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Calcium in PDB 3mdo: Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution, PDB code: 3mdo was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.62 / 1.91
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.945, 99.945, 163.020, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19

Other elements in 3mdo:

The structure of Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution also contains other interesting chemical elements:

Arsenic (As) 1 atom
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution (pdb code 3mdo). 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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution, PDB code: 3mdo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3mdo

Go back to Calcium Binding Sites List in 3mdo
Calcium binding site 1 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca389

b:31.0
occ:1.00
 O A:HOH580 2.2 31.5 1.0
O A:GLN322 2.3 19.4 1.0
O A:HOH583 2.4 26.9 1.0
O A:HOH584 2.4 24.6 1.0
O A:HOH581 2.4 21.3 1.0
O A:HOH579 2.4 24.6 1.0
O A:HOH582 2.5 31.8 1.0
C A:GLN322 3.5 21.9 1.0
CA A:GLN322 4.4 19.4 1.0
O A:SER239 4.5 20.3 1.0
N A:SER323 4.5 22.7 1.0
O A:ASP214 4.6 20.1 1.0
CA A:SER323 4.6 24.2 1.0
C A:SER323 4.7 24.0 1.0
OG A:SER239 4.7 21.9 1.0
O A:SER323 4.8 24.3 1.0
OE1 A:GLN322 4.9 23.6 1.0
O A:GLU321 4.9 22.1 1.0
CA A:GLY240 5.0 22.2 1.0

Calcium binding site 2 out of 7 in 3mdo

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Calcium binding site 2 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca390

b:66.3
occ:1.00
 OD1 A:ASP55 2.4 36.5 1.0
O A:HOH519 2.5 48.3 1.0
O B:HOH617 2.5 53.2 1.0
OE2 B:GLU146 2.9 45.1 0.5
O A:HOH552 2.9 42.8 1.0
CG A:ASP55 3.5 37.8 1.0
CD B:GLU146 3.6 40.3 0.5
OE1 B:GLU146 3.7 39.2 0.5
O A:HOH563 3.7 56.3 1.0
OD2 A:ASP55 3.8 46.4 1.0
CE A:MSE87 4.2 37.5 1.0
O B:HOH618 4.2 53.3 1.0
O A:GLY56 4.6 25.6 1.0
N A:GLY56 4.6 27.3 1.0
CB A:ASP55 4.8 26.9 1.0
CA A:ASP55 5.0 26.9 1.0

Calcium binding site 3 out of 7 in 3mdo

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Calcium binding site 3 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca391

b:51.1
occ:1.00
 O A:HOH621 2.3 36.2 1.0
OD2 A:ASP55 2.4 46.4 1.0
OD2 A:ASP91 2.5 28.0 1.0
O A:HOH630 2.6 40.4 1.0
O4 A:PGE403 3.0 63.7 1.0
O B:HOH593 3.0 49.4 1.0
CG A:ASP91 3.4 32.5 1.0
CG A:ASP55 3.6 37.8 1.0
OD1 A:ASP91 3.7 28.2 1.0
O A:MSE87 3.7 32.2 1.0
CE1 A:HIS53 3.9 38.9 1.0
C6 A:PGE403 4.2 63.6 1.0
OG A:SER288 4.3 31.7 0.5
OD1 A:ASP55 4.3 36.5 1.0
NE2 A:HIS53 4.3 40.9 1.0
O A:HOH563 4.4 56.3 1.0
CE A:MSE87 4.4 37.5 1.0
C5 A:PGE403 4.5 57.8 1.0
CB A:ASP55 4.6 26.9 1.0
OG A:SER288 4.6 31.4 0.5
C A:MSE87 4.7 27.3 1.0
CB A:ASP91 4.7 27.7 1.0
CB A:SER288 4.9 25.5 0.5

Calcium binding site 4 out of 7 in 3mdo

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Calcium binding site 4 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca392

b:60.5
occ:1.00
 O B:HOH595 2.4 25.5 0.5
OD1 B:ASP55 2.5 35.4 1.0
O A:HOH595 2.6 49.4 1.0
O B:HOH595 2.8 28.8 0.5
O A:HOH566 2.8 41.8 1.0
OE1 A:GLU146 2.9 40.5 0.5
OXT B:ACT395 3.1 65.6 1.0
OE2 A:GLU146 3.4 48.6 0.5
CG B:ASP55 3.5 35.8 1.0
O B:ACT395 3.5 63.8 1.0
CD A:GLU146 3.6 43.7 0.5
C B:ACT395 3.7 65.4 1.0
OD2 B:ASP55 3.8 40.0 1.0
CE B:MSE87 4.1 38.0 1.0
O B:GLY56 4.6 22.6 1.0
N B:GLY56 4.7 24.9 1.0
CB B:ASP55 4.8 25.7 1.0
O A:HOH633 4.8 34.4 0.5
CA B:CA389 4.9 50.0 1.0
CA B:ASP55 5.0 25.8 1.0
O A:HOH588 5.0 29.1 1.0

