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Magnesium in PDB 3k5h: Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp

Enzymatic activity of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp

All present enzymatic activity of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp:
4.1.1.21;

Protein crystallography data

The structure of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp, PDB code: 3k5h 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 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.900, 134.400, 99.600, 90.00, 107.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp (pdb code 3k5h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp, PDB code: 3k5h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3k5h

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Magnesium binding site 1 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


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 Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.4
occ:1.00
 O1G A:ATP400 1.9 16.2 1.0
OE2 A:GLU267 2.0 24.4 1.0
O1A A:ATP400 2.1 18.5 1.0
O A:HOH432 2.1 14.3 1.0
OE1 A:GLU254 2.2 16.6 1.0
OE2 A:GLU254 2.3 16.4 1.0
CD A:GLU254 2.6 15.9 1.0
CD A:GLU267 3.1 9.9 1.0
PG A:ATP400 3.2 30.3 1.0
O A:HOH526 3.5 39.1 1.0
O3B A:ATP400 3.5 25.4 1.0
PA A:ATP400 3.6 29.2 1.0
CG A:GLU267 3.7 13.4 1.0
O3G A:ATP400 3.8 23.1 1.0
CG A:GLU254 4.0 6.4 1.0
OE1 A:GLU267 4.1 30.7 1.0
O2B A:ATP400 4.1 14.7 1.0
O A:HOH430 4.1 24.6 1.0
C5' A:ATP400 4.2 32.1 1.0
PB A:ATP400 4.2 23.9 1.0
MG A:MG402 4.2 24.2 1.0
O3A A:ATP400 4.3 12.2 1.0
O2G A:ATP400 4.4 12.8 1.0
O5' A:ATP400 4.4 15.2 1.0
O3' A:ATP400 4.5 9.9 1.0
O2A A:ATP400 4.6 16.6 1.0
CB A:GLU254 4.7 10.0 1.0
SG A:CYS266 4.7 19.1 1.0
O A:HOH490 4.8 28.7 1.0
O A:HOH445 4.8 14.4 1.0
CB A:GLU267 4.9 11.4 1.0
C3' A:ATP400 4.9 17.6 1.0

Magnesium binding site 2 out of 8 in 3k5h

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Magnesium binding site 2 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


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 Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.2
occ:1.00
 O3G A:ATP400 2.0 23.1 1.0
OE1 A:GLU267 2.1 30.7 1.0
O A:HOH445 2.1 14.4 1.0
O A:HOH423 2.1 25.7 1.0
O2B A:ATP400 2.2 14.7 1.0
OE2 A:GLU267 2.5 24.4 1.0
CD A:GLU267 2.5 9.9 1.0
PG A:ATP400 3.3 30.3 1.0
PB A:ATP400 3.5 23.9 1.0
O A:HOH526 3.5 39.1 1.0
O3B A:ATP400 3.8 25.4 1.0
O1G A:ATP400 3.8 16.2 1.0
CG A:GLU267 3.9 13.4 1.0
O A:HOH578 4.0 33.5 1.0
OE2 A:GLU75 4.0 32.9 1.0
NZ A:LYS104 4.0 28.2 1.0
OE1 A:GLU75 4.0 29.3 1.0
O A:HOH566 4.2 43.6 1.0
O1A A:ATP400 4.2 18.5 1.0
MG A:MG401 4.2 14.4 1.0
O1B A:ATP400 4.3 33.5 1.0
CD A:LYS104 4.4 14.2 1.0
CD A:GLU75 4.4 0.0 1.0
O2G A:ATP400 4.5 12.8 1.0
O3A A:ATP400 4.6 12.2 1.0
O A:ALA151 4.6 64.3 1.0
O A:HOH510 4.7 23.5 1.0
CE A:LYS104 4.7 22.8 1.0
CB A:GLU267 4.9 11.4 1.0
CB A:ALA151 4.9 23.1 1.0
C A:ALA151 4.9 26.1 1.0
PA A:ATP400 5.0 29.2 1.0

Magnesium binding site 3 out of 8 in 3k5h

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Magnesium binding site 3 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


