Atomistry » Magnesium » PDB 4q8b-4qgr » 4qbl
Atomistry »
  Magnesium »
    PDB 4q8b-4qgr »
      4qbl »

Magnesium in PDB 4qbl: VRR_NUC Domain Protein

Protein crystallography data

The structure of VRR_NUC Domain Protein, PDB code: 4qbl was solved by S.J.Smerdon, S.Pennell, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 213.143, 51.180, 127.267, 90.00, 125.49, 90.00
R / Rfree (%) 17.5 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the VRR_NUC Domain Protein (pdb code 4qbl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the VRR_NUC Domain Protein, PDB code: 4qbl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4qbl

Go back to Magnesium Binding Sites List in 4qbl
Magnesium binding site 1 out of 6 in the VRR_NUC Domain Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of VRR_NUC Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:34.8
occ:1.00
 OE2 A:GLU89 2.2 30.9 1.0
OE2 A:GLU10 2.3 49.9 1.0
O A:ILE90 2.4 32.8 1.0
O A:HOH313 2.4 42.5 1.0
O A:HOH326 2.4 61.0 1.0
OD2 A:ASP73 2.4 36.4 1.0
CD A:GLU10 3.0 52.0 1.0
CD A:GLU89 3.2 34.0 1.0
CG A:ASP73 3.2 38.6 1.0
OE1 A:GLU10 3.3 53.4 1.0
OD1 A:ASP73 3.3 42.8 1.0
C A:ILE90 3.5 30.4 1.0
N A:ILE90 3.8 28.3 1.0
OE1 A:GLU89 3.8 39.9 1.0
CA A:ILE90 4.1 26.9 1.0
NZ A:LYS91 4.1 34.2 1.0
CG A:GLU89 4.3 30.4 1.0
CG A:GLU10 4.3 43.2 1.0
CB A:ILE90 4.4 34.5 1.0
O A:HOH320 4.4 47.5 1.0
CD A:LYS91 4.5 38.7 1.0
CE A:LYS91 4.5 38.8 1.0
C A:GLU89 4.5 31.8 1.0
N A:LYS91 4.6 29.6 1.0
CB A:ASP73 4.7 26.6 1.0
NE2 A:GLN102 4.8 39.1 1.0
CA A:LYS91 5.0 33.8 1.0
CA A:GLU89 5.0 27.7 1.0

Magnesium binding site 2 out of 6 in 4qbl

Go back to Magnesium Binding Sites List in 4qbl
Magnesium binding site 2 out of 6 in the VRR_NUC Domain Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of VRR_NUC Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:54.8
occ:1.00
 O B:HOH321 2.3 65.6 1.0
O B:ILE90 2.4 53.0 1.0
OE2 B:GLU10 2.4 73.8 1.0
OE2 B:GLU89 2.5 61.5 1.0
O B:HOH325 2.5 57.3 1.0
OD2 B:ASP73 2.5 57.9 1.0
CD B:GLU10 3.1 68.4 1.0
CG B:ASP73 3.2 56.4 1.0
OD1 B:ASP73 3.3 53.4 1.0
OE1 B:GLU10 3.4 70.9 1.0
CD B:GLU89 3.4 63.2 1.0
C B:ILE90 3.5 58.3 1.0
N B:ILE90 3.8 48.6 1.0
OE1 B:GLU89 3.9 67.8 1.0
CA B:ILE90 4.1 54.7 1.0
CD B:LYS91 4.3 63.0 1.0
CG B:GLU10 4.3 58.5 1.0
NZ B:LYS91 4.3 62.3 1.0
CG B:GLU89 4.4 58.9 1.0
CB B:ILE90 4.4 52.3 1.0
CE B:LYS91 4.5 64.8 1.0
C B:GLU89 4.6 53.2 1.0
N B:LYS91 4.6 56.6 1.0
CB B:ASP73 4.7 51.0 1.0
CA B:LYS91 4.9 57.7 1.0
CA B:GLU89 5.0 45.7 1.0

Magnesium binding site 3 out of 6 in 4qbl

Go back to Magnesium Binding Sites List in 4qbl
Magnesium binding site 3 out of 6 in the VRR_NUC Domain Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of VRR_NUC Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:40.5
occ:1.00
 OE2 D:GLU89 2.2 36.6 1.0
OE2 D:GLU10 2.3 54.0 1.0
OD2 D:ASP73 2.3 41.5 1.0
O D:HOH340 2.4 62.0 1.0
O D:ILE90 2.4 43.4 1.0
O D:HOH308 2.4 41.3 1.0
CD D:GLU10 3.1 56.0 1.0
CD D:GLU89 3.2 37.5 1.0
CG D:ASP73 3.2 41.5 1.0
OD1 D:ASP73 3.4 47.0 1.0
OE1 D:GLU10 3.5 52.9 1.0
C D:ILE90 3.5 38.5 1.0
OE1 D:GLU89 3.7 50.3 1.0
N D:ILE90 3.8 31.8 1.0
O D:HOH346 3.9 63.5 1.0
CA D:ILE90 4.1 33.0 1.0
NZ D:LYS91 4.2 41.6 1.0
O D:HOH343 4.2 48.6 1.0
CG D:GLU89 4.3 34.4 1.0
CG D:GLU10 4.3 54.9 1.0
CE D:LYS91 4.4 44.2 1.0
CB D:ILE90 4.5 34.0 1.0
CD D:LYS91 4.6 43.1 1.0
C D:GLU89 4.6 34.7 1.0
CB D:ASP73 4.6 31.3 1.0
N D:LYS91 4.7 36.2 1.0
NE2 D:GLN102 4.8 36.7 1.0
CA D:GLU89 5.0 31.0 1.0

