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Zinc in PDB 6ku2: The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412

Protein crystallography data

The structure of The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412, PDB code: 6ku2 was solved by L.Wu, P.H.Liu, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.34 / 2.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.683, 88.240, 90.771, 90.00, 90.35, 90.00
R / Rfree (%) 17.1 / 22.8

Other elements in 6ku2:

The structure of The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Bromine (Br) 2 atoms
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412 (pdb code 6ku2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412, PDB code: 6ku2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6ku2

Go back to Zinc Binding Sites List in 6ku2
Zinc binding site 1 out of 2 in the The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:30.5
occ:0.57
O A:HOH705 1.7 26.1 1.0
NE2 A:HIS391 1.8 25.7 1.0
NE2 A:HIS74 2.0 21.8 1.0
OD2 A:ASP150 2.2 31.5 1.0
CE1 A:HIS391 2.7 22.9 1.0
CD2 A:HIS391 2.9 22.5 1.0
CE1 A:HIS74 3.0 22.9 1.0
CD2 A:HIS74 3.0 22.6 1.0
CG A:ASP150 3.1 29.2 1.0
CB A:ASP150 3.3 26.6 1.0
OH A:TYR390 3.4 22.8 1.0
ND1 A:HIS391 3.8 22.5 1.0
CG A:HIS391 3.9 22.2 1.0
ND1 A:HIS74 4.1 22.4 1.0
CZ A:TYR390 4.1 23.5 1.0
CG A:HIS74 4.1 21.9 1.0
OD1 A:ASP150 4.2 32.2 1.0
OH A:TYR61 4.5 21.6 1.0
N A:GLY77 4.5 23.7 1.0
CA A:ASP150 4.5 24.6 1.0
C A:ASP150 4.6 24.2 1.0
CE1 A:TYR390 4.7 22.8 1.0
CE2 A:TYR390 4.8 22.4 1.0
N A:ARG151 4.9 25.2 1.0
O A:ALA78 4.9 23.3 1.0
O A:ASP150 5.0 22.2 1.0

Zinc binding site 2 out of 2 in 6ku2

Go back to Zinc Binding Sites List in 6ku2
Zinc binding site 2 out of 2 in the The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn508

b:34.7
occ:0.61
O E:HOH644 2.0 31.3 1.0
NE2 E:HIS391 2.0 34.6 1.0
NE2 E:HIS74 2.0 27.2 1.0
OD2 E:ASP150 2.3 35.5 1.0
CE1 E:HIS391 2.9 30.8 1.0
CE1 E:HIS74 3.0 25.4 1.0
CD2 E:HIS74 3.0 25.2 1.0
CD2 E:HIS391 3.1 31.2 1.0
CG E:ASP150 3.1 31.2 1.0
CB E:ASP150 3.2 29.7 1.0
OH E:TYR390 3.4 31.8 1.0
ND1 E:HIS391 4.0 32.5 1.0
ND1 E:HIS74 4.1 24.1 1.0
CG E:HIS391 4.1 31.7 1.0
CZ E:TYR390 4.1 29.9 1.0
OD1 E:ASP150 4.2 32.0 1.0
CG E:HIS74 4.2 22.8 1.0
CA E:ASP150 4.4 27.5 1.0
N E:GLY77 4.4 28.5 1.0
OH E:TYR61 4.5 23.0 1.0
C E:ASP150 4.5 25.2 1.0
CE1 E:TYR390 4.8 29.9 1.0
CE2 E:TYR390 4.8 30.4 1.0
O E:HOH659 4.9 32.2 1.0
O E:ALA78 4.9 37.8 1.0
O E:ASP150 4.9 25.7 1.0
N E:ARG151 4.9 25.8 1.0

Reference:

R.Cheng, L.Wu, R.Lai, C.Peng, N.Naowarojna, W.Hu, X.Li, S.A.Whelan, N.Lee, J.Lopez, C.Zhao, Y.Yong, J.Xue, X.Jiang, M.W.Grinstaff, Z.Deng, J.Chen, Q.Cui, J.H.Zhou, P.Liu. Single-Step Replacement of An Unreactive C-H Bond By A C-S Bond Using Polysulfide As the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis Acs Catalysis V. 10 8981 2020.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.0C01809
Page generated: Wed Dec 16 12:10:10 2020

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