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Calcium in PDB 3r5x: Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp

Enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp

All present enzymatic activity of Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp, PDB code: 3r5x was solved by Y.Kim, R.Mulligan, J.Hasseman, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.77 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 56.336, 68.992, 92.387, 73.36, 84.96, 75.46
R / Rfree (%) 17.7 / 22.1

Other elements in 3r5x:

The structure of Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp (pdb code 3r5x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp, PDB code: 3r5x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3r5x

Go back to Calcium Binding Sites List in 3r5x
Calcium binding site 1 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:58.8
occ:1.00
 O2B A:ATP402 2.1 47.3 0.7
OE2 A:GLU260 2.1 69.0 1.0
O2A A:ATP402 2.2 53.4 0.7
OD2 A:ASP248 2.2 38.9 1.0
O A:HOH706 3.0 60.0 1.0
CD A:GLU260 3.2 59.9 1.0
CG A:ASP248 3.4 36.2 1.0
PB A:ATP402 3.4 52.7 0.7
CG A:GLU260 3.5 55.5 1.0
PA A:ATP402 3.5 39.2 0.7
O3A A:ATP402 3.9 64.7 0.7
CB A:ASP248 4.1 32.4 1.0
O A:HOH501 4.2 61.9 1.0
O3B A:ATP402 4.2 0.9 0.7
OE1 A:GLU260 4.3 61.7 1.0
OD1 A:ASP248 4.3 40.0 1.0
O A:HOH505 4.3 49.5 1.0
O1G A:ATP402 4.4 53.9 0.8
NH1 A:ARG246 4.4 45.3 1.0
ND2 A:ASN262 4.5 41.7 1.0
O5' A:ATP402 4.5 41.9 0.7
C5' A:ATP402 4.5 38.2 0.7
O3G A:ATP402 4.5 65.6 0.7
O3' A:ATP402 4.6 34.8 0.7
O1A A:ATP402 4.6 37.8 0.7
O1B A:ATP402 4.7 48.8 0.7
OD1 A:ASN262 4.7 52.9 1.0
PG A:ATP402 4.7 64.3 0.6
CB A:GLU260 4.9 50.2 1.0

Calcium binding site 2 out of 7 in 3r5x

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Calcium binding site 2 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:1.0
occ:1.00
 OE2 B:GLU260 2.4 99.3 1.0
OD2 B:ASP248 2.4 53.9 1.0
O3A B:ATP402 3.2 1.0 1.0
CD B:GLU260 3.3 88.9 1.0
CG B:ASP248 3.5 48.8 1.0
CG B:GLU260 3.6 74.1 1.0
O5' B:ATP402 3.7 0.8 1.0
O1A B:ATP402 3.8 0.7 1.0
PA B:ATP402 3.9 0.1 1.0
O3B B:ATP402 4.0 0.4 1.0
CB B:ASP248 4.0 42.9 1.0
O B:HOH594 4.1 80.8 1.0
PB B:ATP402 4.3 0.9 1.0
NH1 B:ARG246 4.4 56.3 1.0
O B:HOH610 4.4 58.7 1.0
OE1 B:GLU260 4.4 86.2 1.0
C5' B:ATP402 4.4 0.9 1.0
ND2 B:ASN262 4.5 52.3 0.3
OD1 B:ASP248 4.5 50.5 1.0
ND2 B:ASN262 4.6 51.1 0.7
C3' B:ATP402 4.6 0.0 1.0
OD1 B:ASN262 4.9 60.9 0.3
OD1 B:ASN262 4.9 64.5 0.7
CB B:GLU260 4.9 69.5 1.0
O3' B:ATP402 4.9 0.7 1.0
O1B B:ATP402 5.0 0.8 1.0

Calcium binding site 3 out of 7 in 3r5x

Go back to Calcium Binding Sites List in 3r5x
Calcium binding site 3 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:69.6
occ:1.00
 O B:GLY281 2.6 47.1 1.0
O B:HOH619 2.7 55.3 1.0
O B:HOH621 2.7 55.4 1.0
O B:HOH620 2.8 59.8 1.0
O B:HOH622 3.0 76.2 1.0
C B:GLY281 3.7 51.3 1.0
ND1 B:HIS283 4.1 63.7 1.0
CA B:GLY281 4.2 54.6 1.0
O B:HOH516 4.2 45.6 1.0
CE1 B:HIS283 4.8 66.8 1.0
N B:ILE282 4.9 49.4 1.0

