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Magnesium in PDB 4nji: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+

Enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+:
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+, PDB code: 4nji was solved by D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.89 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.126, 119.126, 104.310, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18

Other elements in 4nji:

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ (pdb code 4nji). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+, PDB code: 4nji:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4nji

Go back to Magnesium Binding Sites List in 4nji
Magnesium binding site 1 out of 2 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:52.1
occ:1.00
 O A:HOH424 2.4 56.3 1.0
O A:HOH425 2.8 38.3 1.0
O6A A:2K8303 2.9 47.4 1.0
OG1 A:THR51 2.9 47.8 1.0
N5 A:2K8303 2.9 50.9 1.0
O4 A:2K8303 2.9 48.1 1.0
O A:HOH426 3.1 44.6 1.0
NH2 A:ARG27 3.6 34.1 1.0
C4 A:2K8303 3.7 46.9 1.0
C6A A:2K8303 3.7 45.1 1.0
C6 A:2K8303 3.8 47.9 1.0
OD1 A:ASP50 3.8 41.9 1.0
C4A A:2K8303 3.8 47.5 1.0
NH1 A:ARG27 3.9 35.1 1.0
CZ A:ARG27 4.0 36.4 1.0
CB A:THR51 4.2 46.0 1.0
O A:HOH473 4.4 46.4 1.0
CG2 A:THR51 4.4 45.1 1.0
CG A:ASP50 4.5 40.8 1.0
OD2 A:ASP50 4.5 39.1 1.0
CE A:SAM302 4.8 39.5 1.0
NE2 A:HIS204 4.8 35.3 1.0
O6B A:2K8303 4.9 40.5 1.0
CA A:THR51 4.9 41.1 1.0
O A:HOH439 4.9 41.3 1.0

Magnesium binding site 2 out of 2 in 4nji

Go back to Magnesium Binding Sites List in 4nji
Magnesium binding site 2 out of 2 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+


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 Quee From Burkholderia Multivorans in Complex with Adomet, 6-Carboxy-5,6,7,8-Tetrahydropterin, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:59.0
occ:1.00
 O B:HOH421 2.7 43.1 1.0
OG1 B:THR51 2.7 40.8 1.0
O B:HOH422 2.8 52.3 1.0
N5 B:2K8303 2.9 48.9 1.0
O4 B:2K8303 2.9 46.4 1.0
O6B B:2K8303 3.0 52.6 1.0
O B:HOH423 3.2 47.1 1.0
NH2 B:ARG27 3.5 34.9 1.0
C4 B:2K8303 3.7 46.2 1.0
C4A B:2K8303 3.8 46.9 1.0
C6 B:2K8303 3.8 47.4 1.0
C6A B:2K8303 3.8 46.6 1.0
NH1 B:ARG27 3.8 34.7 1.0
OD1 B:ASP50 3.9 45.3 1.0
CZ B:ARG27 3.9 37.9 1.0
CB B:THR51 4.0 43.0 1.0
CG2 B:THR51 4.3 40.8 1.0
O B:HOH467 4.3 44.5 1.0
CG B:ASP50 4.5 45.7 1.0
OD2 B:ASP50 4.5 46.9 1.0
CE B:SAM302 4.7 44.5 1.0
CA B:THR51 4.8 39.7 1.0
O B:HOH445 4.8 41.8 1.0
NE B:ARG27 5.0 35.5 1.0
O B:ASP50 5.0 42.3 1.0

Reference:

D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan. Radical Sam Enzyme Quee Defines A New Minimal Core Fold and Metal-Dependent Mechanism. Nat.Chem.Biol. V. 10 106 2014.
ISSN: ISSN 1552-4450
PubMed: 24362703
DOI: 10.1038/NCHEMBIO.1426
Page generated: Mon Aug 19 23:35:57 2024

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