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Calcium in PDB 4ecg: Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution, PDB code: 4ecg 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) 29.12 / 2.30
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 113.892, 113.892, 75.219, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.3

Other elements in 4ecg:

The structure of Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution (pdb code 4ecg). 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 A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution, PDB code: 4ecg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4ecg

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Calcium binding site 1 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:55.1
occ:1.00
 OE1 A:GLN249 2.2 53.7 1.0
O A:HOH686 2.3 50.9 1.0
O A:SER243 2.3 57.1 1.0
O A:HOH678 2.3 46.7 1.0
O A:HOH676 2.4 57.0 1.0
O A:HOH679 2.6 50.4 1.0
O A:HOH688 2.7 47.7 1.0
CD A:GLN249 3.2 53.1 1.0
C A:SER243 3.6 61.3 1.0
NE2 A:GLN249 4.0 50.0 1.0
CB A:SER243 4.1 66.9 1.0
CG A:GLN249 4.2 54.9 1.0
O A:HOH652 4.2 47.2 1.0
CA A:SER243 4.4 65.2 1.0
CB A:GLN249 4.4 54.5 1.0
N A:GLY245 4.5 60.1 1.0
N A:ILE244 4.5 62.3 1.0
CA A:ILE244 4.6 60.0 1.0
O A:HOH681 4.8 46.1 1.0
O A:HOH677 4.9 54.1 1.0
O A:HOH687 4.9 51.0 1.0

Calcium binding site 2 out of 9 in 4ecg

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Calcium binding site 2 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:65.6
occ:1.00
 O A:HOH624 2.2 43.4 1.0
O A:HOH689 2.3 48.5 1.0
OE1 A:GLU187 2.3 68.5 1.0
OD1 A:ASP185 2.3 59.3 1.0
O A:HOH690 2.6 53.5 1.0
OD2 A:ASP185 2.9 60.9 1.0
CG A:ASP185 2.9 67.3 1.0
CD A:GLU187 3.5 66.3 1.0
CB A:GLU187 4.3 59.4 1.0
CG A:GLU187 4.3 63.1 1.0
OE2 A:GLU187 4.4 65.4 1.0
CB A:ASP185 4.4 65.7 1.0
O A:HOH632 4.5 49.8 1.0
N A:GLU187 4.6 58.9 1.0
O A:HOH701 4.9 66.2 1.0
OG1 A:THR188 4.9 68.3 1.0
N A:THR188 5.0 63.8 1.0

Calcium binding site 3 out of 9 in 4ecg

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Calcium binding site 3 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:1.0
occ:1.00
 O A:HOH691 2.4 69.6 1.0
O A:HOH673 2.8 59.6 1.0
CA A:CA504 2.9 93.5 1.0
O A:HOH674 2.9 55.4 1.0
OE1 A:GLU114 3.8 71.7 1.0
OD1 A:ASP127 3.9 57.1 1.0
OE2 A:GLU114 4.0 79.5 1.0
CD A:GLU114 4.3 68.3 1.0
OD2 A:ASP131 4.3 59.6 1.0
OE2 A:GLU299 4.5 60.4 1.0
O A:HOH709 4.5 62.6 1.0
OD2 A:ASP127 4.5 59.5 1.0
OE1 A:GLU299 4.6 60.5 1.0
CE A:LYS272 4.6 51.1 1.0
NZ A:LYS272 4.7 52.5 1.0
O A:ASP131 4.7 49.6 1.0
CG A:ASP127 4.7 53.9 1.0
OE2 A:GLU267 4.8 72.0 1.0

Calcium binding site 4 out of 9 in 4ecg

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Calcium binding site 4 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:93.5
occ:1.00
 OD2 A:ASP131 2.5 59.6 1.0
OE2 A:GLU114 2.7 79.5 1.0
CA A:CA503 2.9 1.0 1.0
OE2 A:GLU299 3.0 60.4 1.0
O A:HOH616 3.1 62.2 1.0
OE2 A:GLU111 3.3 65.1 1.0
O A:HOH674 3.5 55.4 1.0
CG A:ASP131 3.7 58.5 1.0
NZ A:LYS272 3.7 52.5 1.0
CD A:GLU114 3.7 68.3 1.0
OE1 A:GLU111 3.8 60.8 1.0
CD A:GLU299 3.9 64.7 1.0
NH2 A:ARG107 3.9 51.6 1.0
OE1 A:GLU114 4.0 71.7 1.0
CD A:GLU111 4.0 52.4 1.0
O A:HOH691 4.0 69.6 1.0
OE1 A:GLU299 4.1 60.5 1.0
OD1 A:ASP131 4.3 53.1 1.0
CE A:LYS272 4.5 51.1 1.0
NE1 A:TRP110 4.5 52.4 1.0
CB A:ASP131 4.7 52.6 1.0
O A:ASP131 4.9 49.6 1.0
CZ A:ARG107 4.9 48.8 1.0

