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Cadmium in PDB 5azf: Crystal Structure of Lgg-1 Complexed with A Weel Peptide

Protein crystallography data

The structure of Crystal Structure of Lgg-1 Complexed with A Weel Peptide, PDB code: 5azf was solved by Y.Watanabe, N.N.Noda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.280, 112.146, 35.859, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 21.8

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide (pdb code 5azf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide, PDB code: 5azf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 1 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:14.7
occ:1.00
 NE2 A:HIS42 2.2 11.8 1.0
O A:HOH435 2.7 25.0 1.0
CE1 A:HIS42 3.0 15.9 1.0
CD2 A:HIS42 3.2 16.7 1.0
ND1 A:HIS42 4.2 16.0 1.0
O A:HOH379 4.3 15.9 1.0
CG A:HIS42 4.3 14.9 1.0
O A:HOH420 4.6 30.9 1.0

Cadmium binding site 2 out of 13 in 5azf

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Cadmium binding site 2 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:23.6
occ:1.00
 O A:HOH451 2.3 32.7 1.0
O A:HOH338 2.3 18.2 1.0
O A:HOH439 2.3 30.1 1.0
NE2 A:HIS98 2.4 17.9 1.0
O A:HOH490 2.4 30.4 1.0
O A:HOH432 2.5 26.8 1.0
CE1 A:HIS98 3.2 17.7 1.0
CD2 A:HIS98 3.4 16.5 1.0
O A:HOH479 4.0 35.0 1.0
O A:HOH447 4.1 33.0 1.0
OD2 A:ASP97 4.1 15.2 1.0
O A:HOH458 4.2 21.8 1.0
CB A:ASP97 4.3 13.1 1.0
ND1 A:HIS98 4.4 16.1 1.0
CG A:HIS98 4.5 17.3 1.0
O A:HOH396 4.5 18.9 1.0
CG A:ASP97 4.6 14.9 1.0
O A:HOH368 4.6 34.1 1.0
CD2 A:LEU94 4.9 10.8 1.0

Cadmium binding site 3 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 3 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:33.2
occ:0.65
 CD A:CD205 1.9 27.3 0.3
NE2 A:HIS99 2.2 20.3 1.0
O A:HOH445 2.6 40.2 1.0
O A:HOH374 2.7 26.8 1.0
O A:HOH461 2.8 40.8 1.0
O A:HOH462 2.8 32.6 1.0
CD2 A:HIS99 3.2 19.1 1.0
CE1 A:HIS99 3.2 19.3 1.0
O A:HOH434 3.5 20.9 1.0
ND1 A:HIS99 4.2 17.0 1.0
CG A:HIS99 4.3 18.4 1.0

Cadmium binding site 4 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 4 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:14.3
occ:1.00
 NE2 A:HIS0 2.2 12.7 1.0
O B:HOH396 2.2 21.3 1.0
N B:GLY-2 2.3 10.8 1.0
O A:GLY116 2.3 16.9 1.0
O B:GLY-2 2.5 13.9 1.0
OXT A:GLY116 2.9 17.8 1.0
C A:GLY116 2.9 18.5 1.0
O B:HOH394 3.0 25.1 1.0
CE1 A:HIS0 3.1 19.0 1.0
CA B:GLY-2 3.2 13.0 1.0
CD2 A:HIS0 3.2 15.4 1.0
C B:GLY-2 3.2 14.4 1.0
O B:HOH320 3.5 26.6 1.0
O A:HOH388 4.1 19.9 1.0
ND1 A:HIS0 4.2 17.1 1.0
CG A:HIS0 4.3 15.8 1.0
CA A:GLY116 4.4 17.0 1.0
O B:ASN82 4.4 18.0 1.0
N B:PRO-1 4.5 14.7 1.0
CB B:ASN82 4.6 23.8 1.0
O B:HOH419 4.6 18.2 1.0
O B:HOH323 4.7 33.4 1.0
O B:TYR115 4.9 18.0 1.0
CB B:TYR115 5.0 14.3 1.0
O A:HOH356 5.0 23.1 1.0

Cadmium binding site 5 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 5 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:27.3
occ:0.35
 CD A:CD203 1.9 33.2 0.7
O A:HOH374 2.4 26.8 1.0
NE2 A:HIS99 2.6 20.3 1.0
O A:HOH434 2.7 20.9 1.0
O A:HOH445 3.2 40.2 1.0
CE1 A:HIS99 3.5 19.3 1.0
CD2 A:HIS99 3.5 19.1 1.0
O A:HOH461 4.2 40.8 1.0
O A:GLN96 4.2 13.7 1.0
O A:HOH462 4.4 32.6 1.0
ND1 A:HIS99 4.6 17.0 1.0
CG A:HIS99 4.7 18.4 1.0
O A:HOH371 4.8 28.8 1.0

