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Magnesium 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:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of N5-Carboxyaminoimidazole Synthase From Aspergillus Clavatus in Complex with Adp and 5-Aminoimadazole Ribonucleotide, PDB code: 3k5i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3k5i

Go back to Magnesium Binding Sites List in 3k5i
Magnesium binding site 1 out of 4 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 Magnesium with other atoms in the Mg 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:Mg401

b:14.1
occ:1.00
OE2 A:GLU254 1.9 16.7 1.0
O A:HOH393 2.0 23.7 1.0
OE2 A:GLU267 2.0 20.7 1.0
O1A A:ADP400 2.2 6.7 1.0
O3B A:ADP400 2.2 10.5 1.0
O A:HOH392 2.3 30.4 1.0
CD A:GLU254 2.8 17.4 1.0
OE1 A:GLU254 3.0 65.6 1.0
CD A:GLU267 3.1 40.7 1.0
PA A:ADP400 3.4 20.8 1.0
PB A:ADP400 3.7 15.1 1.0
O3A A:ADP400 3.8 28.0 1.0
CG A:GLU267 3.8 39.4 1.0
O A:HOH405 3.9 23.5 1.0
C5' A:ADP400 4.0 21.8 1.0
OE1 A:GLU267 4.0 53.1 1.0
O5' A:ADP400 4.2 14.7 1.0
O2B A:ADP400 4.2 29.8 1.0
CG A:GLU254 4.2 28.6 1.0
O A:HOH399 4.3 9.3 1.0
O2A A:ADP400 4.5 19.4 1.0
O A:HOH583 4.6 15.2 1.0
CB A:GLU254 4.8 24.4 1.0
O3' A:ADP400 4.8 12.1 1.0
O A:HOH561 4.8 10.7 1.0
CB A:GLU267 4.9 45.8 1.0
C4' A:ADP400 4.9 30.9 1.0
SG A:CYS266 4.9 26.9 1.0
O A:HOH453 4.9 36.9 1.0
NE2 A:HIS273 5.0 13.4 1.0
O1B A:ADP400 5.0 16.8 1.0

Magnesium binding site 2 out of 4 in 3k5i

Go back to Magnesium Binding Sites List in 3k5i
Magnesium binding site 2 out of 4 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 Magnesium with other atoms in the Mg binding site number 2 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
B:Mg401

b:27.2
occ:1.00
OE2 B:GLU254 2.0 15.2 1.0
O B:HOH397 2.1 34.5 1.0
OE2 B:GLU267 2.1 28.6 1.0
O1A B:ADP400 2.5 37.8 1.0
O3B B:ADP400 2.6 49.7 1.0
CD B:GLU254 2.9 99.8 1.0
O B:HOH398 2.9 34.0 1.0
OE1 B:GLU254 3.0 39.8 1.0
CD B:GLU267 3.2 7.7 1.0
PB B:ADP400 3.5 50.8 1.0
O2B B:ADP400 3.6 94.6 1.0
PA B:ADP400 3.8 39.3 1.0
O B:HOH595 3.8 26.3 1.0
CG B:GLU267 3.8 16.4 1.0
O3A B:ADP400 3.9 42.0 1.0
OE1 B:GLU267 4.3 31.4 1.0
CG B:GLU254 4.3 18.7 1.0
C5' B:ADP400 4.4 25.8 1.0
O3' B:ADP400 4.4 35.1 1.0
O5' B:ADP400 4.7 61.8 1.0
O2A B:ADP400 4.9 29.1 1.0
O B:HOH722 4.9 51.4 1.0
O B:HOH564 5.0 41.6 1.0
O1B B:ADP400 5.0 47.7 1.0
CB B:GLU254 5.0 15.3 1.0

Magnesium binding site 3 out of 4 in 3k5i

Go back to Magnesium Binding Sites List in 3k5i
Magnesium binding site 3 out of 4 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 Magnesium with other atoms in the Mg binding site number 3 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
C:Mg401

b:18.2
occ:1.00
OE2 C:GLU267 1.9 19.3 1.0
O C:HOH386 2.0 29.5 1.0
OE2 C:GLU254 2.1 30.2 1.0
O1A C:ADP400 2.3 7.7 1.0
O3B C:ADP400 2.4 9.9 1.0
O C:HOH385 2.4 37.0 1.0
CD C:GLU267 2.9 13.7 1.0
CD C:GLU254 2.9 36.2 1.0
OE1 C:GLU254 3.1 57.4 1.0
CG C:GLU267 3.5 21.4 1.0
PB C:ADP400 3.6 20.5 1.0
PA C:ADP400 3.6 27.2 1.0
O2B C:ADP400 3.7 27.4 1.0
O3A C:ADP400 3.9 40.3 1.0
OE1 C:GLU267 3.9 21.4 1.0
C5' C:ADP400 3.9 19.8 1.0
O C:HOH574 4.0 38.6 1.0
O C:HOH540 4.1 15.7 1.0
CG C:GLU254 4.3 15.5 1.0
O5' C:ADP400 4.4 14.1 1.0
O2A C:ADP400 4.6 32.5 1.0
O C:HOH388 4.6 16.5 1.0
O C:HOH556 4.6 10.3 1.0
O C:HOH532 4.6 14.2 1.0
CB C:GLU267 4.6 16.7 1.0
O3' C:ADP400 4.7 15.9 1.0
NE2 C:HIS273 4.8 32.2 1.0
O1B C:ADP400 4.8 20.5 1.0
CB C:GLU254 4.9 19.2 1.0
SG C:CYS266 4.9 20.4 1.0
C4' C:ADP400 5.0 23.6 1.0

Magnesium binding site 4 out of 4 in 3k5i

Go back to Magnesium Binding Sites List in 3k5i
Magnesium binding site 4 out of 4 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 Magnesium with other atoms in the Mg binding site number 4 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
D:Mg401

b:31.2
occ:1.00
O D:HOH393 2.0 33.8 1.0
OE2 D:GLU267 2.0 22.0 1.0
O1A D:ADP400 2.1 30.0 1.0
OE2 D:GLU254 2.2 29.4 1.0
O3B D:ADP400 2.5 46.7 1.0
O D:HOH395 2.6 35.9 1.0
CD D:GLU254 2.9 35.9 1.0
OE1 D:GLU254 2.9 68.9 1.0
CD D:GLU267 3.1 16.6 1.0
PA D:ADP400 3.4 43.8 1.0
PB D:ADP400 3.4 56.3 1.0
O2B D:ADP400 3.5 98.9 1.0
O D:HOH619 3.6 51.8 1.0
O3A D:ADP400 3.7 36.8 1.0
CG D:GLU267 3.7 19.9 1.0
O D:HOH533 3.9 45.1 1.0
OE1 D:GLU267 4.1 37.1 1.0
O D:HOH520 4.3 37.4 1.0
C5' D:ADP400 4.3 31.2 1.0
O D:HOH543 4.3 45.5 1.0
O5' D:ADP400 4.4 65.2 1.0
CG D:GLU254 4.4 18.7 1.0
O2A D:ADP400 4.5 25.7 1.0
O3' D:ADP400 4.8 29.5 1.0
O1B D:ADP400 4.9 41.8 1.0
OE1 D:GLN211 5.0 99.8 1.0
CB D:GLU254 5.0 24.9 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: Mon Dec 14 08:21:29 2020

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