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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

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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: Tue Aug 20 01:52:22 2024

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