Magnesium 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:

Zinc (Zn) 2 atoms
Bromine (Br) 2 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of Eanb/Y353A Complex with Ergothioneine Covalent Linked with Persulfide CYS412, PDB code: 6ku2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ku2

Go back to Magnesium Binding Sites List in 6ku2
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502

b:27.2
occ:1.00
O A:ASP437 2.2 23.5 1.0
O A:THR414 2.2 24.6 1.0
O A:TRP216 2.2 23.3 1.0
OD1 A:ASN217 2.2 29.9 1.0
OD1 A:ASP437 2.3 25.7 1.0
O A:HOH716 2.7 26.8 1.0
C A:ASP437 2.9 23.2 1.0
C A:TRP216 3.2 22.8 1.0
C A:THR414 3.2 26.1 1.0
CG A:ASP437 3.2 21.5 1.0
CG A:ASN217 3.4 29.2 1.0
CA A:ASN217 3.5 25.3 1.0
N A:GLY438 3.6 24.8 1.0
N A:ASN217 3.7 24.0 1.0
CA A:ASP437 3.7 23.0 1.0
NH1 A:ARG266 3.8 25.6 1.0
CA A:GLY438 3.9 24.4 1.0
CA A:THR414 3.9 26.4 1.0
CB A:ASP437 3.9 23.0 1.0
CB A:ASN217 4.0 26.1 1.0
O A:HOH709 4.0 31.1 1.0
OD2 A:ASP437 4.1 18.7 1.0
N A:GLY415 4.2 25.2 1.0
C A:GLY438 4.2 28.3 1.0
O A:GLY438 4.3 28.1 1.0
CB A:THR414 4.3 27.2 1.0
O A:THR215 4.4 27.4 1.0
CA A:TRP216 4.4 23.5 1.0
ND2 A:ASN217 4.4 32.4 1.0
CA A:GLY415 4.4 27.1 1.0
CZ A:ARG266 4.5 23.9 1.0
NH2 A:ARG266 4.5 23.7 1.0
CB A:TRP216 4.5 22.8 1.0
C A:ASN217 4.7 27.3 1.0
O A:HOH650 4.8 19.9 1.0

Magnesium binding site 2 out of 2 in 6ku2

Go back to Magnesium Binding Sites List in 6ku2
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg503

b:32.3
occ:1.00
OD1 E:ASN217 2.2 29.2 1.0
O E:TRP216 2.2 35.6 1.0
OD1 E:ASP437 2.2 29.2 1.0
O E:THR414 2.2 27.6 1.0
O E:ASP437 2.2 30.4 1.0
O E:HOH682 2.4 26.3 1.0
C E:ASP437 3.0 30.4 1.0
C E:TRP216 3.1 33.3 1.0
CG E:ASP437 3.2 29.8 1.0
C E:THR414 3.2 29.4 1.0
CG E:ASN217 3.3 34.0 1.0
CA E:ASN217 3.5 32.1 1.0
N E:ASN217 3.6 32.8 1.0
N E:GLY438 3.7 31.4 1.0
CA E:ASP437 3.8 33.1 1.0
CA E:GLY438 3.9 29.7 1.0
NH1 E:ARG266 3.9 33.3 1.0
CA E:THR414 3.9 29.7 1.0
CB E:ASP437 3.9 31.3 1.0
CB E:ASN217 4.0 32.4 1.0
OD2 E:ASP437 4.1 27.6 1.0
O E:HOH634 4.1 29.8 1.0
C E:GLY438 4.2 30.6 1.0
O E:GLY438 4.2 26.3 1.0
N E:GLY415 4.2 29.2 1.0
CA E:TRP216 4.3 33.8 1.0
CB E:THR414 4.3 32.6 1.0
ND2 E:ASN217 4.4 36.1 1.0
O E:THR215 4.4 32.4 1.0
CB E:TRP216 4.4 34.1 1.0
CA E:GLY415 4.6 29.2 1.0
CZ E:ARG266 4.6 31.1 1.0
NH2 E:ARG266 4.6 30.6 1.0
C E:ASN217 4.7 33.3 1.0
O E:HOH674 4.8 27.6 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: Mon Jan 25 08:49:19 2021

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