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Calcium in PDB 4dlk: Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase

Enzymatic activity of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase

All present enzymatic activity of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase:
4.1.1.21;

Protein crystallography data

The structure of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 4dlk was solved by L.W.Fung, M.L.Tuntland, B.D.Santarsiero, M.E.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.368, 84.476, 167.269, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase (pdb code 4dlk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 4dlk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4dlk

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Calcium binding site 1 out of 5 in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:16.8
occ:1.00
 O2B A:ATP404 2.3 18.6 1.0
O A:HOH529 2.3 19.1 1.0
OE2 A:GLU268 2.3 16.3 1.0
O A:HOH549 2.4 21.3 1.0
O A:HOH526 2.4 19.0 1.0
O1G A:ATP404 2.5 18.0 1.0
OE1 A:GLU268 2.7 16.5 1.0
CD A:GLU268 2.9 16.3 1.0
O A:HOH561 3.1 22.8 1.0
PB A:ATP404 3.5 18.9 1.0
PG A:ATP404 3.5 18.6 1.0
CA A:CA402 3.7 19.2 1.0
O3A A:ATP404 3.8 19.7 1.0
O3G A:ATP404 3.9 18.1 1.0
O3B A:ATP404 3.9 18.6 1.0
NH1 A:ARG107 4.3 16.7 1.0
CG A:GLU268 4.4 16.0 1.0
NH2 A:ARG107 4.5 16.7 1.0
O A:GLY152 4.6 20.2 1.0
O2A A:ATP404 4.8 20.7 1.0
PA A:ATP404 4.8 20.1 1.0
O1B A:ATP404 4.8 18.8 1.0
O3G A:ATP405 4.9 24.5 1.0
CZ A:ARG107 4.9 17.0 1.0
O2G A:ATP404 4.9 18.3 1.0
O A:HOH537 4.9 19.8 1.0

Calcium binding site 2 out of 5 in 4dlk

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Calcium binding site 2 out of 5 in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:19.2
occ:1.00
 O3G A:ATP405 2.4 24.5 1.0
O1G A:ATP404 2.4 18.0 1.0
OE2 A:GLU268 2.4 16.3 1.0
O A:HOH537 2.5 19.8 1.0
O A:HOH534 2.5 19.6 1.0
OE1 A:GLU255 2.5 14.4 1.0
OE2 A:GLU255 2.6 14.7 1.0
O A:HOH561 2.9 22.8 1.0
CD A:GLU255 2.9 14.3 1.0
CD A:GLU268 3.6 16.3 1.0
PG A:ATP404 3.6 18.6 1.0
PG A:ATP405 3.7 25.0 1.0
CA A:CA401 3.7 16.8 1.0
O2G A:ATP404 3.8 18.3 1.0
CG A:GLU268 4.2 16.0 1.0
O2G A:ATP405 4.2 24.7 1.0
O3A A:ATP404 4.3 19.7 1.0
O1G A:ATP405 4.3 23.3 1.0
NE2 A:HIS274 4.3 14.0 1.0
O A:HOH517 4.4 17.0 1.0
CG A:GLU255 4.4 13.9 1.0
OE1 A:GLU268 4.6 16.5 1.0
O1A A:ATP404 4.6 20.3 1.0
O3B A:ATP404 4.7 18.6 1.0
O3G A:ATP404 4.7 18.1 1.0
O A:HOH549 4.7 21.3 1.0
O3B A:ATP405 4.8 23.8 1.0
O A:HOH529 4.9 19.1 1.0
CE1 A:HIS274 4.9 13.9 1.0
O2B A:ATP404 4.9 18.6 1.0
CB A:GLU255 5.0 13.8 1.0

