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Magnesium in PDB 5dcx: Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation

Enzymatic activity of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation

All present enzymatic activity of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation:
3.6.4.12;

Protein crystallography data

The structure of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation, PDB code: 5dcx was solved by F.N.Musayev, F.Zarate-Perez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.81 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.644, 178.706, 130.358, 90.00, 91.66, 90.00
R / Rfree (%) 19.1 / 23.8

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation (pdb code 5dcx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation, PDB code: 5dcx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 5dcx

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Magnesium binding site 1 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:95.8
occ:1.00
 OE2 A:GLU83 2.2 59.5 1.0
NE2 A:HIS90 2.5 52.1 1.0
NE2 A:HIS92 2.5 45.0 1.0
CE1 A:HIS90 3.2 59.9 1.0
CE1 A:HIS92 3.3 45.2 1.0
CD A:GLU83 3.3 56.4 1.0
CD2 A:HIS90 3.6 43.1 1.0
CD2 A:HIS92 3.6 34.9 1.0
OE1 A:GLU83 3.8 57.0 1.0
ND1 A:HIS90 4.4 41.8 1.0
ND1 A:HIS92 4.5 44.0 1.0
CG A:GLU83 4.5 41.0 1.0
CG A:HIS90 4.6 33.7 1.0
CB A:GLU83 4.7 33.1 1.0
CG A:HIS92 4.7 34.7 1.0
OE2 A:GLU164 4.7 53.4 1.0
NZ A:LYS160 4.8 71.6 1.0
CE A:LYS160 4.8 54.3 1.0

Magnesium binding site 2 out of 11 in 5dcx

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Magnesium binding site 2 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:0.8
occ:1.00
 OE2 B:GLU83 2.3 47.8 1.0
NE2 B:HIS90 2.3 44.9 1.0
NE2 B:HIS92 2.4 43.1 1.0
CE1 B:HIS90 3.1 50.3 1.0
CE1 B:HIS92 3.2 47.0 1.0
O B:HOH405 3.3 62.5 1.0
CD2 B:HIS90 3.3 39.5 1.0
CD B:GLU83 3.4 47.6 1.0
CD2 B:HIS92 3.6 29.4 1.0
OE1 B:GLU83 3.9 49.1 1.0
NZ B:LYS160 4.1 69.5 1.0
ND1 B:HIS90 4.2 37.6 1.0
CG B:HIS90 4.4 34.0 1.0
ND1 B:HIS92 4.4 40.7 1.0
CG B:HIS92 4.6 37.8 1.0
CG B:GLU83 4.6 38.2 1.0
CB B:GLU83 4.7 33.2 1.0
OE2 B:GLU164 4.8 59.7 1.0

Magnesium binding site 3 out of 11 in 5dcx

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Magnesium binding site 3 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:34.3
occ:1.00
 NE2 C:HIS90 2.2 45.3 1.0
OE1 C:GLU83 2.2 40.9 1.0
NE2 C:HIS92 2.2 46.7 1.0
CE1 C:HIS92 3.0 46.8 1.0
CE1 C:HIS90 3.0 58.9 1.0
CD2 C:HIS90 3.3 40.8 1.0
CD C:GLU83 3.4 40.2 1.0
CD2 C:HIS92 3.4 37.0 1.0
OE2 C:GLU83 3.9 49.0 1.0
ND1 C:HIS90 4.2 53.1 1.0
ND1 C:HIS92 4.2 42.4 1.0
CG C:HIS90 4.3 39.5 1.0
CG C:HIS92 4.4 36.2 1.0
O C:HOH410 4.5 46.4 1.0
CG C:GLU83 4.6 38.1 1.0
CB C:GLU83 4.6 33.2 1.0
OE2 C:GLU164 4.9 64.6 1.0
NZ C:LYS160 4.9 53.5 1.0
CE C:LYS160 5.0 40.8 1.0