Calcium binding site 5 out of 7 in 3mdo

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Calcium binding site 5 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca389

b:50.0
occ:1.00
 OD2 B:ASP55 2.3 40.0 1.0
O B:HOH616 2.4 48.7 1.0
O B:HOH564 2.4 33.8 1.0
OXT B:ACT395 2.5 65.6 1.0
OD2 B:ASP91 2.5 33.2 1.0
O B:HOH522 2.7 35.3 1.0
O A:HOH588 2.7 29.1 1.0
C B:ACT395 3.3 65.4 1.0
CH3 B:ACT395 3.4 64.3 1.0
CG B:ASP91 3.5 32.7 1.0
CG B:ASP55 3.6 35.8 1.0
OD1 B:ASP91 3.8 34.7 1.0
O B:MSE87 3.9 32.1 1.0
NE2 B:HIS53 4.0 39.1 1.0
OD1 B:ASP55 4.3 35.4 1.0
CE B:MSE87 4.4 38.0 1.0
OG B:SER288 4.4 48.3 1.0
C1 B:PGE402 4.4 65.3 1.0
O B:ACT395 4.5 63.8 1.0
CB B:ASP55 4.6 25.7 1.0
OE1 A:GLU146 4.6 40.5 0.5
O1 B:PGE402 4.7 68.5 1.0
CE1 B:HIS53 4.7 41.6 1.0
CB B:ASP91 4.8 27.5 1.0
C2 B:PGE402 4.8 54.0 1.0
C B:MSE87 4.9 30.0 1.0
CA A:CA392 4.9 60.5 1.0

Calcium binding site 6 out of 7 in 3mdo

Go back to Calcium Binding Sites List in 3mdo
Calcium binding site 6 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca390

b:32.5
occ:1.00
 O1 B:CAC394 2.3 20.4 0.5
O B:HOH586 2.3 22.5 1.0
O B:HOH583 2.3 20.4 1.0
O B:HOH582 2.5 17.0 1.0
O B:GLN322 2.5 22.8 1.0
O B:HOH585 2.6 20.7 1.0
O B:HOH584 2.7 28.0 1.0
C B:GLN322 3.6 22.8 1.0
AS B:CAC394 3.6 37.8 0.5
C1 B:CAC394 4.1 28.9 0.5
O B:SER239 4.3 22.0 1.0
CA B:GLN322 4.4 21.4 1.0
O B:HOH525 4.4 30.6 1.0
C2 B:CAC394 4.4 32.6 0.5
O B:ASP214 4.4 24.3 1.0
N B:SER323 4.5 22.0 1.0
CA B:SER323 4.6 21.4 1.0
C B:SER323 4.6 22.2 1.0
O B:SER323 4.8 21.5 1.0
OG B:SER239 4.8 19.6 1.0
O B:GLU321 4.9 19.1 1.0
CA B:GLY240 4.9 23.5 1.0
OE1 B:GLN322 5.0 25.8 1.0
C4 B:PGE403 5.0 49.9 1.0

Calcium binding site 7 out of 7 in 3mdo

Go back to Calcium Binding Sites List in 3mdo
Calcium binding site 7 out of 7 in the Crystal Structure of A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution


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 A Putative Phosphoribosylformylglycinamidine Cyclo-Ligase (BDI_2101) From Parabacteroides Distasonis Atcc 8503 at 1.91 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca391

b:85.0
occ:1.00
 O B:HOH448 2.5 40.6 1.0
O B:HOH450 2.6 53.4 1.0
O B:HOH459 2.6 44.9 1.0
O B:HOH449 2.9 57.4 1.0
O B:HOH447 3.1 50.5 1.0
O B:GLY145 3.2 38.0 1.0
C B:GLY145 4.0 33.7 1.0
N B:GLY145 4.0 34.0 1.0
O B:HOH602 4.1 36.8 1.0
CA B:GLY144 4.6 34.9 1.0
CA B:GLY145 4.7 32.3 1.0
C B:GLY144 4.8 34.3 1.0
N B:GLU146 4.8 29.3 1.0
OE1 B:GLU146 4.9 39.1 0.5
CA B:GLU146 5.0 28.4 0.5
CA B:GLU146 5.0 28.5 0.5

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Tue Jul 8 14:34:23 2025

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