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Sodium 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:

Magnesium (Mg) 2 atoms
Iron (Fe) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 4nji

Go back to Sodium Binding Sites List in 4nji
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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
B:Na306

b:38.8
occ:1.00
 O B:HOH448 2.4 47.5 1.0
O B:HOH480 2.6 47.4 1.0
O B:GLN154 2.7 36.2 1.0
O B:HOH408 2.9 34.5 1.0
O B:HOH435 3.3 34.5 1.0
C B:GLN154 3.7 36.1 1.0
CB B:GLN157 4.2 31.7 1.0
N B:GLN154 4.3 32.5 1.0
CA B:ASP155 4.3 34.0 1.0
N B:ASP155 4.3 32.9 1.0
O B:HOH508 4.5 43.8 1.0
OE1 B:GLN157 4.6 40.8 1.0
CB B:PRO153 4.6 34.7 1.0
N B:GLN157 4.6 35.0 1.0
CA B:GLN154 4.6 33.5 1.0
O B:HOH506 4.7 35.5 1.0
C B:ASP155 4.7 35.9 1.0
O B:HOH507 4.8 42.7 1.0
O B:GLN157 4.8 32.9 1.0
N B:ASN156 4.9 36.2 1.0
CA B:GLN157 5.0 31.0 1.0
CA B:PRO153 5.0 31.2 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 Oct 7 17:13:18 2024

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