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Calcium in PDB 8u38: Structure of A Bacterial Multi-Ubiquitin Domain Protein

Protein crystallography data

The structure of Structure of A Bacterial Multi-Ubiquitin Domain Protein, PDB code: 8u38 was solved by Q.Ye, M.Gong, K.D.Corbett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.80 / 3.04
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.024, 136.024, 105.807, 90, 90, 120
R / Rfree (%) 23.6 / 27.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Bacterial Multi-Ubiquitin Domain Protein (pdb code 8u38). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of A Bacterial Multi-Ubiquitin Domain Protein, PDB code: 8u38:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8u38

Go back to Calcium Binding Sites List in 8u38
Calcium binding site 1 out of 6 in the Structure of A Bacterial Multi-Ubiquitin Domain Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Bacterial Multi-Ubiquitin Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:113.8
occ:1.00
 O A:LEU142 2.5 124.3 1.0
OE2 A:GLU148 2.6 89.5 1.0
O A:GLY146 2.9 103.1 1.0
O A:ARG144 3.2 133.7 1.0
CG A:GLU148 3.3 82.0 1.0
CD A:GLU148 3.4 85.4 1.0
C A:LEU142 3.6 101.5 1.0
O D:ASP85 3.6 104.2 1.0
O A:ARG89 3.8 94.2 1.0
C A:GLY146 4.1 101.5 1.0
CA A:LEU142 4.3 96.2 1.0
C A:ARG144 4.3 137.7 1.0
CB D:ASP85 4.4 98.7 1.0
N A:GLU148 4.4 113.2 1.0
CB A:LEU142 4.5 84.5 1.0
N A:ARG144 4.5 126.9 1.0
OE1 A:GLU148 4.6 91.4 1.0
N A:ALA143 4.6 99.3 1.0
C D:ASP85 4.6 111.0 1.0
C A:ALA143 4.7 116.5 1.0
CA A:VAL147 4.7 86.5 1.0
CB A:TYR88 4.7 95.8 1.0
OD2 D:ASP85 4.7 102.5 1.0
CB A:GLU148 4.7 91.0 1.0
CA A:ALA143 4.7 112.0 1.0
N A:ARG89 4.8 111.6 1.0
CG D:ASP85 4.8 110.2 1.0
CD2 A:TYR88 4.9 91.3 1.0
N A:VAL147 4.9 105.5 1.0
C A:ARG89 4.9 93.1 1.0
CA A:ARG144 5.0 131.7 1.0
N A:GLY146 5.0 127.5 1.0

Calcium binding site 2 out of 6 in 8u38

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Calcium binding site 2 out of 6 in the Structure of A Bacterial Multi-Ubiquitin Domain Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Bacterial Multi-Ubiquitin Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:111.4
occ:1.00
 O B:LEU142 2.6 121.8 1.0
OE2 B:GLU148 2.6 116.5 1.0
O B:GLY146 2.7 129.8 1.0
O B:ARG144 3.1 151.1 1.0
CG B:GLU148 3.3 102.7 1.0
CD B:GLU148 3.4 118.3 1.0
C B:LEU142 3.7 104.2 1.0
C B:GLY146 3.9 120.0 1.0
O C:ASP85 3.9 100.6 1.0
O B:ARG89 4.1 94.2 1.0
C B:ARG144 4.2 153.4 1.0
N B:GLU148 4.3 115.1 1.0
CA B:LEU142 4.4 111.1 1.0
CB C:ASP85 4.4 109.8 1.0
N B:ARG144 4.4 149.0 1.0
CA B:VAL147 4.5 112.9 1.0
OE1 B:GLU148 4.6 121.6 1.0
OD2 C:ASP85 4.6 121.5 1.0
CB B:LEU142 4.6 101.5 1.0
N B:VAL147 4.6 128.8 1.0
CB B:GLU148 4.7 108.8 1.0
N B:ALA143 4.7 112.1 1.0
C B:ALA143 4.7 126.8 1.0
CG C:ASP85 4.8 115.0 1.0
N B:GLY146 4.8 137.0 1.0
C B:VAL147 4.8 117.4 1.0
CA B:ARG144 4.8 151.1 1.0
C C:ASP85 4.9 105.9 1.0
CA B:ALA143 4.9 116.0 1.0
CA B:GLY146 5.0 130.4 1.0

Calcium binding site 3 out of 6 in 8u38

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Calcium binding site 3 out of 6 in the Structure of A Bacterial Multi-Ubiquitin Domain Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Bacterial Multi-Ubiquitin Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:166.9
occ:1.00
 OD1 B:ASP131 2.5 131.2 1.0
O B:ASP129 2.6 121.7 1.0
OD1 A:ASP131 2.8 115.0 1.0
CG B:ASP131 3.0 129.6 1.0
O A:ASP129 3.0 123.0 1.0
OD2 A:ASP131 3.2 125.3 1.0
CG A:ASP131 3.2 123.2 1.0
OD2 B:ASP131 3.3 128.7 1.0
O B:ILE126 3.4 109.0 1.0
O A:ILE126 3.6 104.7 1.0
N B:ASP131 3.7 138.4 1.0
C B:ASP129 3.8 137.3 1.0
CB B:ASP131 4.1 126.6 1.0
CA B:ASP130 4.1 138.6 1.0
C B:ASP130 4.1 130.3 1.0
C A:ASP129 4.2 131.9 1.0
N A:ASP131 4.2 130.4 1.0
CA B:ASP131 4.3 129.4 1.0
CB A:ASP131 4.4 104.2 1.0
N B:ASP130 4.4 149.2 1.0
C B:ILE126 4.5 114.8 1.0
C A:ILE126 4.7 121.2 1.0
C A:ASP130 4.7 127.4 1.0
N B:ILE126 4.7 105.3 1.0
CA A:ASP130 4.7 130.1 1.0
CA A:ASP131 4.8 116.9 1.0
N B:ASP129 4.8 135.6 1.0
N A:ASP129 4.9 136.8 1.0
O B:ASP130 4.9 111.0 1.0
N A:ASP130 5.0 142.2 1.0
CA B:ASP129 5.0 130.1 1.0

