Magnesium in PDB 6h99: Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form.

Protein crystallography data

The structure of Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form., PDB code: 6h99 was solved by F.Leisinger, R.Burn, M.Meury, P.Lukat, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.54 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.760, 43.183, 88.740, 90.00, 108.46, 90.00
R / Rfree (%) 16.3 / 19.5

Other elements in 6h99:

The structure of Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form. also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form. (pdb code 6h99). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form., PDB code: 6h99:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6h99

Go back to Magnesium Binding Sites List in 6h99
Magnesium binding site 1 out of 4 in the Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:12.4
occ:1.00
O A:ASP437 2.2 11.3 1.0
O A:THR414 2.3 13.5 1.0
OD1 A:ASN217 2.3 12.8 1.0
O A:TRP216 2.3 11.0 1.0
O A:HOH835 2.5 12.0 1.0
OD1 A:ASP437 2.6 12.0 1.0
C A:ASP437 3.0 11.6 1.0
C A:TRP216 3.2 13.3 1.0
C A:THR414 3.3 11.2 1.0
CG A:ASP437 3.4 10.5 1.0
CG A:ASN217 3.5 15.7 1.0
CA A:ASN217 3.5 10.3 1.0
N A:ASN217 3.7 11.1 1.0
NH2 A:ARG266 3.8 11.5 1.0
N A:GLY438 3.8 11.4 1.0
CA A:THR414 3.8 10.2 1.0
CA A:ASP437 3.9 10.8 1.0
CA A:GLY438 3.9 12.9 1.0
CB A:ASP437 4.1 10.1 1.0
CB A:ASN217 4.1 11.8 1.0
CB A:THR414 4.1 16.2 1.0
C A:GLY438 4.2 15.0 1.0
O A:GLY438 4.2 13.2 1.0
O A:HOH627 4.2 17.0 1.0
OD2 A:ASP437 4.2 12.1 1.0
N A:GLY415 4.3 11.2 1.0
CB A:TRP216 4.3 11.9 1.0
CA A:TRP216 4.4 11.7 1.0
ND2 A:ASN217 4.6 25.7 1.0
CZ A:ARG266 4.6 13.6 1.0
CA A:GLY415 4.6 11.7 1.0
O A:THR215 4.6 13.7 1.0
NH1 A:ARG266 4.6 12.3 1.0
O A:HOH754 4.8 11.4 1.0
C A:ASN217 4.8 11.4 1.0
OG1 A:THR414 5.0 20.1 1.0
N A:GLY439 5.0 9.8 1.0

Magnesium binding site 2 out of 4 in 6h99

Go back to Magnesium Binding Sites List in 6h99
Magnesium binding site 2 out of 4 in the Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:25.6
occ:1.00
OG1 A:THR305 2.7 23.9 1.0
O A:LYS303 2.9 17.9 1.0
N A:THR305 3.4 16.3 1.0
CB A:THR305 3.6 21.1 1.0
O A:HOH924 3.6 30.4 1.0
C A:LYS303 3.8 17.4 1.0
C A:THR304 3.8 17.1 1.0
CA A:THR304 3.9 13.6 1.0
CA A:THR305 4.0 15.9 1.0
N A:THR304 4.3 15.4 1.0
O A:HOH648 4.6 32.9 1.0
O A:THR304 4.7 22.5 1.0
CG2 A:THR305 4.9 28.4 1.0
CA A:LYS303 5.0 17.3 1.0

Magnesium binding site 3 out of 4 in 6h99

Go back to Magnesium Binding Sites List in 6h99
Magnesium binding site 3 out of 4 in the Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:28.1
occ:1.00
O A:HOH669 2.0 26.2 1.0
O A:HOH802 2.1 28.9 1.0
O A:HOH606 2.1 32.0 1.0
O A:HOH1010 2.1 33.1 1.0
O A:HOH785 2.1 26.1 1.0
OE1 A:GLU172 3.8 42.6 1.0
O A:HOH805 4.0 23.4 1.0
O A:HOH853 4.1 29.3 1.0
OD1 A:ASP177 4.1 26.8 1.0
O A:TYR176 4.2 22.2 1.0
O A:HOH1069 4.2 35.0 1.0
O A:ILE173 4.3 21.6 1.0
O A:HOH1012 4.7 33.8 1.0
O A:HOH619 4.9 32.5 1.0
CD A:GLU172 5.0 40.5 0.4
CG A:ASP177 5.0 27.6 1.0

Magnesium binding site 4 out of 4 in 6h99

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Magnesium binding site 4 out of 4 in the Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Anaerobic Ergothioneine Biosynthesis Enzyme From Chlorobium Limicola in Persulfide Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:33.8
occ:1.00
O A:HOH847 2.9 13.4 1.0
OH A:TYR355 3.0 35.7 1.0
CE2 A:TYR188 3.7 11.6 1.0
CD2 A:TYR188 3.8 9.7 1.0
CZ A:TYR355 3.8 22.1 1.0
CE1 A:TYR375 3.9 18.0 1.0
CE1 A:TYR355 3.9 23.8 1.0
CA A:GLY256 3.9 10.1 1.0
N A:GLY256 4.2 11.3 1.0
CZ A:TYR188 4.5 12.7 1.0
OH A:TYR375 4.6 26.6 1.0
CG A:TYR188 4.7 11.1 1.0
O A:HOH666 4.7 20.6 1.0
CD1 A:TYR375 4.7 21.5 1.0
CZ A:TYR375 4.7 18.3 1.0
O A:HOH782 4.7 16.0 1.0
C A:GLY256 4.9 12.9 1.0
CZ2 A:TRP416 4.9 10.7 1.0
CE2 A:TRP416 5.0 11.6 1.0
OH A:TYR188 5.0 13.1 1.0

Reference:

F.Leisinger, R.Burn, M.Meury, P.Lukat, F.P.Seebeck. Structural and Mechanistic Basis For Anaerobic Ergothioneine Biosynthesis. J.Am.Chem.Soc. V. 141 6906 2019.
ISSN: ESSN 1520-5126
PubMed: 30943021
DOI: 10.1021/JACS.8B12596
Page generated: Mon Dec 14 22:48:39 2020

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