Magnesium binding site 4 out of 6 in 4qbl

Go back to Magnesium Binding Sites List in 4qbl
Magnesium binding site 4 out of 6 in the VRR_NUC Domain Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of VRR_NUC Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg201

b:25.0
occ:1.00
 OE2 E:GLU89 2.2 28.6 1.0
OD2 E:ASP73 2.3 21.7 1.0
OE2 E:GLU10 2.3 32.8 1.0
O E:ILE90 2.4 24.2 1.0
O E:HOH308 2.5 29.9 1.0
O E:HOH325 2.5 36.1 1.0
CD E:GLU10 3.1 37.9 1.0
CG E:ASP73 3.1 26.4 1.0
CD E:GLU89 3.2 28.3 1.0
OD1 E:ASP73 3.3 32.2 1.0
OE1 E:GLU10 3.4 37.1 1.0
C E:ILE90 3.5 25.0 1.0
N E:ILE90 3.7 20.1 1.0
OE1 E:GLU89 3.8 30.5 1.0
CA E:ILE90 4.0 19.9 1.0
NZ E:LYS91 4.1 27.9 1.0
O E:HOH348 4.1 36.6 1.0
CE E:LYS91 4.3 27.1 1.0
CG E:GLU89 4.3 22.9 1.0
CB E:ILE90 4.4 19.8 1.0
CG E:GLU10 4.4 30.3 1.0
O E:HOH333 4.5 39.9 1.0
C E:GLU89 4.5 21.4 1.0
CB E:ASP73 4.5 27.7 1.0
CD E:LYS91 4.6 26.8 1.0
N E:LYS91 4.6 16.9 1.0
NE2 E:GLN102 4.8 33.8 1.0
CA E:GLU89 4.9 23.4 1.0
CA E:LYS91 5.0 18.2 1.0

Magnesium binding site 5 out of 6 in 4qbl

Go back to Magnesium Binding Sites List in 4qbl
Magnesium binding site 5 out of 6 in the VRR_NUC Domain Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of VRR_NUC Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:51.3
occ:1.00
 OE2 F:GLU10 2.1 81.5 1.0
OD2 F:ASP73 2.3 49.0 1.0
O F:ILE90 2.4 55.0 1.0
OE2 F:GLU89 2.4 64.7 1.0
O F:HOH305 2.6 62.3 1.0
CD F:GLU10 3.0 75.9 1.0
CG F:ASP73 3.0 51.0 1.0
OD1 F:ASP73 3.2 54.0 1.0
CD F:GLU89 3.4 62.3 1.0
OE1 F:GLU10 3.4 74.1 1.0
C F:ILE90 3.5 53.4 1.0
N F:ILE90 3.7 47.0 1.0
OE1 F:GLU89 3.9 62.7 1.0
CA F:ILE90 4.0 49.4 1.0
CG F:GLU10 4.2 67.9 1.0
CB F:ILE90 4.3 48.0 1.0
CB F:ASP73 4.5 50.1 1.0
NZ F:LYS91 4.5 62.3 1.0
CG F:GLU89 4.5 56.4 1.0
C F:GLU89 4.6 48.7 1.0
CE F:LYS91 4.6 63.4 1.0
N F:LYS91 4.7 53.3 1.0
CD F:LYS91 4.7 59.9 1.0

Magnesium binding site 6 out of 6 in 4qbl

Go back to Magnesium Binding Sites List in 4qbl
Magnesium binding site 6 out of 6 in the VRR_NUC Domain Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of VRR_NUC Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:37.8
occ:1.00
 OE2 C:GLU10 2.1 54.6 1.0
O C:ILE90 2.3 30.8 1.0
OE2 C:GLU89 2.3 39.4 1.0
OD2 C:ASP73 2.4 37.3 1.0
O C:HOH329 2.5 42.5 1.0
O C:HOH394 2.6 53.9 1.0
CD C:GLU10 2.9 56.4 1.0
CG C:ASP73 3.2 35.1 1.0
OE1 C:GLU10 3.3 62.7 1.0
CD C:GLU89 3.3 38.5 1.0
C C:ILE90 3.4 30.2 1.0
OD1 C:ASP73 3.4 37.5 1.0
N C:ILE90 3.7 27.5 1.0
CA C:ILE90 3.9 27.9 1.0
OE1 C:GLU89 4.0 36.5 1.0
CG C:GLU10 4.2 49.6 1.0
NZ C:LYS91 4.2 46.2 1.0
CB C:ILE90 4.2 29.3 1.0
CG C:GLU89 4.3 30.6 1.0
O C:HOH331 4.3 48.9 1.0
CD C:LYS91 4.4 43.8 1.0
O C:HOH387 4.4 51.8 1.0
C C:GLU89 4.5 27.5 1.0
N C:LYS91 4.5 27.3 1.0
CE C:LYS91 4.6 42.6 1.0
CB C:ASP73 4.6 25.6 1.0
CA C:LYS91 4.9 30.1 1.0
CA C:GLU89 4.9 33.0 1.0

Reference:

S.Pennell, A.C.Declais, J.Li, L.F.Haire, W.Berg, J.W.Saldanha, I.A.Taylor, J.Rouse, D.M.Lilley, S.J.Smerdon. FAN1 Activity on Asymmetric Repair Intermediates Is Mediated By An Atypical Monomeric Virus-Type Replication-Repair Nuclease Domain. Cell Rep V. 8 84 2014.
ISSN: ESSN 2211-1247
PubMed: 24981866
DOI: 10.1016/J.CELREP.2014.06.001
Page generated: Mon Dec 14 19:22:16 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