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Zinc in PDB 5gv3: Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)

Protein crystallography data

The structure of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2), PDB code: 5gv3 was solved by Y.Tomabechi, H.Ehara, M.Kukimoto-Niino, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.49 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 59.610, 103.930, 129.180, 90.00, 90.00, 90.00
R / Rfree (%) 26.9 / 30.8

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) (pdb code 5gv3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 15 binding sites of Zinc where determined in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2), PDB code: 5gv3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 15 in 5gv3

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Zinc binding site 1 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:45.3
occ:1.00
OE1 A:GLU41 2.0 51.4 1.0
OE2 A:GLU41 2.0 81.2 1.0
O A:HOH323 2.1 61.3 1.0
CD A:GLU41 2.3 55.1 1.0
OH A:TYR39 3.8 46.8 1.0
CG A:GLU41 3.9 54.3 1.0
CG A:HIS168 4.5 39.3 1.0
ND1 A:HIS168 4.6 42.3 1.0
CB A:GLU41 4.7 37.7 1.0
CZ A:TYR39 4.8 45.5 1.0
CB A:HIS168 4.8 30.7 1.0
CE2 A:TYR39 4.9 46.9 1.0
CD2 A:HIS168 4.9 42.9 1.0
CE1 A:HIS168 4.9 52.3 1.0

Zinc binding site 2 out of 15 in 5gv3

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Zinc binding site 2 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:50.0
occ:0.66
NE2 A:HIS70 2.0 71.6 1.0
O A:HOH343 2.1 77.3 1.0
O A:HOH339 2.1 65.8 1.0
O A:HOH328 2.1 71.4 1.0
O A:HOH311 2.1 69.7 1.0
CE1 A:HIS70 2.5 78.9 1.0
CD2 A:HIS70 3.3 60.7 1.0
ND1 A:HIS70 3.7 62.4 1.0
CG A:HIS70 4.2 51.6 1.0
O A:HOH337 4.5 59.4 1.0

Zinc binding site 3 out of 15 in 5gv3

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Zinc binding site 3 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:90.1
occ:0.81
OE1 A:GLU43 2.0 63.5 1.0
OE2 A:GLU43 2.0 74.7 1.0
CD A:GLU43 2.3 36.9 1.0
CG A:GLU43 3.8 46.9 1.0
NE1 A:TRP165 4.1 36.0 1.0
CZ2 A:TRP165 4.5 41.5 1.0
CB A:GLU43 4.6 36.7 1.0
CE2 A:TRP165 4.7 43.5 1.0

Zinc binding site 4 out of 15 in 5gv3

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Zinc binding site 4 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:68.6
occ:0.00
CD2 A:HIS131 1.9 55.2 1.0
CG A:HIS131 1.9 61.8 1.0
ND1 A:HIS131 2.0 79.2 1.0
NE2 A:HIS131 2.0 72.9 1.0
O A:HOH319 2.1 92.8 1.0
O A:HOH301 2.1 66.2 1.0
O A:HOH345 2.1 69.6 1.0
CE1 A:HIS131 2.2 84.5 1.0
CB A:HIS131 2.9 44.8 1.0
O A:HOH330 3.7 49.8 1.0
O A:HOH347 3.9 67.0 1.0
OH A:TYR114 4.0 54.9 1.0
CA A:HIS131 4.2 53.3 1.0
CZ A:TYR114 4.6 47.2 1.0
CE2 A:TYR114 4.6 41.0 1.0
N A:HIS131 4.9 50.4 1.0

Zinc binding site 5 out of 15 in 5gv3

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Zinc binding site 5 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn205

b:80.1
occ:0.00
OD1 A:ASP118 2.0 68.9 1.0
OD2 A:ASP118 2.0 77.5 1.0
OG1 A:THR120 2.0 83.5 1.0
O A:HOH305 2.1 71.7 1.0
CG A:ASP118 2.3 77.0 1.0
CG2 A:THR120 2.3 68.2 1.0
CD2 A:PHE90 2.3 79.6 1.0
CB A:THR120 2.7 77.8 1.0
CE2 A:PHE90 2.8 90.8 1.0
CG A:PHE90 3.5 88.0 1.0
CB A:ASP118 3.8 72.2 1.0
CA A:THR120 4.0 64.4 1.0
CB A:PHE90 4.0 86.1 1.0
N A:THR120 4.1 73.5 1.0
CZ A:PHE90 4.2 97.9 1.0
CA A:ASP118 4.5 58.5 1.0
CD1 A:PHE90 4.7 87.9 1.0
N A:PHE90 4.8 80.8 1.0
C A:ASP118 4.8 64.3 1.0
C A:THR120 4.9 67.5 1.0
CE1 A:PHE90 5.0 92.5 1.0

Zinc binding site 6 out of 15 in 5gv3

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Zinc binding site 6 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn206

b:64.5
occ:0.26
OE1 A:GLN189 4.6 80.5 1.0
O A:GLU187 4.9 63.3 1.0

Zinc binding site 7 out of 15 in 5gv3

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Zinc binding site 7 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn207

b:0.7
occ:0.44
ZN A:ZN209 2.3 79.8 0.0
O A:HOH331 4.2 57.0 1.0
O A:HOH338 4.6 58.5 1.0

Zinc binding site 8 out of 15 in 5gv3

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Zinc binding site 8 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:69.4
occ:0.29
OD1 A:ASN181 4.9 50.5 1.0

Zinc binding site 9 out of 15 in 5gv3

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Zinc binding site 9 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn209

b:79.8
occ:0.00
ZN A:ZN207 2.3 0.7 0.4

Zinc binding site 10 out of 15 in 5gv3

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Zinc binding site 10 out of 15 in the Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Membrane-Distal Domain of Mouse Lysosome- Associated Membrane Protein 2 (Lamp-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:38.0
occ:1.00
OD1 B:ASP109 2.0 56.5 1.0
OD2 B:ASP109 2.0 63.6 1.0
CD2 B:HIS108 2.0 74.9 1.0
NE2 B:HIS108 2.0 70.8 1.0
O B:HOH302 2.1 59.9 1.0
CG B:ASP109 2.2 47.4 1.0
CG B:HIS108 2.3 80.0 1.0
CE1 B:HIS108 2.3 51.2 1.0
ND1 B:HIS108 2.4 77.0 1.0
CB B:HIS108 3.4 42.4 1.0
CB B:ASP109 3.6 56.0 1.0
N B:ASP109 3.6 53.1 1.0
CA B:ASP109 4.1 47.6 1.0
C B:HIS108 4.2 53.6 1.0
CA B:HIS108 4.3 58.2 1.0
ND2 B:ASN138 4.8 76.0 1.0

Reference:

K.Terasawa, Y.Tomabechi, M.Ikeda, H.Ehara, M.Kukimoto-Niino, M.Wakiyama, K.A.Podyma-Inoue, A.R.Rajapakshe, T.Watabe, M.Shirouzu, M.Hara-Yokoyama. Lysosome-Associated Membrane Proteins-1 and -2 (Lamp-1 and Lamp-2) Assemble Via Distinct Modes. Biochem. Biophys. Res. V. 479 489 2016COMMUN..
ISSN: ESSN 1090-2104
PubMed: 27663661
DOI: 10.1016/J.BBRC.2016.09.093
Page generated: Wed Dec 16 06:19:48 2020

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