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Nickel in PDB 5yir: Crystal Structure of Ankb Lir/Gabarap Complex

Protein crystallography data

The structure of Crystal Structure of Ankb Lir/Gabarap Complex, PDB code: 5yir was solved by J.Li, R.Zhu, K.Chen, H.Zheng, C.Yuan, H.Zhang, C.Wang, M.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.59 / 2.75
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 84.637, 84.637, 89.344, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 22.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Ankb Lir/Gabarap Complex (pdb code 5yir). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 10 binding sites of Nickel where determined in the Crystal Structure of Ankb Lir/Gabarap Complex, PDB code: 5yir:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 10 in 5yir

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Nickel binding site 1 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni201

b:44.9
occ:1.00
 NE2 D:HIS99 2.2 34.0 1.0
CD2 D:HIS99 3.1 36.6 1.0
CE1 D:HIS99 3.2 42.4 1.0
CG D:HIS99 4.3 37.2 1.0
ND1 D:HIS99 4.3 31.9 1.0
O D:GLU100 5.0 41.5 1.0

Nickel binding site 2 out of 10 in 5yir

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Nickel binding site 2 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni202

b:0.2
occ:1.00
 OE1 D:GLU97 2.4 86.9 1.0
NE2 D:HIS98 2.8 71.3 1.0
CE1 D:HIS98 3.4 69.8 1.0
CD D:GLU97 3.7 97.9 1.0
CD2 D:HIS98 3.9 39.6 1.0
OE2 D:GLU97 4.3 0.7 1.0
CB D:GLU97 4.6 37.0 1.0
ND1 D:HIS98 4.6 46.5 1.0
CG D:GLU97 4.7 70.0 1.0
CG D:HIS98 4.9 44.6 1.0

Nickel binding site 3 out of 10 in 5yir

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Nickel binding site 3 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni203

b:42.7
occ:1.00
 CD2 D:HIS9 2.2 41.3 1.0
O C:HOH2101 2.2 35.4 1.0
O G:HOH2103 2.3 31.8 1.0
OE2 G:GLU1995 2.3 75.1 1.0
OE1 G:GLU1995 2.9 84.3 1.0
CD G:GLU1995 3.0 80.1 1.0
CG D:HIS9 3.1 40.0 1.0
NE2 D:HIS9 3.2 41.4 1.0
CB D:HIS9 3.5 44.3 1.0
O D:HOH301 3.5 58.1 1.0
ND1 D:HIS9 4.2 42.5 1.0
CE1 D:HIS9 4.3 39.7 1.0
CA D:HIS9 4.4 43.7 1.0
CG G:GLU1995 4.5 78.1 1.0

Nickel binding site 4 out of 10 in 5yir

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Nickel binding site 4 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni201

b:45.4
occ:1.00
 O A:HOH301 2.2 42.6 1.0
O A:HOH303 2.2 35.4 1.0
OE1 A:GLU112 2.2 70.2 1.0
OE2 A:GLU112 2.4 55.5 1.0
CD A:GLU112 2.6 59.6 1.0
CG A:GLU112 4.1 52.3 1.0

Nickel binding site 5 out of 10 in 5yir

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Nickel binding site 5 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:66.6
occ:1.00
 O B:HOH301 2.0 40.4 1.0
O A:HOH304 2.2 66.8 1.0
NE2 A:HIS69 2.2 78.5 1.0
NE2 B:HIS69 2.4 56.0 1.0
CE1 B:HIS69 2.5 55.6 1.0
CD2 A:HIS69 3.0 52.9 1.0
CE1 A:HIS69 3.3 84.5 1.0
CD2 B:HIS69 3.7 48.9 1.0
ND1 B:HIS69 3.9 54.2 1.0
CG A:HIS69 4.2 70.1 1.0
ND1 A:HIS69 4.3 84.2 1.0
CG B:HIS69 4.5 53.3 1.0
OD2 A:ASP45 4.5 63.1 1.0
O A:ARG67 4.6 49.6 1.0

