Atomistry » Magnesium » PDB 3jxq-3k9f » 3k5i
Atomistry »
  Magnesium »
    PDB 3jxq-3k9f »
      3k5i »

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: Wed Aug 14 17:56:34 2024

Last articles

Na in 7Q78
Na in 7Q77
Na in 7Q76
Na in 7Q6Q
Na in 7Q75
Na in 7Q5F
Na in 7Q47
Na in 7Q3Z
Na in 7Q5E
Na in 7Q36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy