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Zinc in PDB 3qnf: Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1

Protein crystallography data

The structure of Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1, PDB code: 3qnf was solved by M.Vollmar, G.Kochan, T.Krojer, D.Harvey, A.Chaikuad, C.Allerston, J.R.C.Muniz, J.Raynor, E.Ugochukwu, G.Berridge, B.P.Wordsworth, F.Vondelft, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Kavanagh, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.246, 132.816, 233.687, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 (pdb code 3qnf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1, PDB code: 3qnf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3qnf

Go back to Zinc Binding Sites List in 3qnf
Zinc binding site 1 out of 3 in the Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1


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 Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5000

b:26.9
occ:1.00
OE2 A:GLU376 2.0 17.7 1.0
NE2 A:HIS353 2.1 18.3 1.0
NE2 A:HIS357 2.1 29.4 1.0
OE1 A:GLU376 2.3 40.4 1.0
CD A:GLU376 2.4 25.7 1.0
CD2 A:HIS357 2.8 20.7 1.0
CD2 A:HIS353 3.0 17.3 1.0
CE1 A:HIS353 3.1 29.3 1.0
CE1 A:HIS357 3.2 36.6 1.0
OE2 A:GLU320 3.5 20.2 1.0
OE1 A:GLU320 3.7 47.1 1.0
CD A:GLU320 3.9 34.9 1.0
CG A:GLU376 3.9 24.5 1.0
CG A:HIS357 4.0 23.1 1.0
ND1 A:HIS357 4.1 23.6 1.0
CG A:HIS353 4.2 17.1 1.0
ND1 A:HIS353 4.2 28.8 1.0
CB A:ALA379 4.3 25.8 1.0
OE2 A:GLU354 4.6 38.1 1.0
CA A:GLU376 4.6 25.1 1.0
CB A:GLU376 4.7 25.1 1.0
OE1 A:GLU354 4.7 38.2 1.0

Zinc binding site 2 out of 3 in 3qnf

Go back to Zinc Binding Sites List in 3qnf
Zinc binding site 2 out of 3 in the Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1


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 Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5000

b:25.3
occ:1.00
OE2 B:GLU376 2.0 17.6 1.0
NE2 B:HIS353 2.1 27.4 1.0
NE2 B:HIS357 2.1 29.2 1.0
OE1 B:GLU376 2.3 40.4 1.0
CD B:GLU376 2.4 25.7 1.0
CD2 B:HIS357 2.9 20.7 1.0
CD2 B:HIS353 3.0 22.8 1.0
CE1 B:HIS353 3.1 30.5 1.0
CE1 B:HIS357 3.2 36.5 1.0
OE2 B:GLU320 3.7 20.3 1.0
OE1 B:GLU320 3.9 47.0 1.0
CG B:GLU376 3.9 24.5 1.0
CD B:GLU320 4.1 34.9 1.0
CG B:HIS357 4.1 23.0 1.0
CG B:HIS353 4.2 19.1 1.0
CB B:ALA379 4.2 25.6 1.0
ND1 B:HIS353 4.2 28.2 1.0
ND1 B:HIS357 4.2 23.6 1.0
OE2 B:GLU354 4.4 43.6 1.0
CA B:GLU376 4.6 25.1 1.0
CB B:GLU376 4.6 25.0 1.0
OE1 B:GLU354 4.7 23.7 1.0
CD B:GLU354 4.9 25.4 1.0

Zinc binding site 3 out of 3 in 3qnf

Go back to Zinc Binding Sites List in 3qnf
Zinc binding site 3 out of 3 in the Crystal Structure of the Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1


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 Open State of Human Endoplasmic Reticulum Aminopeptidase 1 ERAP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn5000

b:32.0
occ:1.00
OE2 C:GLU376 2.0 17.7 1.0
NE2 C:HIS353 2.1 31.5 1.0
NE2 C:HIS357 2.1 29.5 1.0
OE1 C:GLU376 2.2 40.4 1.0
CD C:GLU376 2.4 25.7 1.0
CD2 C:HIS357 2.9 20.6 1.0
CD2 C:HIS353 3.0 30.5 1.0
CE1 C:HIS353 3.1 30.4 1.0
CE1 C:HIS357 3.2 36.9 1.0
OE2 C:GLU320 3.5 20.3 1.0
OE1 C:GLU320 3.6 47.1 1.0
CD C:GLU320 3.9 35.0 1.0
CG C:GLU376 3.9 24.5 1.0
CG C:HIS357 4.0 23.1 1.0
ND1 C:HIS357 4.1 23.7 1.0
CG C:HIS353 4.2 27.1 1.0
ND1 C:HIS353 4.2 26.9 1.0
CB C:ALA379 4.3 25.9 1.0
OE2 C:GLU354 4.6 33.1 1.0
CB C:GLU376 4.7 25.1 1.0
CA C:GLU376 4.7 25.3 1.0
OE1 C:GLU354 4.8 28.1 1.0

Reference:

G.Kochan, T.Krojer, D.Harvey, R.Fischer, L.Chen, M.Vollmar, F.Von Delft, K.L.Kavanagh, M.A.Brown, P.Bowness, P.Wordsworth, B.M.Kessler, U.Oppermann. Crystal Structures of the Endoplasmic Reticulum Aminopeptidase-1 (ERAP1) Reveal the Molecular Basis For N-Terminal Peptide Trimming. Proc.Natl.Acad.Sci.Usa V. 108 7745 2011.
ISSN: ISSN 0027-8424
PubMed: 21508329
DOI: 10.1073/PNAS.1101262108
Page generated: Wed Dec 16 04:45:46 2020

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