Nickel binding site 6 out of 10 in 5yir

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Nickel binding site 6 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni203

b:93.3
occ:1.00
 NE2 A:HIS9 2.2 72.1 1.0
O A:HOH305 2.2 63.7 1.0
OE1 G:GLU1987 2.3 78.3 1.0
O G:HOH2101 2.4 56.0 1.0
CD2 A:HIS9 3.1 60.4 1.0
CE1 A:HIS9 3.1 64.2 1.0
CD G:GLU1987 3.1 93.9 1.0
CG G:GLU1987 3.6 81.5 1.0
OE2 G:GLU1987 4.1 79.8 1.0
ND1 A:HIS9 4.2 63.3 1.0
CG A:HIS9 4.3 54.4 1.0
O G:HOH2102 4.4 69.0 1.0
CB G:GLU1987 4.8 71.5 1.0

Nickel binding site 7 out of 10 in 5yir

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Nickel binding site 7 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni204

b:0.5
occ:1.00
 NE2 A:HIS98 2.5 60.2 1.0
CE1 A:HIS98 3.2 58.8 1.0
CD2 A:HIS98 3.6 46.2 1.0
CB A:GLU97 4.2 39.9 1.0
ND1 A:HIS98 4.3 55.3 1.0
CG A:HIS98 4.5 51.1 1.0

Nickel binding site 8 out of 10 in 5yir

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Nickel binding site 8 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni201

b:47.9
occ:1.00
 O H:HOH2101 2.0 36.9 1.0
NE2 D:HIS69 2.1 58.5 1.0
NE2 B:HIS9 2.1 46.1 1.0
O D:HOH307 2.5 55.0 1.0
CD2 D:HIS69 3.0 48.3 1.0
CE1 B:HIS9 3.1 43.1 1.0
CE1 D:HIS69 3.1 62.9 1.0
CD2 B:HIS9 3.2 39.2 1.0
OE2 H:GLU1987 3.5 44.1 1.0
CG H:GLU1987 3.9 60.0 1.0
CD H:GLU1987 4.1 67.9 1.0
CG D:HIS69 4.2 67.7 1.0
ND1 B:HIS9 4.2 45.7 1.0
ND1 D:HIS69 4.2 63.7 1.0
CG B:HIS9 4.3 41.7 1.0
O D:ARG67 4.7 57.7 1.0

Nickel binding site 9 out of 10 in 5yir

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Nickel binding site 9 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni202

b:45.3
occ:1.00
 NE2 B:HIS99 2.2 41.0 1.0
CD2 B:HIS99 3.1 34.4 1.0
CE1 B:HIS99 3.2 43.3 1.0
CG B:HIS99 4.3 39.3 1.0
ND1 B:HIS99 4.3 41.0 1.0
O B:GLU100 5.0 47.9 1.0

Nickel binding site 10 out of 10 in 5yir

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Nickel binding site 10 out of 10 in the Crystal Structure of Ankb Lir/Gabarap Complex


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Ankb Lir/Gabarap Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni203

b:94.9
occ:1.00
 OE1 B:GLU97 2.6 82.2 1.0
NE2 B:HIS98 2.7 68.5 1.0
CE1 B:HIS98 3.3 59.2 1.0
CD B:GLU97 3.8 91.5 1.0
CD2 B:HIS98 3.9 39.4 1.0
OE2 B:GLU97 4.5 88.7 1.0
ND1 B:HIS98 4.6 50.6 1.0
CB B:GLU97 4.7 50.6 1.0
CG B:GLU97 4.8 66.6 1.0
CG B:HIS98 4.9 49.4 1.0

Reference:

J.Li, R.Zhu, K.Chen, H.Zheng, H.Zhao, C.Yuan, H.Zhang, C.Wang, M.Zhang. Potent and Specific ATG8-Targeting Autophagy Inhibitory Peptides From Giant Ankyrins. Nat. Chem. Biol. V. 14 778 2018.
ISSN: ESSN 1552-4469
PubMed: 29867141
DOI: 10.1038/S41589-018-0082-8
Page generated: Thu Oct 10 08:17:05 2024

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