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Zinc in PDB 1y8q: Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex

Protein crystallography data

The structure of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex, PDB code: 1y8q was solved by L.M.Lois, C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.245, 116.667, 106.078, 90.00, 112.67, 90.00
R / Rfree (%) 20.8 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex (pdb code 1y8q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex, PDB code: 1y8q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y8q

Go back to Zinc Binding Sites List in 1y8q
Zinc binding site 1 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn642

b:26.1
occ:1.00
SG B:CYS444 2.1 26.5 1.0
SG B:CYS161 2.3 26.0 1.0
SG B:CYS441 2.3 28.5 1.0
SG B:CYS158 2.4 25.3 1.0
CB B:CYS441 3.1 27.6 1.0
CB B:CYS444 3.2 26.8 1.0
CB B:CYS158 3.2 23.3 1.0
CB B:CYS161 3.4 26.3 1.0
N B:CYS161 3.5 27.8 1.0
CA B:CYS161 3.5 32.6 1.0
N B:CYS444 3.7 27.0 1.0
N B:CYS158 3.8 23.6 1.0
CA B:CYS158 4.0 25.4 1.0
CA B:CYS444 4.0 27.1 1.0
C B:GLU160 4.1 28.0 1.0
O B:HOH850 4.5 28.9 1.0
C B:CYS158 4.5 25.9 1.0
CA B:CYS441 4.5 28.8 1.0
O B:GLU160 4.7 28.5 1.0
O B:CYS158 4.7 30.6 1.0
CB B:VAL443 4.8 27.8 1.0
N B:GLU160 4.8 27.3 1.0
O B:HOH822 4.8 31.8 1.0
C B:VAL443 4.8 27.3 1.0
CA B:GLU160 4.8 29.1 1.0
C B:CYS444 4.8 27.4 1.0
C B:GLU157 4.9 26.8 1.0
C B:CYS161 5.0 38.2 1.0

Zinc binding site 2 out of 2 in 1y8q

Go back to Zinc Binding Sites List in 1y8q
Zinc binding site 2 out of 2 in the Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sumo E1 Activating Enzyme SAE1-SAE2-Mg-Atp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn642

b:31.7
occ:1.00
SG D:CYS441 2.2 34.4 1.0
SG D:CYS444 2.2 34.0 1.0
SG D:CYS158 2.3 33.0 1.0
SG D:CYS161 2.3 37.3 1.0
CB D:CYS441 3.1 39.1 1.0
CB D:CYS444 3.3 33.5 1.0
N D:CYS161 3.5 34.8 1.0
CB D:CYS161 3.5 35.1 1.0
CB D:CYS158 3.5 33.2 1.0
CA D:CYS161 3.6 37.6 1.0
N D:CYS444 3.7 35.6 1.0
N D:CYS158 3.8 35.1 1.0
CA D:CYS444 4.1 37.0 1.0
CA D:CYS158 4.1 35.0 1.0
C D:GLU160 4.2 34.5 1.0
O D:CYS158 4.5 35.9 1.0
C D:CYS158 4.5 35.2 1.0
O D:HOH857 4.6 28.6 1.0
CA D:CYS441 4.6 40.6 1.0
CB D:VAL443 4.6 33.6 1.0
N D:GLU160 4.8 36.1 1.0
O D:GLU160 4.8 32.7 1.0
C D:VAL443 4.8 36.5 1.0
CA D:GLU160 4.8 35.0 1.0
C D:GLU157 4.9 36.7 1.0
C D:CYS444 4.9 37.6 1.0
O D:HOH985 4.9 37.4 1.0
O D:ASN438 5.0 45.6 1.0

Reference:

L.M.Lois, C.D.Lima. Structures of the Sumo E1 Provide Mechanistic Insights Into Sumo Activation and E2 Recruitment to E1 Embo J. V. 24 439 2005.
ISSN: ISSN 0261-4189
PubMed: 15660128
DOI: 10.1038/SJ.EMBOJ.7600552
Page generated: Sat Sep 26 00:28:55 2020
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