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Sodium in PDB 3k5i: Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide

Enzymatic activity of Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide

All present enzymatic activity of Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide:
4.1.1.21;

Protein crystallography data

The structure of Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide, PDB code: 3k5i was solved by J.B.Thoden, H.M.Holden, H.Paritala, S.M.Firestine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.500, 134.200, 98.500, 90.00, 105.60, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3k5i:

The structure of Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide (pdb code 3k5i). 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 N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide, PDB code: 3k5i:

Sodium binding site 1 out of 1 in 3k5i

Go back to Sodium Binding Sites List in 3k5i
Sodium binding site 1 out of 1 in the Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide


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 N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na384

b:37.1
occ:1.00
O A:HOH460 2.5 57.4 1.0
O A:GLN211 2.5 25.1 1.0
O A:HOH461 2.5 37.9 1.0
O A:HOH558 2.6 16.8 1.0
O A:HOH504 2.9 47.4 1.0
O A:HOH706 2.9 35.8 1.0
C A:GLN211 3.6 24.5 1.0
O A:HOH605 4.1 23.2 1.0
N A:GLN211 4.1 12.5 1.0
CE2 A:PHE186 4.3 10.3 1.0
CA A:GLN211 4.3 20.4 1.0
O A:HOH589 4.4 20.1 1.0
CZ A:PHE186 4.4 17.9 1.0
CB A:GLN211 4.4 39.4 1.0
OE1 A:GLU189 4.6 18.2 1.0
N A:GLU212 4.6 12.1 1.0
O2' A:ADP400 4.7 14.7 1.0
O A:HOH462 4.8 40.7 1.0
CG1 A:VAL210 4.8 82.9 1.0
CA A:GLU212 4.8 40.9 1.0
O A:HOH521 4.8 34.9 1.0

Reference:

J.B.Thoden, H.M.Holden, H.Paritala, S.M.Firestine. Structural and Functional Studies of Aspergillus Clavatus N(5)-Carboxyaminoimidazole Ribonucleotide Synthetase Biochemistry V. 49 752 2010.
ISSN: ISSN 0006-2960
PubMed: 20050602
DOI: 10.1021/BI901599U
Page generated: Tue Dec 15 06:16:01 2020

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