Magnesium binding site 4 out of 11 in 5dcx

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Magnesium binding site 4 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:32.2
occ:1.00
 OE1 D:GLU83 2.0 33.1 1.0
NE2 D:HIS92 2.2 33.9 1.0
NE2 D:HIS90 2.2 50.8 1.0
CE1 D:HIS92 3.0 30.0 1.0
CE1 D:HIS90 3.1 51.2 1.0
CD D:GLU83 3.2 37.7 1.0
CD2 D:HIS90 3.3 47.2 1.0
CD2 D:HIS92 3.3 28.5 1.0
OE2 D:GLU83 3.6 44.3 1.0
ND1 D:HIS92 4.2 38.6 1.0
ND1 D:HIS90 4.3 40.8 1.0
CG D:HIS92 4.4 40.8 1.0
CG D:HIS90 4.4 41.5 1.0
CG D:GLU83 4.4 29.1 1.0
OE2 D:GLU164 4.4 47.3 1.0
CB D:GLU83 4.6 32.5 1.0
CE D:LYS160 4.9 60.5 1.0
NZ D:LYS160 5.0 73.8 1.0

Magnesium binding site 5 out of 11 in 5dcx

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Magnesium binding site 5 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:36.1
occ:1.00
 OE2 E:GLU83 2.0 65.5 1.0
O E:HOH410 2.1 53.9 1.0
NE2 E:HIS92 2.3 43.2 1.0
NE2 E:HIS90 2.3 45.5 1.0
CD E:GLU83 2.9 53.7 1.0
CE1 E:HIS90 3.2 55.1 1.0
CE1 E:HIS92 3.2 45.3 1.0
OE1 E:GLU83 3.2 50.8 1.0
CD2 E:HIS92 3.2 43.3 1.0
CD2 E:HIS90 3.4 45.1 1.0
CG E:GLU83 4.2 46.4 1.0
NZ E:LYS160 4.3 77.5 1.0
ND1 E:HIS90 4.3 47.5 1.0
ND1 E:HIS92 4.4 44.9 1.0
CG E:HIS92 4.4 37.6 1.0
OE2 E:GLU164 4.4 73.8 1.0
CB E:GLU83 4.4 38.9 1.0
CG E:HIS90 4.5 38.0 1.0
CE E:LYS160 4.6 69.4 1.0

Magnesium binding site 6 out of 11 in 5dcx

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Magnesium binding site 6 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:39.7
occ:1.00
 NE2 F:HIS92 2.2 53.8 1.0
NE2 F:HIS90 2.2 52.5 1.0
OE2 F:GLU83 2.3 49.6 1.0
CE1 F:HIS92 2.9 39.9 1.0
CE1 F:HIS90 3.1 60.7 1.0
CD2 F:HIS90 3.3 41.3 1.0
CD2 F:HIS92 3.4 57.7 1.0
CD F:GLU83 3.4 51.5 1.0
OE1 F:GLU83 4.0 54.7 1.0
ND1 F:HIS92 4.2 39.5 1.0
ND1 F:HIS90 4.3 44.6 1.0
CG F:HIS90 4.4 42.1 1.0
CG F:HIS92 4.4 43.5 1.0
CG F:GLU83 4.6 42.9 1.0
CB F:GLU83 4.6 43.1 1.0
OE2 F:GLU164 4.6 60.0 1.0

Magnesium binding site 7 out of 11 in 5dcx

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Magnesium binding site 7 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg301

b:36.1
occ:1.00
 OE2 G:GLU83 2.2 44.5 1.0
NE2 G:HIS90 2.3 70.3 1.0
NE2 G:HIS92 2.3 47.3 1.0
CE1 G:HIS90 3.1 72.7 1.0
CE1 G:HIS92 3.1 42.6 1.0
CD G:GLU83 3.3 55.3 1.0
CD2 G:HIS90 3.3 64.0 1.0
CD2 G:HIS92 3.4 46.6 1.0
OE1 G:GLU83 3.9 50.1 1.0
ND1 G:HIS90 4.2 68.5 1.0
ND1 G:HIS92 4.3 45.8 1.0
OE2 G:GLU164 4.4 80.3 1.0
CG G:HIS90 4.4 61.9 1.0
CG G:HIS92 4.5 47.4 1.0
CG G:GLU83 4.5 57.2 1.0
CB G:GLU83 4.7 53.8 1.0