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 Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:22.6
occ:1.00
 OE2 B:GLU267 1.8 15.6 1.0
O1A B:ATP400 1.9 25.8 1.0
O B:HOH497 2.0 18.7 1.0
O1G B:ATP400 2.0 34.4 1.0
OE2 B:GLU254 2.3 22.6 1.0
OE1 B:GLU254 2.5 32.0 1.0
CD B:GLU254 2.8 29.4 1.0
O3B B:ATP400 3.0 27.6 1.0
CD B:GLU267 3.0 57.2 1.0
PG B:ATP400 3.0 33.7 1.0
PA B:ATP400 3.3 34.5 1.0
MG B:MG402 3.7 25.1 1.0
O2B B:ATP400 3.7 7.3 1.0
CG B:GLU267 3.8 8.2 1.0
O3G B:ATP400 3.8 24.5 1.0
OE1 B:GLU267 3.9 15.2 1.0
O3A B:ATP400 3.9 22.4 1.0
PB B:ATP400 3.9 20.2 1.0
O B:HOH445 3.9 31.7 1.0
O2G B:ATP400 4.1 34.0 1.0
CG B:GLU254 4.2 4.9 1.0
O2A B:ATP400 4.3 11.9 1.0
O B:HOH507 4.3 18.9 1.0
O5' B:ATP400 4.3 34.1 1.0
O B:HOH547 4.4 34.1 1.0
C5' B:ATP400 4.4 44.2 1.0
O3' B:ATP400 4.5 30.9 1.0
O B:HOH784 4.7 28.5 1.0
CB B:GLU254 4.9 6.2 1.0
SG B:CYS266 4.9 17.3 1.0

Magnesium binding site 4 out of 8 in 3k5h

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Magnesium binding site 4 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


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 Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:25.1
occ:1.00
 O3G B:ATP400 1.9 24.5 1.0
O B:HOH485 2.0 29.2 1.0
O2B B:ATP400 2.2 7.3 1.0
OE1 B:GLU267 2.2 15.2 1.0
O B:HOH507 2.2 18.9 1.0
OE2 B:GLU267 2.4 15.6 1.0
CD B:GLU267 2.6 57.2 1.0
PG B:ATP400 3.0 33.7 1.0
PB B:ATP400 3.2 20.2 1.0
O3B B:ATP400 3.4 27.6 1.0
O1G B:ATP400 3.4 34.4 1.0
MG B:MG401 3.7 22.6 1.0
NZ B:LYS104 3.8 18.2 1.0
O B:ALA151 3.9 38.4 1.0
CG B:GLU267 4.1 8.2 1.0
O B:HOH443 4.1 26.8 1.0
O B:HOH547 4.2 34.1 1.0
O1B B:ATP400 4.2 34.7 1.0
O1A B:ATP400 4.2 25.8 1.0
O3A B:ATP400 4.3 22.4 1.0
O2G B:ATP400 4.4 34.0 1.0
CE B:LYS104 4.5 11.3 1.0
C B:ALA151 4.6 19.5 1.0
PA B:ATP400 4.7 34.5 1.0
CA B:TYR152 4.7 31.7 1.0
OE1 B:GLU254 4.9 32.0 1.0
CD B:LYS104 4.9 30.4 1.0
CB B:GLU267 5.0 8.1 1.0

Magnesium binding site 5 out of 8 in 3k5h

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Magnesium binding site 5 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:40.5
occ:1.00
 O1G C:ATP400 1.7 25.9 1.0
OE2 C:GLU267 1.9 21.3 1.0
O C:HOH398 1.9 28.9 1.0
O1A C:ATP400 2.0 21.4 1.0
OE1 C:GLU254 2.4 32.4 1.0
OE2 C:GLU254 2.5 26.3 1.0
PG C:ATP400 2.7 29.6 1.0
O3B C:ATP400 2.8 27.4 1.0
CD C:GLU254 2.8 22.3 1.0
CD C:GLU267 3.0 21.1 1.0
PA C:ATP400 3.3 32.8 1.0
O C:HOH505 3.3 31.1 1.0
MG C:MG402 3.5 22.9 1.0
O2B C:ATP400 3.5 35.9 1.0
O3G C:ATP400 3.5 33.6 1.0
PB C:ATP400 3.6 36.6 1.0
O3A C:ATP400 3.7 28.3 1.0
CG C:GLU267 3.8 20.9 1.0
OE1 C:GLU267 3.8 29.9 1.0
C5' C:ATP400 3.9 30.1 1.0
O2G C:ATP400 3.9 28.3 1.0
O C:HOH535 3.9 22.5 1.0
O C:HOH387 4.2 38.3 1.0
O5' C:ATP400 4.2 31.0 1.0
O2A C:ATP400 4.3 21.4 1.0
CG C:GLU254 4.4 15.9 1.0
O C:HOH467 4.4 18.1 1.0
O3' C:ATP400 4.6 46.0 1.0
C4' C:ATP400 4.9 83.0 1.0
CB C:GLU267 5.0 24.6 1.0
C3' C:ATP400 5.0 19.8 1.0

