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Zinc in PDB 3kyd: Human Sumo E1~SUMO1-Amp Tetrahedral Intermediate Mimic

Protein crystallography data

The structure of Human Sumo E1~SUMO1-Amp Tetrahedral Intermediate Mimic, PDB code: 3kyd was solved by C.D.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.61
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.717, 115.608, 90.837, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 28.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Sumo E1~SUMO1-Amp Tetrahedral Intermediate Mimic (pdb code 3kyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Human Sumo E1~SUMO1-Amp Tetrahedral Intermediate Mimic, PDB code: 3kyd:

Zinc binding site 1 out of 1 in 3kyd

Go back to Zinc Binding Sites List in 3kyd
Zinc binding site 1 out of 1 in the Human Sumo E1~SUMO1-Amp Tetrahedral Intermediate Mimic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Sumo E1~SUMO1-Amp Tetrahedral Intermediate Mimic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn550

b:50.4
occ:1.00
SG B:CYS158 2.3 23.3 1.0
SG B:CYS161 2.3 25.4 1.0
SG B:CYS444 2.3 24.1 1.0
SG B:CYS441 2.3 23.2 1.0
CB B:CYS441 3.2 23.8 1.0
CB B:CYS158 3.3 23.3 1.0
CB B:CYS444 3.3 24.2 1.0
CB B:CYS161 3.5 24.9 1.0
N B:CYS158 3.6 23.4 1.0
CA B:CYS161 3.6 24.9 1.0
N B:CYS161 3.6 24.5 1.0
N B:CYS444 3.8 24.2 1.0
CA B:CYS158 3.9 23.4 1.0
CA B:CYS444 4.1 24.3 1.0
C B:GLU160 4.2 24.2 1.0
O B:CYS158 4.3 23.7 1.0
C B:CYS158 4.4 23.6 1.0
CA B:CYS441 4.6 23.8 1.0
O B:GLU160 4.7 24.1 1.0
N B:GLU160 4.7 24.0 1.0
C B:GLU157 4.8 23.3 1.0
CB B:VAL443 4.8 24.1 1.0
CA B:GLU160 4.9 24.2 1.0
C B:VAL443 4.9 24.1 1.0
C B:CYS444 4.9 24.5 1.0

Reference:

S.K.Olsen, A.D.Capili, X.Lu, D.S.Tan, C.D.Lima. Active Site Remodelling Accompanies Thioester Bond Formation in the Sumo E1. Nature V. 463 906 2010.
ISSN: ISSN 0028-0836
PubMed: 20164921
DOI: 10.1038/NATURE08765
Page generated: Wed Dec 16 04:31:23 2020

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