Calcium binding site 4 out of 7 in 3r5x

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Calcium binding site 4 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:82.4
occ:1.00
 OD2 C:ASP248 2.5 46.9 1.0
O C:HOH616 2.7 75.5 1.0
OE1 C:GLU260 2.7 78.4 1.0
O1A C:ATP402 2.8 75.4 1.0
O2B C:ATP402 2.8 0.3 1.0
O3G C:ATP402 3.6 0.6 1.0
NH1 C:ARG246 3.6 44.4 1.0
O C:HOH646 3.6 97.6 1.0
CG C:ASP248 3.8 44.0 1.0
OD1 C:ASN262 3.8 52.8 1.0
CD C:GLU260 3.9 84.4 1.0
PB C:ATP402 4.1 0.4 1.0
ND2 C:ASN262 4.1 52.8 1.0
PA C:ATP402 4.1 80.0 1.0
CG C:ASN262 4.4 53.4 1.0
CB C:GLU260 4.5 60.4 1.0
O3B C:ATP402 4.5 0.5 1.0
O3A C:ATP402 4.5 0.9 1.0
CG C:GLU260 4.6 73.6 1.0
OD1 C:ASP248 4.6 45.0 1.0
CB C:ASP248 4.6 37.9 1.0
PG C:ATP402 4.7 0.9 1.0
OE2 C:GLU260 4.9 94.6 1.0
CZ C:ARG246 4.9 47.4 1.0

Calcium binding site 5 out of 7 in 3r5x

Go back to Calcium Binding Sites List in 3r5x
Calcium binding site 5 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:53.0
occ:1.00
 OE1 C:GLU108 2.5 48.6 1.0
OE2 C:GLU108 2.6 41.3 1.0
O C:HOH637 2.6 54.9 1.0
CD C:GLU108 2.9 49.7 1.0
O C:HOH636 3.4 84.9 1.0
O C:HOH657 4.4 64.2 1.0
CG C:GLU108 4.4 47.8 1.0
O C:HOH624 4.9 49.5 1.0

Calcium binding site 6 out of 7 in 3r5x

Go back to Calcium Binding Sites List in 3r5x
Calcium binding site 6 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:36.5
occ:1.00
 O3A D:ATP402 2.3 33.0 1.0
OD2 D:ASP248 2.3 32.0 1.0
O D:HOH660 2.3 26.6 1.0
OE2 D:GLU260 2.5 34.5 1.0
O3B D:ATP402 3.0 0.1 1.0
PB D:ATP402 3.3 0.9 1.0
CG D:ASP248 3.4 37.9 1.0
PA D:ATP402 3.4 34.3 1.0
CD D:GLU260 3.5 36.6 1.0
O2A D:ATP402 3.6 34.6 1.0
CB D:ASP248 3.8 33.7 1.0
O5' D:ATP402 3.8 38.2 1.0
O1B D:ATP402 4.0 0.8 1.0
CG D:GLU260 4.0 37.5 1.0
NH1 D:ARG246 4.2 27.7 1.0
C5' D:ATP402 4.3 32.7 1.0
ND2 D:ASN262 4.4 32.9 1.0
O2B D:ATP402 4.4 0.8 1.0
OE1 D:GLU260 4.5 42.9 1.0
OD1 D:ASP248 4.5 32.0 1.0
PG D:ATP402 4.5 73.3 1.0
O1A D:ATP402 4.6 31.0 1.0
O3G D:ATP402 4.7 31.1 1.0
O3' D:ATP402 4.8 39.4 1.0
O D:HOH661 4.9 41.2 1.0
O1G D:ATP402 4.9 82.8 1.0

Calcium binding site 7 out of 7 in 3r5x

Go back to Calcium Binding Sites List in 3r5x
Calcium binding site 7 out of 7 in the Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp


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 D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:51.0
occ:1.00
 O D:HOH667 2.4 46.5 1.0
O D:TYR208 2.5 52.8 1.0
OE1 D:GLU200 2.6 42.7 1.0
OD2 D:ASP203 2.6 42.7 0.5
OE2 D:GLU200 2.6 49.1 1.0
O D:HOH668 2.7 50.4 1.0
OD2 D:ASP203 2.9 44.7 0.6
CD D:GLU200 2.9 51.4 1.0
CG D:ASP203 3.5 46.0 0.5
OD1 D:ASP203 3.6 52.1 0.5
C D:TYR208 3.6 64.4 1.0
CG D:ASP203 3.9 43.4 0.6
N D:TYR208 4.2 61.3 1.0
CA D:ALA206 4.2 65.3 1.0
CB D:ASP203 4.3 47.4 0.6
CA D:TYR208 4.3 54.7 1.0
CG D:GLU200 4.4 45.2 1.0
O D:HOH603 4.5 46.6 1.0
C D:ALA206 4.6 68.2 1.0
CB D:TYR208 4.7 54.0 1.0
N D:ASP209 4.7 70.3 0.5
N D:ASP209 4.7 70.2 0.5
CA D:ASP209 4.8 70.1 0.5
O D:HOH669 4.9 46.8 1.0
O D:ASP203 4.9 50.1 0.5
CB D:ASP203 4.9 50.7 0.5
CA D:ASP209 4.9 70.0 0.5
OD1 D:ASP209 4.9 71.2 0.5
CB D:ALA206 4.9 67.5 1.0
N D:LYS207 5.0 60.4 1.0
OD1 D:ASP203 5.0 39.3 0.6

Reference:

Y.Kim, J.Hasseman, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of D-Alanine--D-Alanine Ligase From Bacillus Anthracis Complexed with Atp To Be Published.
Page generated: Tue Jul 8 16:11:40 2025

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