Magnesium binding site 8 out of 11 in 5dcx

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Magnesium binding site 8 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg301

b:46.1
occ:1.00
 OE2 H:GLU83 2.3 55.9 1.0
NE2 H:HIS90 2.3 71.3 1.0
NE2 H:HIS92 2.4 60.7 1.0
CE1 H:HIS90 3.2 73.2 1.0
CE1 H:HIS92 3.2 52.3 1.0
CD2 H:HIS90 3.3 66.9 1.0
CD H:GLU83 3.4 56.0 1.0
CD2 H:HIS92 3.6 65.6 1.0
OE1 H:GLU83 3.9 52.2 1.0
NZ H:LYS160 4.2 65.2 1.0
OE2 H:GLU164 4.2 81.7 1.0
ND1 H:HIS90 4.3 66.2 1.0
ND1 H:HIS92 4.4 58.4 1.0
CG H:HIS90 4.4 57.2 1.0
CG H:GLU83 4.6 52.5 1.0
CG H:HIS92 4.6 64.5 1.0
CB H:GLU83 4.7 48.9 1.0

Magnesium binding site 9 out of 11 in 5dcx

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Magnesium binding site 9 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg301

b:57.1
occ:1.00
 NE2 I:HIS92 2.3 66.4 1.0
NE2 I:HIS90 2.4 70.5 1.0
OE2 I:GLU83 2.5 69.8 1.0
CE1 I:HIS92 2.7 66.1 1.0
CD2 I:HIS90 3.3 67.8 1.0
CE1 I:HIS90 3.4 74.0 1.0
CD2 I:HIS92 3.6 61.9 1.0
CD I:GLU83 3.6 73.1 1.0
ND1 I:HIS92 4.0 60.4 1.0
OE1 I:GLU83 4.2 80.7 1.0
NZ I:LYS160 4.4 82.4 1.0
CG I:HIS92 4.5 59.5 1.0
ND1 I:HIS90 4.5 64.2 1.0
CG I:HIS90 4.5 60.7 1.0
CG I:GLU83 4.8 70.0 1.0
CB I:GLU83 4.9 66.9 1.0
CE I:LYS160 4.9 74.7 1.0

Magnesium binding site 10 out of 11 in 5dcx

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Magnesium binding site 10 out of 11 in the Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg301

b:48.6
occ:1.00
 OE2 J:GLU83 2.0 64.0 1.0
NE2 J:HIS92 2.3 55.5 1.0
NE2 J:HIS90 2.4 63.7 1.0
CE1 J:HIS92 2.9 54.5 1.0
CD J:GLU83 3.2 70.4 1.0
CE1 J:HIS90 3.2 61.3 1.0
CD2 J:HIS90 3.4 62.9 1.0
CD2 J:HIS92 3.5 61.6 1.0
CG J:GLU83 4.0 67.8 1.0
OE1 J:GLU83 4.1 66.5 1.0
ND1 J:HIS92 4.1 54.7 1.0
ND1 J:HIS90 4.4 55.2 1.0
CG J:HIS92 4.5 57.4 1.0
CG J:HIS90 4.5 57.4 1.0

Reference:

F.N.Musayev, F.Zarate-Perez, M.Bardelli, C.Bishop, E.F.Saniev, R.M.Linden, E.Henckaerts, C.R.Escalante. Structural Studies of AAV2 REP68 Reveal A Partially Structured Linker and Compact Domain Conformation. Biochemistry V. 54 5907 2015.
ISSN: ISSN 0006-2960
PubMed: 26314310
DOI: 10.1021/ACS.BIOCHEM.5B00610
Page generated: Mon Dec 14 20:10:59 2020

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