Cadmium binding site 6 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 6 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:15.8
occ:1.00
 NE2 B:HIS42 2.2 10.1 1.0
O B:HOH445 2.8 23.9 1.0
CE1 B:HIS42 3.0 14.4 1.0
CD2 B:HIS42 3.3 14.1 1.0
ND1 B:HIS42 4.2 16.0 1.0
O B:HOH349 4.3 19.0 1.0
CG B:HIS42 4.3 13.8 1.0
O B:HOH422 4.6 30.4 1.0
O B:HOH472 4.9 18.9 1.0

Cadmium binding site 7 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 7 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:27.8
occ:1.00
 O B:HOH455 2.3 28.9 1.0
NE2 B:HIS98 2.3 19.0 1.0
O B:HOH482 2.4 33.8 1.0
O B:HOH319 2.5 18.1 1.0
O B:HOH436 2.5 29.0 1.0
O B:HOH452 2.5 25.4 1.0
CE1 B:HIS98 3.2 18.9 1.0
CD2 B:HIS98 3.4 16.4 1.0
OD2 B:ASP97 4.1 14.6 1.0
O B:HOH464 4.2 22.5 1.0
CB B:ASP97 4.3 13.2 1.0
ND1 B:HIS98 4.4 17.8 1.0
CG B:HIS98 4.5 16.4 1.0
O B:HOH417 4.6 32.7 1.0
CG B:ASP97 4.6 15.7 1.0
O B:HOH343 4.8 42.5 1.0
O B:HOH338 4.9 20.1 1.0
CD2 B:LEU94 4.9 12.1 1.0

Cadmium binding site 8 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 8 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:21.1
occ:0.55
 CD B:CD207 1.9 24.4 0.5
NE2 B:HIS99 2.4 19.8 1.0
O B:HOH467 2.8 32.7 1.0
O B:HOH369 2.8 32.4 1.0
O B:HOH458 2.8 34.0 1.0
CE1 B:HIS99 3.2 19.4 1.0
CD2 B:HIS99 3.3 18.6 1.0
O B:HOH412 3.3 21.5 1.0
ND1 B:HIS99 4.3 18.2 1.0
CG B:HIS99 4.3 17.2 1.0
NH1 B:ARG22 4.4 25.9 1.0

Cadmium binding site 9 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 9 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:14.1
occ:1.00
 O A:HOH388 2.2 19.9 1.0
NE2 B:HIS0 2.2 12.0 1.0
N A:GLY-2 2.2 9.7 1.0
OXT B:GLY116 2.3 15.7 1.0
O A:GLY-2 2.6 12.7 1.0
O B:GLY116 2.6 15.9 1.0
O A:HOH337 2.7 16.4 1.0
C B:GLY116 2.8 17.8 1.0
CE1 B:HIS0 3.1 17.9 1.0
CA A:GLY-2 3.2 11.5 1.0
CD2 B:HIS0 3.3 15.4 1.0
C A:GLY-2 3.3 12.1 1.0
O B:HOH396 4.0 21.3 1.0
O A:ASN82 4.2 14.2 1.0
ND1 B:HIS0 4.3 16.3 1.0
O A:HOH398 4.3 13.2 1.0
CA B:GLY116 4.3 16.2 1.0
CG B:HIS0 4.4 14.6 1.0
O B:HOH324 4.5 20.1 1.0
N A:PRO-1 4.6 13.6 1.0
O B:HOH323 4.6 33.4 1.0
O A:TYR115 4.6 17.9 1.0
O B:HOH463 4.7 35.5 1.0
CB A:ASN82 4.7 14.9 1.0
O B:HOH356 4.8 19.1 1.0

Cadmium binding site 10 out of 13 in 5azf

Go back to Cadmium Binding Sites List in 5azf
Cadmium binding site 10 out of 13 in the Crystal Structure of Lgg-1 Complexed with A Weel Peptide


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Lgg-1 Complexed with A Weel Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:20.3
occ:1.00
 O B:HOH410 2.1 37.0 1.0
OD1 B:ASP27 2.3 17.5 1.0
O B:HOH437 2.4 29.2 1.0
OD2 B:ASP27 2.6 20.9 1.0
CG B:ASP27 2.8 19.4 1.0
CG B:ARG28 4.3 24.2 1.0
O B:HOH443 4.3 37.2 1.0
CB B:ASP27 4.3 18.6 1.0
NE B:ARG28 4.5 29.1 1.0
O B:HOH424 4.7 31.9 1.0
N B:ASP27 5.0 17.1 1.0
O B:HOH321 5.0 32.9 1.0

Reference:

F.Wu, Y.Watanabe, X.Y.Guo, X.Qi, P.Wang, H.Y.Zhao, Z.Wang, Y.Fujioka, H.Zhang, J.Q.Ren, T.C.Fang, Y.X.Shen, W.Feng, J.J.Hu, N.N.Noda, H.Zhang. Structural Basis of the Differential Function of the Two C. Elegans ATG8 Homologs, Lgg-1 and Lgg-2, in Autophagy Mol.Cell V. 60 914 2015.
ISSN: ISSN 1097-2765
DOI: 10.1016/J.MOLCEL.2015.11.019
Page generated: Fri Jul 19 18:11:02 2024

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