Calcium binding site 5 out of 9 in 4ecg

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Calcium binding site 5 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:87.1
occ:1.00
 O A:HOH692 2.2 59.2 1.0
O A:HOH680 2.5 58.6 1.0
OD1 A:ASP157 2.7 65.5 1.0
OD1 A:ASP159 3.0 92.0 1.0
OD2 A:ASP157 3.2 70.8 1.0
CG A:ASP157 3.3 67.5 1.0
OD2 A:ASP159 3.7 83.4 1.0
CG A:ASP159 3.7 81.8 1.0
CB A:ASP157 4.7 60.1 1.0

Calcium binding site 6 out of 9 in 4ecg

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Calcium binding site 6 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:76.4
occ:1.00
 O A:HOH672 2.5 58.7 1.0
O A:HOH671 2.5 69.0 1.0
OD1 A:ASP275 2.6 63.6 1.0
O A:SER270 2.6 65.9 1.0
O A:HOH670 2.8 47.4 1.0
CG A:ASP275 3.5 61.1 1.0
C A:SER270 3.6 49.6 1.0
OD2 A:ASP275 3.7 70.0 1.0
CB A:SER270 4.1 50.9 1.0
CA A:SER270 4.3 52.1 1.0
N A:ALA271 4.4 50.6 1.0
CA A:ALA271 4.4 48.8 1.0
O A:HOH693 4.8 52.5 1.0
CG2 A:THR274 4.8 52.8 1.0
CB A:THR274 4.9 52.1 1.0
CB A:ASP275 4.9 55.1 1.0

Calcium binding site 7 out of 9 in 4ecg

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Calcium binding site 7 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 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 Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:74.3
occ:1.00
 O A:HOH700 2.5 73.4 1.0
O A:HOH617 2.6 57.1 1.0
OE1 A:GLU182 2.7 77.2 1.0
O A:HOH701 2.8 66.2 1.0
CD A:GLU182 3.6 73.6 1.0
CB A:GLU182 4.3 61.9 1.0
O A:PRO183 4.3 50.7 1.0
OE2 A:GLU182 4.3 74.5 1.0
CG A:GLU182 4.5 69.1 1.0

Calcium binding site 8 out of 9 in 4ecg

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Calcium binding site 8 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution


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 A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:99.4
occ:1.00
 O A:HOH714 1.8 95.4 1.0
O A:HOH711 2.5 67.7 1.0
O A:HOH713 2.5 74.5 1.0
O A:HOH712 2.8 60.5 1.0
OE2 A:GLU182 3.2 74.5 1.0
CD A:GLU182 3.9 73.6 1.0
CG A:GLU182 4.5 69.1 1.0
OE1 A:GLU182 4.6 77.2 1.0
CH2 A:TRP304 5.0 50.0 1.0

Calcium binding site 9 out of 9 in 4ecg

Go back to Calcium Binding Sites List in 4ecg
Calcium binding site 9 out of 9 in the Crystal Structure of A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution


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 A Putative Iron-Regulated Protein A Precursor (BDI_2603) From Parabacteroides Distasonis Atcc 8503 at 2.30 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca509

b:79.9
occ:1.00
 O A:TRP133 2.3 52.3 1.0
O A:HOH708 2.4 50.9 1.0
O A:HOH710 2.4 72.5 1.0
O A:HOH709 2.5 62.6 1.0
C A:TRP133 3.6 49.0 1.0
O A:HOH704 4.2 47.6 1.0
CD A:PRO134 4.3 51.8 1.0
N A:PRO134 4.4 51.6 1.0
N A:TRP133 4.5 49.3 1.0
CA A:TRP133 4.6 46.5 1.0
O A:HOH673 4.7 59.6 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Jul 13 23:53:59 2024

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