.0 1.0
N A:ASN84 4.9 82.6 1.0

Magnesium binding site 3 out of 4 in 5f3w

Go back to Magnesium Binding Sites List in 5f3w
Magnesium binding site 3 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:93.2
occ:1.00
OD2 C:ASP49 1.8 0.1 1.0
CD2 C:HIS186 2.1 0.7 1.0
ND2 C:ASN84 2.1 95.0 1.0
NE2 C:HIS158 2.8 0.2 1.0
MG C:MG402 2.8 85.8 1.0
CG C:HIS186 2.9 0.7 1.0
CG C:ASP49 2.9 0.1 1.0
NE2 C:HIS186 3.1 0.0 1.0
CG C:ASN84 3.2 0.6 1.0
CA C:HIS186 3.3 0.5 1.0
CB C:HIS186 3.4 0.4 1.0
OD1 C:ASP49 3.4 92.2 1.0
CE1 C:HIS158 3.5 88.9 1.0
O C:HOH501 3.7 73.5 1.0
OD1 C:ASN84 3.7 0.2 1.0
O C:HIS186 3.9 0.3 1.0
CD2 C:HIS158 3.9 87.0 1.0
ND1 C:HIS186 4.0 0.8 1.0
OD2 C:ASP8 4.0 96.4 1.0
CE1 C:HIS186 4.0 0.3 1.0
C C:HIS186 4.1 1.0 1.0
CB C:ASP49 4.1 96.7 1.0
CD2 C:HIS85 4.3 80.8 1.0
N C:HIS186 4.3 0.6 1.0
CB C:ASN84 4.4 97.2 1.0
NE2 C:HIS85 4.7 98.0 1.0
ND1 C:HIS158 4.7 65.4 1.0
N C:ASN84 4.7 92.9 1.0
NE2 C:HIS10 4.7 88.0 1.0
CE1 C:HIS10 4.9 88.9 1.0
CG C:HIS158 4.9 66.8 1.0
CG C:ASP8 4.9 87.9 1.0

Magnesium binding site 4 out of 4 in 5f3w

Go back to Magnesium Binding Sites List in 5f3w
Magnesium binding site 4 out of 4 in the Structure of the Atprs-MRE11/RAD50-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Atprs-MRE11/RAD50-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:85.8
occ:1.00
NE2 C:HIS10 2.3 88.0 1.0
OD2 C:ASP8 2.3 96.4 1.0
NE2 C:HIS188 2.4 85.0 1.0
OD2 C:ASP49 2.5 0.1 1.0
CE1 C:HIS10 2.8 88.9 1.0
MG C:MG401 2.8 93.2 1.0
O C:HOH501 3.2 73.5 1.0
CE1 C:HIS188 3.3 99.1 1.0
CD2 C:HIS188 3.4 75.5 1.0
CG C:ASP49 3.5 0.1 1.0
CG C:ASP8 3.6 87.9 1.0
CD2 C:HIS10 3.6 82.0 1.0
CD2 C:HIS186 4.0 0.7 1.0
CB C:ASP49 4.1 96.7 1.0
O C:HIS186 4.1 0.3 1.0
ND1 C:HIS10 4.1 87.4 1.0
CA C:HIS186 4.3 0.5 1.0
OD1 C:ASP8 4.3 90.5 1.0
OD1 C:ASP49 4.4 92.2 1.0
C C:HIS186 4.4 1.0 1.0
CD2 C:HIS85 4.5 80.8 1.0
ND1 C:HIS188 4.5 99.8 1.0
CG C:HIS10 4.5 67.4 1.0
CG C:HIS188 4.6 84.0 1.0
CB C:ASP8 4.6 83.8 1.0
ND2 C:ASN84 4.6 95.0 1.0
NE2 C:HIS85 4.6 98.0 1.0
NE2 C:HIS186 5.0 0.0 1.0
CG C:HIS186 5.0 0.7 1.0

Reference:

Y.Liu, S.Sung, Y.Kim, F.Li, G.Gwon, A.Jo, A.K.Kim, T.Kim, O.K.Song, S.E.Lee, Y.Cho. Atp-Dependent Dna Binding, Unwinding, and Resection By the MRE11/RAD50 Complex Embo J. V. 35 743 2016.
ISSN: ESSN 1460-2075
PubMed: 26717941
DOI: 10.15252/EMBJ.201592462
Page generated: Mon Dec 14 20:17:19 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