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Calcium in PDB 3vot: Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis

Enzymatic activity of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis

All present enzymatic activity of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis:
6.3.2.28;

Protein crystallography data

The structure of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis, PDB code: 3vot was solved by M.Suzuki, Y.Takahashi, A.Noguchi, T.Arai, M.Yagasaki, K.Kino, J.Saito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.46 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.090, 90.030, 154.910, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.1

Other elements in 3vot:

The structure of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis (pdb code 3vot). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis, PDB code: 3vot:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3vot

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Calcium binding site 1 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


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 L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:43.2
occ:1.00
 OE1 A:GLU205 2.3 20.5 1.0
O3' A:ADP501 2.3 25.0 1.0
O A:HOH1154 2.4 33.1 1.0
O A:HOH1280 2.5 38.9 1.0
O A:HOH1217 2.6 36.0 1.0
O A:HOH1174 2.6 38.9 1.0
O2' A:ADP501 2.8 25.4 1.0
CD A:GLU205 3.2 20.9 1.0
C3' A:ADP501 3.3 25.6 1.0
OE2 A:GLU205 3.5 22.2 1.0
C2' A:ADP501 3.6 25.3 1.0
C4' A:ADP501 3.9 26.9 1.0
O A:HOH1084 4.2 26.7 1.0
OE2 A:GLU235 4.4 40.0 1.0
OE1 A:GLU273 4.4 32.2 1.0
CG A:GLU205 4.5 19.5 1.0
CD A:GLU235 4.7 38.7 1.0
NZ A:LYS225 4.8 27.6 1.0
C1' A:ADP501 4.8 25.8 1.0
OE1 A:GLU235 4.8 38.5 1.0
O A:HOH1186 4.8 41.6 1.0
O A:PHE233 4.8 40.1 1.0
O4' A:ADP501 4.8 27.0 1.0
C5' A:ADP501 4.9 28.2 1.0
O A:HOH1218 4.9 38.1 1.0

Calcium binding site 2 out of 9 in 3vot

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Calcium binding site 2 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:49.2
occ:1.00
 O2B A:ADP501 1.9 38.2 1.0
OE1 A:GLU286 2.0 26.1 1.0
O1A A:ADP501 2.3 31.2 1.0
O A:HOH1186 2.4 41.6 1.0
O A:HOH1153 2.6 27.7 1.0
OE1 A:GLU273 2.8 32.2 1.0
OE2 A:GLU273 2.9 32.1 1.0
O A:HOH1291 3.1 42.1 1.0
CD A:GLU273 3.2 28.4 1.0
CD A:GLU286 3.3 25.5 1.0
PB A:ADP501 3.3 43.0 1.0
CA A:CA504 3.5 42.8 1.0
PA A:ADP501 3.6 32.4 1.0
O3A A:ADP501 3.8 37.2 1.0
OE2 A:GLU286 4.0 28.1 1.0
O1B A:ADP501 4.2 42.6 1.0
CB A:GLU286 4.3 20.3 1.0
CG A:GLU286 4.3 22.9 1.0
O3B A:ADP501 4.4 42.4 1.0
C5' A:ADP501 4.4 28.2 1.0
O5' A:ADP501 4.5 30.7 1.0
O3' A:ADP501 4.7 25.0 1.0
O2A A:ADP501 4.7 32.3 1.0
O A:HOH1217 4.7 36.0 1.0
CG A:GLU273 4.7 24.3 1.0
O A:HOH1074 4.8 21.1 1.0
O A:HOH1188 4.9 38.2 1.0

Calcium binding site 3 out of 9 in 3vot

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Calcium binding site 3 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


