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Sodium in PDB 4njh: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin

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

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

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin, PDB code: 4njh 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) 39.01 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 119.129, 119.129, 103.363, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.4

Other elements in 4njh:

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

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 and 6-Carboxy-5,6,7,8-Tetrahydropterin (pdb code 4njh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin, PDB code: 4njh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4njh

Go back to Sodium Binding Sites List in 4njh
Sodium binding site 1 out of 3 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


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 and 6-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:31.0
occ:1.00
 O A:HOH401 2.7 44.3 1.0
O A:HOH503 2.8 35.4 1.0
OG1 A:THR51 2.8 31.0 1.0
O A:HOH504 2.8 27.6 1.0
N5 A:2K8303 2.9 34.0 1.0
O6A A:2K8303 2.9 34.1 1.0
O4 A:2K8303 3.3 33.3 1.0
C6 A:2K8303 3.6 26.9 1.0
NH2 A:ARG27 3.6 25.1 1.0
OD1 A:ASP50 3.7 28.5 1.0
C6A A:2K8303 3.7 28.0 1.0
NH1 A:ARG27 3.9 21.1 1.0
C4A A:2K8303 3.9 29.5 1.0
C4 A:2K8303 4.0 29.4 1.0
CZ A:ARG27 4.0 23.4 1.0
CB A:THR51 4.0 30.9 1.0
O A:HOH604 4.1 56.1 1.0
CG2 A:THR51 4.2 25.1 1.0
CG A:ASP50 4.4 32.1 1.0
OD2 A:ASP50 4.4 30.3 1.0
CE A:SAM302 4.4 29.8 1.0
O A:HOH484 4.6 33.9 1.0
O A:HOH505 4.9 28.2 1.0
CA A:THR51 4.9 29.4 1.0
O6B A:2K8303 4.9 23.8 1.0
NE2 A:HIS204 4.9 21.5 1.0

Sodium binding site 2 out of 3 in 4njh

Go back to Sodium Binding Sites List in 4njh
Sodium binding site 2 out of 3 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:31.8
occ:1.00
 O B:HOH421 2.7 29.6 1.0
O B:HOH406 2.8 38.2 1.0
OG1 B:THR51 2.8 27.1 1.0
O B:HOH424 2.9 35.0 1.0
N5 B:2K8303 2.9 37.6 1.0
O6B B:2K8303 3.0 32.2 1.0
O4 B:2K8303 3.4 28.9 1.0
NH2 B:ARG27 3.6 23.0 1.0
C6 B:2K8303 3.6 27.5 1.0
OD1 B:ASP50 3.7 33.3 1.0
C6A B:2K8303 3.7 26.8 1.0
NH1 B:ARG27 3.9 21.3 1.0
C4A B:2K8303 3.9 30.0 1.0
O B:HOH572 4.0 53.1 1.0
C4 B:2K8303 4.0 30.4 1.0
CZ B:ARG27 4.0 25.6 1.0
CB B:THR51 4.0 30.6 1.0
CG2 B:THR51 4.2 24.7 1.0
OD2 B:ASP50 4.4 38.1 1.0
CG B:ASP50 4.4 35.6 1.0
CE B:SAM302 4.4 29.6 1.0
O B:HOH484 4.6 32.9 1.0
CA B:THR51 4.9 25.2 1.0
O B:HOH422 4.9 27.4 1.0
NE2 B:HIS204 5.0 24.9 1.0
O6A B:2K8303 5.0 27.8 1.0

Sodium binding site 3 out of 3 in 4njh

Go back to Sodium Binding Sites List in 4njh
Sodium binding site 3 out of 3 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet and 6-Carboxy-5,6,7,8-Tetrahydropterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na306

b:25.5
occ:1.00
 O B:HOH554 2.4 25.2 1.0
O B:HOH545 2.5 35.7 1.0
O B:HOH544 2.7 30.6 1.0
O B:GLN154 2.7 22.1 1.0
O B:HOH553 2.8 21.3 1.0
O B:HOH455 3.3 30.6 1.0
O B:HOH567 3.5 39.8 1.0
C B:GLN154 3.7 21.9 1.0
CB B:GLN157 4.1 20.7 1.0
N B:GLN154 4.2 20.0 1.0
CA B:ASP155 4.3 19.0 1.0
OE1 B:GLN157 4.3 26.3 1.0
N B:ASP155 4.4 18.4 1.0
O B:HOH485 4.5 41.1 1.0
N B:GLN157 4.5 21.4 1.0
CB B:PRO153 4.6 20.2 1.0
CA B:GLN154 4.6 21.0 1.0
C B:ASP155 4.7 20.5 1.0
O B:HOH494 4.7 23.9 1.0
O B:GLN157 4.8 23.4 1.0
N B:ASN156 4.8 22.2 1.0
O B:HOH496 4.8 28.4 1.0
CA B:GLN157 4.8 19.8 1.0
CA B:PRO153 5.0 18.6 1.0
C B:PRO153 5.0 22.4 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 17:13:10 2024

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