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Zinc in PDB 1joc: EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate

Protein crystallography data

The structure of EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate, PDB code: 1joc was solved by J.J.Dumas, E.Merithew, D.Rajamani, S.Hayes, D.Lawe, S.Corvera, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 36.528, 85.096, 88.036, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 28.1

Zinc Binding Sites:

The binding sites of Zinc atom in the EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate (pdb code 1joc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate, PDB code: 1joc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1joc

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Zinc binding site 1 out of 4 in the EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:32.6
occ:1.00
SG A:CYS1377 2.2 29.7 1.0
SG A:CYS1402 2.2 25.3 1.0
SG A:CYS1405 2.2 28.3 1.0
SG A:CYS1374 2.4 27.3 1.0
CB A:CYS1405 3.1 29.3 1.0
CB A:CYS1374 3.2 18.7 1.0
CB A:CYS1377 3.3 24.4 1.0
CB A:CYS1402 3.5 25.8 1.0
N A:CYS1377 3.7 24.2 1.0
N A:CYS1402 3.8 24.5 1.0
CA A:CYS1377 4.1 22.9 1.0
N A:CYS1405 4.1 31.4 1.0
CA A:CYS1405 4.2 29.6 1.0
CA A:CYS1402 4.2 25.5 1.0
CE1 A:PHE1381 4.4 24.1 1.0
CB A:GLN1376 4.4 29.5 1.0
CZ A:PHE1381 4.5 20.9 1.0
CA A:CYS1374 4.7 21.5 1.0
C A:GLN1376 4.7 23.9 1.0
C A:CYS1402 4.9 25.4 1.0
O A:CYS1402 4.9 26.0 1.0
C A:VAL1401 5.0 24.3 1.0
CA A:GLN1376 5.0 24.7 1.0

Zinc binding site 2 out of 4 in 1joc

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Zinc binding site 2 out of 4 in the EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:38.6
occ:1.00
SG A:CYS1382 2.3 25.4 1.0
SG A:CYS1358 2.3 26.2 1.0
SG A:CYS1385 2.3 35.6 1.0
SG A:CYS1361 2.4 31.2 1.0
CB A:CYS1358 3.1 22.4 1.0
CB A:CYS1385 3.2 33.5 1.0
CB A:CYS1361 3.4 28.5 1.0
CB A:CYS1382 3.6 16.4 1.0
N A:CYS1361 3.7 32.1 1.0
N A:CYS1382 4.0 22.9 1.0
CA A:CYS1361 4.1 28.9 1.0
N A:CYS1385 4.3 31.0 1.0
CA A:CYS1385 4.4 30.1 1.0
CA A:CYS1382 4.4 22.0 1.0
CE A:LYS1363 4.6 45.2 1.0
CB A:LYS1363 4.6 36.5 1.0
CA A:CYS1358 4.6 29.0 1.0
CB A:ALA1360 4.7 32.8 1.0
NZ A:LYS1363 4.7 56.7 1.0
C A:ALA1360 4.8 33.9 1.0
C A:CYS1361 4.8 28.1 1.0
N A:GLY1362 4.9 25.8 1.0
C A:CYS1382 4.9 26.7 1.0
O A:CYS1382 5.0 26.9 1.0
N A:LYS1363 5.0 30.5 1.0

Zinc binding site 3 out of 4 in 1joc

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Zinc binding site 3 out of 4 in the EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:43.6
occ:1.00
SG B:CYS1377 2.1 40.7 1.0
SG B:CYS1402 2.3 38.6 1.0
SG B:CYS1374 2.3 27.8 1.0
SG B:CYS1405 2.4 50.1 1.0
CB B:CYS1405 3.2 49.0 1.0
CB B:CYS1374 3.3 30.4 1.0
CB B:CYS1377 3.4 38.5 1.0
CB B:CYS1402 3.7 37.9 1.0
N B:CYS1377 3.9 32.6 1.0
N B:CYS1402 3.9 38.7 1.0
N B:CYS1405 4.3 49.5 1.0
CA B:CYS1377 4.3 33.5 1.0
CA B:CYS1405 4.4 46.5 1.0
CA B:CYS1402 4.4 40.1 1.0
CZ B:PHE1381 4.4 35.2 1.0
CE1 B:PHE1381 4.5 38.6 1.0
CB B:GLN1376 4.6 37.0 1.0
CA B:CYS1374 4.7 33.4 1.0
C B:GLN1376 4.8 31.7 1.0
O B:CYS1402 4.9 38.2 1.0
C B:VAL1401 5.0 36.4 1.0

Zinc binding site 4 out of 4 in 1joc

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Zinc binding site 4 out of 4 in the EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of EEA1 Homodimer of C-Terminal Fyve Domain Bound to Inositol 1,3-Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:56.5
occ:1.00
SG B:CYS1361 2.2 62.0 1.0
SG B:CYS1358 2.3 42.0 1.0
SG B:CYS1382 2.4 44.0 1.0
SG B:CYS1385 2.4 47.3 1.0
CB B:CYS1385 3.0 44.2 1.0
CB B:CYS1358 3.1 50.2 1.0
CB B:CYS1361 3.4 54.3 1.0
CB B:CYS1382 3.7 38.4 1.0
N B:CYS1361 3.8 52.9 1.0
N B:CYS1382 4.0 35.7 1.0
N B:CYS1385 4.1 43.5 1.0
CA B:CYS1385 4.2 43.4 1.0
CA B:CYS1361 4.2 55.9 1.0
CE B:LYS1363 4.3 55.1 1.0
CB B:LYS1363 4.4 52.8 1.0
CA B:CYS1382 4.4 38.0 1.0
NZ B:LYS1363 4.5 48.4 1.0
CB B:ALA1360 4.5 52.9 1.0
CA B:CYS1358 4.5 48.2 1.0
C B:ALA1360 4.7 53.8 1.0
CD B:LYS1363 4.7 49.8 1.0
O B:CYS1382 4.9 35.0 1.0
C B:CYS1361 4.9 58.1 1.0
CA B:ALA1360 5.0 53.0 1.0
C B:CYS1382 5.0 36.7 1.0

Reference:

J.J.Dumas, E.Merithew, E.Sudharshan, D.Rajamani, S.Hayes, D.Lawe, S.Corvera, D.G.Lambright. Multivalent Endosome Targeting By Homodimeric EEA1. Mol.Cell V. 8 947 2001.
ISSN: ISSN 1097-2765
PubMed: 11741531
DOI: 10.1016/S1097-2765(01)00385-9
Page generated: Wed Dec 16 02:53:58 2020

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