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 L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:42.8
occ:1.00
 O A:HOH1153 2.3 27.7 1.0
OE2 A:GLU84 2.4 24.9 1.0
O A:HOH1187 2.4 36.7 1.0
OE2 A:GLU286 2.6 28.1 1.0
O2B A:ADP501 2.6 38.2 1.0
O3B A:ADP501 2.9 42.4 1.0
OE1 A:GLU286 3.0 26.1 1.0
CD A:GLU286 3.2 25.5 1.0
PB A:ADP501 3.3 43.0 1.0
CD A:GLU84 3.3 23.6 1.0
CA A:CA503 3.5 49.2 1.0
O A:HOH1142 3.5 35.9 1.0
OE1 A:GLU84 3.6 25.1 1.0
O A:GLY155 4.0 50.3 1.0
O A:HOH1244 4.0 30.4 1.0
NZ A:LYS113 4.2 28.3 1.0
O3A A:ADP501 4.3 37.2 1.0
O A:HOH1188 4.4 38.2 1.0
O1B A:ADP501 4.5 42.6 1.0
C A:GLY155 4.6 48.9 1.0
CG A:GLU286 4.6 22.9 1.0
CG A:GLU84 4.7 21.2 1.0
O A:HOH1035 4.7 29.2 1.0
O1A A:ADP501 4.8 31.2 1.0
O A:HOH1291 5.0 42.1 1.0

Calcium binding site 4 out of 9 in 3vot

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Calcium binding site 4 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


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 L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:27.9
occ:1.00
 O A:HOH1165 2.3 20.1 1.0
OE1 A:GLN214 2.3 18.9 1.0
O B:HOH730 2.3 24.7 1.0
O A:HOH1176 2.4 27.1 1.0
O B:HOH759 2.4 39.3 1.0
O A:HOH1175 2.6 25.9 1.0
OD1 B:ASN98 3.0 29.3 1.0
CD A:GLN214 3.4 18.0 1.0
O B:HOH827 3.7 42.8 1.0
CG B:ASN98 4.1 28.0 1.0
O B:HOH682 4.2 28.7 1.0
NE2 A:GLN214 4.2 17.4 1.0
O A:HOH1059 4.2 28.2 1.0
CG A:GLN214 4.4 18.0 1.0
O B:HOH819 4.5 35.4 1.0
OE2 A:GLU322 4.5 19.8 1.0
CB B:ASN98 4.5 27.5 1.0
OE1 A:GLU322 4.6 19.1 1.0
CB A:GLN214 4.7 18.4 1.0
O B:ASN98 4.7 24.6 1.0

Calcium binding site 5 out of 9 in 3vot

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Calcium binding site 5 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


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 L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:59.9
occ:1.00
 O A:HOH1335 2.2 37.5 1.0
OE2 A:GLU169 2.3 43.5 1.0
OD2 A:ASP165 2.6 38.4 1.0
OE1 A:GLU169 3.0 40.4 1.0
CD A:GLU169 3.0 42.3 1.0
CG A:ASP165 3.7 38.3 1.0
NH1 A:ARG163 3.8 38.1 0.5
CB A:ASP165 4.2 40.0 1.0
CG A:GLU169 4.5 43.3 1.0
OD1 A:ASP165 4.8 37.2 1.0
CZ A:ARG163 4.9 36.6 0.5

Calcium binding site 6 out of 9 in 3vot

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Calcium binding site 6 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:39.7
occ:1.00
 O B:HOH779 2.3 30.3 1.0
O B:HOH780 2.4 31.8 1.0
O B:HOH724 2.4 31.3 1.0
O3' B:ADP501 2.4 26.3 1.0
OE2 B:GLU205 2.5 23.6 1.0
O B:HOH728 2.6 34.4 1.0
O2' B:ADP501 2.7 28.1 1.0
CD B:GLU205 3.4 24.4 1.0
C3' B:ADP501 3.4 28.1 1.0
OE1 B:GLU205 3.6 25.9 1.0
C2' B:ADP501 3.6 28.4 1.0
C4' B:ADP501 3.9 29.7 1.0
OE1 B:GLU273 4.3 28.7 1.0
O B:HOH659 4.4 28.5 1.0
O B:PHE233 4.4 48.8 1.0
OE2 B:GLU235 4.5 43.6 1.0
C1' B:ADP501 4.7 29.9 1.0
CD B:GLU235 4.7 43.9 1.0
CG B:GLU205 4.7 23.5 1.0
O4' B:ADP501 4.7 30.4 1.0
OE1 B:GLU235 4.8 43.8 1.0
CB B:PHE233 4.8 46.3 1.0
O B:HOH725 4.9 38.3 1.0
C5' B:ADP501 4.9 31.1 1.0

