Zinc in PDB 6mgq: Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014

Protein crystallography data

The structure of Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014, PDB code: 6mgq was solved by L.J.Stern, Z.Maben, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.06 / 2.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.140, 234.700, 132.280, 90.00, 93.12, 90.00
R / Rfree (%) 19.8 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014 (pdb code 6mgq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014, PDB code: 6mgq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6mgq

Go back to Zinc Binding Sites List in 6mgq
Zinc binding site 1 out of 3 in the Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:25.8
occ:1.00
NE2 A:HIS353 2.0 29.9 1.0
OE1 A:GLU376 2.1 51.1 1.0
O13 D:2X01 2.2 51.2 0.6
NE2 A:HIS357 2.3 32.8 1.0
O12 D:2X01 2.3 36.0 0.6
OE2 A:GLU376 2.6 59.9 1.0
P11 D:2X01 2.7 46.6 0.6
CD A:GLU376 2.7 52.3 1.0
CE1 A:HIS353 2.9 29.3 1.0
CD2 A:HIS357 2.9 33.2 1.0
CD2 A:HIS353 3.1 25.1 1.0
CE1 A:HIS357 3.1 35.8 1.0
N10 D:2X01 3.3 51.6 0.6
C3 D:2X01 3.6 49.8 0.6
CG A:HIS357 4.0 33.0 1.0
ND1 A:HIS357 4.0 34.2 1.0
ND1 A:HIS353 4.0 24.2 1.0
CG A:HIS353 4.1 22.8 1.0
CG A:GLU376 4.2 41.1 1.0
OE2 A:GLU320 4.2 59.8 1.0
OE1 A:GLU320 4.3 61.8 1.0
CB A:ALA379 4.3 20.5 1.0
CD A:GLU320 4.4 57.8 1.0
C6 D:7GA2 4.4 44.4 0.6
C8 D:7GA2 4.4 46.1 0.6
OE2 A:GLU354 4.5 66.6 1.0
C1 D:2X01 4.6 53.8 0.6
CA A:GLU376 4.6 22.1 1.0
CA D:7GA2 4.7 50.7 0.6
C6 D:2X01 4.7 54.6 0.6
CB A:GLU376 4.8 39.0 1.0

Zinc binding site 2 out of 3 in 6mgq

Go back to Zinc Binding Sites List in 6mgq
Zinc binding site 2 out of 3 in the Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:36.3
occ:1.00
NE2 B:HIS353 1.9 60.1 1.0
NE2 B:HIS357 2.0 47.1 1.0
OE1 B:GLU376 2.1 61.3 1.0
O12 E:2X01 2.2 75.8 0.6
O13 E:2X01 2.4 61.5 0.6
CD2 B:HIS357 2.5 42.2 1.0
OE2 B:GLU376 2.5 58.0 1.0
CD B:GLU376 2.7 48.5 1.0
P11 E:2X01 2.9 70.4 0.6
CE1 B:HIS353 2.9 57.1 1.0
CD2 B:HIS353 2.9 54.7 1.0
CE1 B:HIS357 3.3 41.6 1.0
CG B:HIS357 3.8 41.2 1.0
C8 E:7GA2 3.8 49.3 0.6
N10 E:2X01 3.9 68.8 0.6
ND1 B:HIS353 4.0 52.3 1.0
CG B:HIS353 4.1 45.6 1.0
C3 E:2X01 4.1 61.9 0.6
ND1 B:HIS357 4.1 41.6 1.0
CG B:GLU376 4.1 43.5 1.0
CB B:ALA379 4.3 30.1 1.0
OE2 B:GLU354 4.4 53.3 1.0
OE1 B:GLU320 4.4 69.7 1.0
C6 E:7GA2 4.4 68.5 0.6
CA B:GLU376 4.5 37.8 1.0
CD B:GLU320 4.5 67.5 1.0
OE1 B:GLU354 4.5 58.9 1.0
OE2 B:GLU320 4.5 73.2 1.0
CA E:7GA2 4.6 61.0 0.6
CB B:GLU376 4.7 40.8 1.0
CD B:GLU354 4.9 50.8 1.0
C9 E:7GA2 5.0 45.9 0.6

Zinc binding site 3 out of 3 in 6mgq

Go back to Zinc Binding Sites List in 6mgq
Zinc binding site 3 out of 3 in the Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Er Aminopeptidase 1 Bound to 10MER Phosphinic Inhibitor DG014 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:25.9
occ:1.00
NE2 C:HIS353 2.0 28.9 1.0
OE1 C:GLU376 2.0 35.5 1.0
NE2 C:HIS357 2.1 26.3 1.0
O13 F:2X01 2.3 74.3 0.6
O12 F:2X01 2.4 86.6 0.6
OE2 C:GLU376 2.6 38.0 1.0
CD C:GLU376 2.7 33.5 1.0
CD2 C:HIS357 2.7 22.6 1.0
P11 F:2X01 2.8 76.6 0.6
CD2 C:HIS353 2.9 28.3 1.0
CE1 C:HIS353 3.1 29.1 1.0
CE1 C:HIS357 3.2 25.6 1.0
N10 F:2X01 3.7 59.1 0.6
C3 F:2X01 3.9 60.3 0.6
C8 F:7GA2 3.9 60.8 0.6
CG C:HIS357 4.0 25.1 1.0
OE1 C:GLU320 4.1 58.5 1.0
CG C:HIS353 4.1 25.0 1.0
ND1 C:HIS353 4.1 26.7 1.0
CG C:GLU376 4.2 33.8 1.0
ND1 C:HIS357 4.2 24.2 1.0
C6 F:7GA2 4.4 69.8 0.6
CD C:GLU320 4.4 53.1 1.0
OE2 C:GLU354 4.5 52.2 1.0
CA F:7GA2 4.6 67.5 0.6
CA C:GLU376 4.6 30.6 1.0
CB C:ALA379 4.6 25.2 1.0
OE2 C:GLU320 4.6 58.6 1.0
OE1 C:GLU354 4.8 44.6 1.0
CB C:GLU376 4.8 34.3 1.0
C9 F:7GA2 4.8 59.8 0.6
C1 F:2X01 4.9 56.0 0.6

Reference:

L.J.Stern, Z.Maben. Conformational Transitions Drive the ERAP1 Catalytic Cycle and Explain the Effect of Disease-Associated Polymorphism. To Be Published.
Page generated: Wed Dec 16 12:19:36 2020

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