Magnesium binding site 6 out of 8 in 3k5h

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Magnesium binding site 6 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:22.9
occ:1.00
 O2B C:ATP400 1.8 35.9 1.0
O3G C:ATP400 2.0 33.6 1.0
O C:HOH388 2.1 39.5 1.0
O C:HOH467 2.2 18.1 1.0
OE2 C:GLU267 2.3 21.3 1.0
OE1 C:GLU267 2.3 29.9 1.0
CD C:GLU267 2.6 21.1 1.0
PG C:ATP400 3.0 29.6 1.0
PB C:ATP400 3.1 36.6 1.0
O C:HOH505 3.3 31.1 1.0
O1G C:ATP400 3.4 25.9 1.0
O3B C:ATP400 3.4 27.4 1.0
MG C:MG401 3.5 40.5 1.0
NZ C:LYS104 3.8 52.7 1.0
CG C:GLU267 4.0 20.9 1.0
O1B C:ATP400 4.0 36.8 1.0
O C:HOH580 4.1 43.1 1.0
O3A C:ATP400 4.2 28.3 1.0
O1A C:ATP400 4.3 21.4 1.0
O C:ALA151 4.3 40.1 1.0
O2G C:ATP400 4.3 28.3 1.0
OE1 C:GLU75 4.4 48.5 1.0
CD C:LYS104 4.5 21.2 1.0
PA C:ATP400 4.6 32.8 1.0
OE1 C:GLU254 4.7 32.4 1.0
CE C:LYS104 4.8 37.8 1.0
C C:ALA151 4.8 62.5 1.0
O2A C:ATP400 4.9 21.4 1.0
CB C:GLU267 4.9 24.6 1.0
CA C:TYR152 5.0 35.5 1.0
CB C:ALA151 5.0 44.6 1.0

Magnesium binding site 7 out of 8 in 3k5h

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Magnesium binding site 7 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:33.2
occ:1.00
 OE2 D:GLU267 1.9 21.1 1.0
O1A D:ATP400 1.9 28.1 1.0
OE2 D:GLU254 2.0 28.7 1.0
O D:HOH455 2.2 23.0 1.0
OE1 D:GLU254 2.5 37.6 1.0
O1G D:ATP400 2.5 40.7 1.0
CD D:GLU254 2.5 12.9 1.0
CD D:GLU267 2.9 35.4 1.0
PA D:ATP400 3.3 33.8 1.0
PG D:ATP400 3.4 30.1 1.0
CG D:GLU267 3.4 17.5 1.0
O3B D:ATP400 3.6 22.3 1.0
MG D:MG402 3.6 24.5 1.0
O3G D:ATP400 3.8 12.0 1.0
O2A D:ATP400 3.8 33.2 1.0
O3A D:ATP400 3.9 46.6 1.0
PB D:ATP400 3.9 30.5 1.0
OE1 D:GLU267 4.0 19.9 1.0
CG D:GLU254 4.0 27.4 1.0
O2B D:ATP400 4.1 18.2 1.0
O D:HOH415 4.3 25.7 1.0
O D:HOH452 4.3 9.8 1.0
O5' D:ATP400 4.5 30.8 1.0
O3' D:ATP400 4.6 32.0 1.0
SG D:CYS266 4.6 23.4 1.0
CB D:GLU254 4.6 11.8 1.0
C5' D:ATP400 4.6 26.4 1.0
O2G D:ATP400 4.7 56.5 1.0
CB D:GLU267 4.9 20.2 1.0

Magnesium binding site 8 out of 8 in 3k5h

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Magnesium binding site 8 out of 8 in the Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Carboxyaminoimidazole Ribonucleotide Synthase From Asperigillus Clavatus Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:24.5
occ:1.00
 O3G D:ATP400 1.8 12.0 1.0
O D:HOH426 1.9 21.8 1.0
O2B D:ATP400 2.0 18.2 1.0
O D:HOH415 2.0 25.7 1.0
OE1 D:GLU267 2.1 19.9 1.0
OE2 D:GLU267 2.2 21.1 1.0
CD D:GLU267 2.5 35.4 1.0
PG D:ATP400 3.1 30.1 1.0
PB D:ATP400 3.2 30.5 1.0
O3B D:ATP400 3.5 22.3 1.0
NZ D:LYS104 3.5 23.8 1.0
MG D:MG401 3.6 33.2 1.0
O1G D:ATP400 3.7 40.7 1.0
O D:ALA151 3.8 54.0 1.0
O D:HOH452 4.0 9.8 1.0
CG D:GLU267 4.0 17.5 1.0
O3A D:ATP400 4.1 46.6 1.0
O1A D:ATP400 4.1 28.1 1.0
O D:HOH496 4.2 16.1 1.0
O2G D:ATP400 4.3 56.5 1.0
CE D:LYS104 4.3 18.6 1.0
OE2 D:GLU75 4.3 53.0 1.0
O1B D:ATP400 4.3 32.3 1.0
CD D:LYS104 4.4 41.1 1.0
O2A D:ATP400 4.5 33.2 1.0
PA D:ATP400 4.5 33.8 1.0
C D:ALA151 4.7 32.4 1.0
CB D:GLU267 4.8 20.2 1.0
OE1 D:GLU254 4.9 37.6 1.0
CA D:TYR152 4.9 45.3 1.0
OE1 D:GLU75 5.0 0.0 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 17:56:08 2024

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