Calcium binding site 7 out of 9 in 3vot

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Calcium binding site 7 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:43.3
occ:1.00
 O3B B:ADP501 2.0 37.1 1.0
OE1 B:GLU286 2.2 29.1 1.0
O B:HOH725 2.3 38.3 1.0
O B:HOH710 2.3 31.0 1.0
O2A B:ADP501 2.4 33.3 1.0
OE2 B:GLU273 2.7 26.8 1.0
OE1 B:GLU273 3.2 28.7 1.0
CD B:GLU273 3.3 25.9 1.0
CD B:GLU286 3.4 27.6 1.0
CA B:CA504 3.4 46.5 1.0
PB B:ADP501 3.4 40.4 1.0
PA B:ADP501 3.7 34.7 1.0
O3A B:ADP501 3.9 37.8 1.0
OE2 B:GLU286 4.0 28.6 1.0
O2B B:ADP501 4.3 39.4 1.0
C5' B:ADP501 4.4 31.1 1.0
O1B B:ADP501 4.5 40.4 1.0
CG B:GLU286 4.5 25.4 1.0
O5' B:ADP501 4.6 33.7 1.0
CB B:GLU286 4.6 23.4 1.0
O B:HOH841 4.7 34.3 1.0
O3' B:ADP501 4.8 26.3 1.0
CG B:GLU273 4.8 23.4 1.0
OE2 B:GLU84 4.8 29.9 1.0
O1A B:ADP501 4.9 35.3 1.0
O B:HOH644 4.9 23.1 1.0
OE1 B:GLU84 4.9 29.6 1.0

Calcium binding site 8 out of 9 in 3vot

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Calcium binding site 8 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:46.5
occ:1.00
 O B:HOH710 2.3 31.0 1.0
OE2 B:GLU84 2.4 29.9 1.0
O B:HOH841 2.6 34.3 1.0
OE2 B:GLU286 2.6 28.6 1.0
O3B B:ADP501 2.6 37.1 1.0
O2B B:ADP501 2.7 39.4 1.0
OE1 B:GLU286 3.1 29.1 1.0
PB B:ADP501 3.2 40.4 1.0
CD B:GLU286 3.2 27.6 1.0
CD B:GLU84 3.4 27.4 1.0
CA B:CA503 3.4 43.3 1.0
OE1 B:GLU84 3.7 29.6 1.0
O B:GLY155 3.9 62.8 1.0
NZ B:LYS113 4.3 35.0 1.0
O1B B:ADP501 4.3 40.4 1.0
O3A B:ADP501 4.4 37.8 1.0
O B:HOH881 4.5 38.3 1.0
O B:HOH735 4.6 31.2 1.0
CG B:GLU84 4.7 25.2 1.0
CG B:GLU286 4.7 25.4 1.0
O2A B:ADP501 4.8 33.3 1.0
O B:HOH731 4.8 29.3 1.0
C B:GLY155 4.9 63.5 1.0

Calcium binding site 9 out of 9 in 3vot

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Calcium binding site 9 out of 9 in the Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of L-Amino Acid Ligase From Bacillus Licheniformis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:33.8
occ:1.00
 OE1 B:GLN214 2.3 19.6 1.0
O B:HOH824 2.3 34.9 1.0
O B:HOH822 2.5 31.1 1.0
O B:HOH645 2.6 23.6 1.0
O B:HOH823 2.6 28.4 1.0
O A:HOH1314 2.8 42.2 1.0
CD B:GLN214 3.4 19.1 1.0
NE2 B:GLN214 4.2 17.9 1.0
CG B:GLN214 4.3 18.9 1.0
O B:HOH743 4.3 32.2 1.0
OE1 B:GLU322 4.3 20.8 1.0
CB B:GLN214 4.6 19.1 1.0
OE2 B:GLU322 4.7 21.2 1.0
O A:HOH1164 4.8 28.4 1.0
O B:HOH878 4.9 42.4 1.0
O A:HOH1233 4.9 29.6 1.0
CD B:GLU322 5.0 20.7 1.0

Reference:

M.Suzuki, Y.Takahashi, A.Noguchi, T.Arai, M.Yagasaki, K.Kino, J.Saito. The Structure of L-Amino-Acid Ligase From Bacillus Licheniformis Acta Crystallogr.,Sect.D V. 68 1535 2012.
ISSN: ISSN 0907-4449
PubMed: 23090402
DOI: 10.1107/S0907444912038103
Page generated: Tue Jul 8 17:40:10 2025

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