Calcium binding site 4 out of 6 in 8u38

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Calcium binding site 4 out of 6 in the Structure of A Bacterial Multi-Ubiquitin Domain Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Bacterial Multi-Ubiquitin Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:133.5
occ:1.00
 O C:LEU142 2.5 140.8 1.0
O C:GLY146 2.9 139.2 1.0
OE2 C:GLU148 3.1 139.4 1.0
O C:ARG144 3.4 145.1 1.0
O B:ASP85 3.6 120.2 1.0
CG C:GLU148 3.6 111.3 1.0
C C:LEU142 3.7 122.1 1.0
O C:ARG89 3.7 107.5 1.0
CD C:GLU148 3.8 133.5 1.0
C C:GLY146 4.1 133.5 1.0
CB B:ASP85 4.2 97.7 1.0
CA C:LEU142 4.4 120.5 1.0
N C:GLU148 4.4 125.4 1.0
OD2 B:ASP85 4.5 113.8 1.0
C C:ARG144 4.5 149.1 1.0
CA C:VAL147 4.5 102.6 1.0
N C:ARG144 4.5 140.7 1.0
C B:ASP85 4.6 118.0 1.0
N C:ALA143 4.6 122.9 1.0
CG B:ASP85 4.6 111.4 1.0
CB C:LEU142 4.7 110.0 1.0
C C:ALA143 4.7 123.9 1.0
CA C:ALA143 4.7 124.8 1.0
N C:ARG89 4.8 125.0 1.0
N C:VAL147 4.8 124.0 1.0
C C:ARG89 4.8 116.5 1.0
CB C:TYR88 4.9 107.8 1.0
CB C:GLU148 4.9 122.5 1.0
CA B:ASP85 4.9 105.9 1.0
CD2 C:TYR88 5.0 95.9 1.0
C C:VAL147 5.0 118.3 1.0

Calcium binding site 5 out of 6 in 8u38

Go back to Calcium Binding Sites List in 8u38
Calcium binding site 5 out of 6 in the Structure of A Bacterial Multi-Ubiquitin Domain Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A Bacterial Multi-Ubiquitin Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:214.1
occ:1.00
 OD1 C:ASP131 2.7 171.1 1.0
O C:ASP129 3.1 159.7 1.0
CG C:ASP131 3.1 175.1 1.0
OD2 C:ASP131 3.2 178.8 1.0
O C:ILE126 3.8 141.4 1.0
N C:ASP131 4.2 172.7 1.0
C C:ASP129 4.3 163.1 1.0
CB C:ASP131 4.3 173.0 1.0
C C:ASP130 4.6 169.9 1.0
CA C:ASP130 4.7 173.1 1.0
CA C:ASP131 4.7 164.9 1.0
C C:ILE126 4.8 145.6 1.0
N C:ASP130 5.0 171.2 1.0

Calcium binding site 6 out of 6 in 8u38

Go back to Calcium Binding Sites List in 8u38
Calcium binding site 6 out of 6 in the Structure of A Bacterial Multi-Ubiquitin Domain Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A Bacterial Multi-Ubiquitin Domain Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:134.6
occ:1.00
 O D:LEU142 2.6 135.7 1.0
O D:GLY146 2.7 130.1 1.0
OE2 D:GLU148 2.7 109.6 1.0
O D:ARG144 3.0 136.0 1.0
CG D:GLU148 3.4 108.7 1.0
CD D:GLU148 3.5 116.7 1.0
C D:LEU142 3.7 113.9 1.0
O A:ASP85 3.9 113.6 1.0
C D:GLY146 3.9 110.0 1.0
O D:ARG89 4.0 107.8 1.0
C D:ARG144 4.2 139.0 1.0
N D:GLU148 4.4 123.5 1.0
CB A:ASP85 4.4 107.5 1.0
CA D:LEU142 4.4 120.8 1.0
N D:ARG144 4.4 137.5 1.0
CA D:VAL147 4.6 109.3 1.0
OD2 A:ASP85 4.6 112.4 1.0
C D:ALA143 4.6 128.4 1.0
OE1 D:GLU148 4.7 135.6 1.0
N D:ALA143 4.7 105.2 1.0
N D:VAL147 4.7 111.7 1.0
CB D:LEU142 4.7 114.7 1.0
N D:GLY146 4.8 128.3 1.0
CB D:GLU148 4.8 112.1 1.0
CA D:ARG144 4.8 136.7 1.0
CA D:ALA143 4.8 104.2 1.0
CG A:ASP85 4.8 115.2 1.0
C A:ASP85 4.8 111.0 1.0
C D:VAL147 4.9 114.1 1.0
CB D:TYR88 5.0 90.8 1.0
CA D:GLY146 5.0 125.9 1.0
N D:ARG89 5.0 126.8 1.0

Reference:

L.R.Chambers, Q.Ye, M.Gong, K.D.Corbett. Bacteria Encode Eukaryotic-Like Ubiquitination Pathways That Function in Antiviral Defense To Be Published.
Page generated: Thu Jul 10 07:36:55 2025

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