Calcium binding site 3 out of 5 in 4dlk

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Calcium binding site 3 out of 5 in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.5
occ:1.00
 O1G A:ATP405 2.4 23.3 1.0
O A:HOH533 2.4 19.5 1.0
O3G A:ATP404 2.4 18.1 1.0
OD2 A:ASP154 2.4 21.3 1.0
O A:HOH543 2.4 21.0 1.0
O A:HOH551 2.6 21.7 1.0
O A:HOH584 3.4 25.9 1.0
PG A:ATP404 3.5 18.6 1.0
CG A:ASP154 3.6 21.5 1.0
O2G A:ATP404 3.7 18.3 1.0
PG A:ATP405 3.9 25.0 1.0
O A:HOH545 4.0 21.1 1.0
N A:ASP154 4.1 21.5 1.0
O A:HOH529 4.1 19.1 1.0
O3A A:ATP405 4.1 25.2 1.0
O2B A:ATP405 4.3 22.8 1.0
O1G A:ATP404 4.3 18.0 1.0
OD1 A:ASP154 4.3 21.8 1.0
CA A:ASP154 4.4 22.2 1.0
O2G A:ATP405 4.6 24.7 1.0
CB A:ASP154 4.6 21.8 1.0
NZ A:LYS348 4.7 17.3 1.0
O3G A:ATP405 4.7 24.5 1.0
O3B A:ATP404 4.7 18.6 1.0
O3B A:ATP405 4.7 23.8 1.0
PB A:ATP405 4.7 23.5 1.0
O2A A:ATP405 4.8 24.8 1.0
O A:ASN216 4.8 20.2 1.0
CB A:TYR153 5.0 22.1 1.0

Calcium binding site 4 out of 5 in 4dlk

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Calcium binding site 4 out of 5 in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:19.9
occ:1.00
 OE2 B:GLU268 2.1 24.9 1.0
O B:HOH550 2.3 25.5 1.0
O1A B:ATP403 2.4 20.9 1.0
OE1 B:GLU255 2.4 27.4 1.0
O3G B:ATP403 2.4 20.9 1.0
O3B B:ATP403 2.6 20.1 1.0
OE2 B:GLU255 2.6 26.6 1.0
CD B:GLU255 2.9 26.3 1.0
PG B:ATP403 3.2 20.4 1.0
O B:HOH623 3.2 37.2 1.0
CD B:GLU268 3.3 26.3 1.0
PA B:ATP403 3.6 21.3 1.0
PB B:ATP403 3.8 19.9 1.0
O3A B:ATP403 3.9 20.7 1.0
O B:HOH561 4.0 27.1 1.0
CG B:GLU268 4.0 25.6 1.0
OD1 B:ASN267 4.2 25.6 1.0
O1G B:ATP403 4.2 19.8 1.0
O2G B:ATP403 4.2 19.8 1.0
O2B B:ATP403 4.3 19.7 1.0
OE1 B:GLU268 4.3 28.0 1.0
CG B:GLU255 4.4 24.7 1.0
O B:HOH527 4.4 22.7 1.0
C5' B:ATP403 4.5 22.9 1.0
O5' B:ATP403 4.5 22.0 1.0
O3' B:ATP403 4.7 24.5 1.0
CA B:CA402 4.7 31.5 1.0
O2A B:ATP403 4.8 21.7 1.0
NE2 B:HIS213 4.9 21.2 1.0

Calcium binding site 5 out of 5 in 4dlk

Go back to Calcium Binding Sites List in 4dlk
Calcium binding site 5 out of 5 in the Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Atp-Ca++ Complex of Purk: N5- Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:31.5
occ:1.00
 O2B B:ATP403 2.3 19.7 1.0
O1G B:ATP403 2.3 19.8 1.0
OE1 B:GLU268 2.4 28.0 1.0
O B:GLY152 2.9 25.0 1.0
CD B:GLU268 3.2 26.3 1.0
OE2 B:GLU268 3.2 24.9 1.0
PB B:ATP403 3.3 19.9 1.0
PG B:ATP403 3.4 20.4 1.0
O3B B:ATP403 3.4 20.1 1.0
C B:GLY152 4.0 24.0 1.0
O3G B:ATP403 4.1 20.9 1.0
O1B B:ATP403 4.1 19.7 1.0
NH2 B:ARG107 4.3 21.3 1.0
O B:HOH561 4.5 27.1 1.0
CA B:TYR153 4.5 25.0 1.0
NH1 B:ARG107 4.6 21.0 1.0
O2G B:ATP403 4.6 19.8 1.0
O3A B:ATP403 4.6 20.7 1.0
CG B:GLU268 4.6 25.6 1.0
N B:TYR153 4.7 24.7 1.0
CA B:CA401 4.7 19.9 1.0
CZ B:ARG107 4.8 21.6 1.0

Reference:

M.L.Tuntland, B.D.Santarsiero, M.E.Johnson, L.W.Fung. Elucidation of the Bicarbonate Binding Site and Insights Into the Carboxylation Mechanism of (N(5))-Carboxyaminoimidazole Ribonucleotide Synthase (Purk) From Bacillus Anthracis. Acta Crystallogr.,Sect.D V. 70 3057 2014.
ISSN: ISSN 0907-4449
PubMed: 25372694
DOI: 10.1107/S1399004714021166
Page generated: Sat Jul 13 23:30:06 2024

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