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Calcium in PDB 9d5b: Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament (pdb code 9d5b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament, PDB code: 9d5b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 9d5b

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Calcium binding site 1 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


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Stereo pair view

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

b:30.0
occ:1.00
 OE2 A:GLU148 2.4 110.8 1.0
O A:LEU142 2.4 104.5 1.0
O A:GLY146 2.7 99.7 1.0
O A:ARG144 2.8 114.5 1.0
CD A:GLU148 3.3 115.7 1.0
CG A:GLU148 3.5 107.0 1.0
C A:LEU142 3.6 105.7 1.0
C A:GLY146 3.9 104.1 1.0
C A:ARG144 4.0 116.4 1.0
O A:ARG89 4.2 103.4 1.0
CA A:LEU142 4.3 100.5 1.0
N A:ARG144 4.3 113.9 1.0
OE1 A:GLU148 4.5 119.3 1.0
O B:ASP85 4.5 103.2 1.0
C A:ALA143 4.5 119.6 1.0
N A:GLY146 4.6 112.3 1.0
CB A:LEU142 4.6 92.7 1.0
N A:GLU148 4.6 100.5 1.0
N A:ALA143 4.6 112.4 1.0
CA A:VAL147 4.6 94.0 1.0
CA A:ARG144 4.7 112.1 1.0
N A:VAL147 4.7 100.9 1.0
CA A:ALA143 4.7 117.1 1.0
CD1 A:TYR88 4.8 85.4 1.0
C A:LYS145 4.9 115.5 1.0
CB A:TYR88 4.9 79.9 1.0
CA A:GLY146 4.9 107.8 1.0
CB B:ASP85 4.9 112.0 1.0
O A:ALA143 4.9 121.2 1.0
CB A:GLU148 4.9 95.4 1.0
C A:VAL147 4.9 99.8 1.0
OD2 B:ASP85 5.0 119.4 1.0

Calcium binding site 2 out of 10 in 9d5b

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Calcium binding site 2 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:30.0
occ:1.00
 OD2 C:ASP29 2.2 124.1 1.0
O A:VAL31 2.2 126.9 1.0
OD2 A:ASP29 2.2 124.1 1.0
O C:VAL31 2.2 126.9 1.0
OD1 A:ASP29 2.3 129.8 1.0
OD1 C:ASP29 2.5 129.8 1.0
CG A:ASP29 2.6 128.9 1.0
CG C:ASP29 2.7 128.9 1.0
C A:VAL31 3.1 130.3 1.0
C C:VAL31 3.2 130.3 1.0
CA A:VAL31 3.9 129.6 1.0
N A:PRO32 4.0 126.3 1.0
N A:VAL31 4.0 131.8 1.0
N C:PRO32 4.0 126.3 1.0
CA C:VAL31 4.0 129.6 1.0
CB A:VAL31 4.0 130.6 1.0
CA C:PRO32 4.1 126.5 1.0
CB A:ASP29 4.1 130.4 1.0
NE2 C:GLN36 4.1 122.9 1.0
CB C:VAL31 4.1 130.6 1.0
CA A:PRO32 4.1 126.5 1.0
N C:VAL31 4.1 131.8 1.0
CB C:ASP29 4.2 130.4 1.0
NE2 A:GLN36 4.3 122.9 1.0
OE1 C:GLN36 4.8 126.0 1.0
CG1 A:VAL31 4.8 135.2 1.0
CG1 C:VAL31 4.9 135.2 1.0
OE1 A:GLN36 4.9 126.0 1.0
CD C:GLN36 4.9 121.4 1.0
CA A:ASP29 4.9 134.2 1.0
C C:PRO32 5.0 125.8 1.0

Calcium binding site 3 out of 10 in 9d5b

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Calcium binding site 3 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:30.0
occ:1.00
 OD1 A:ASP131 2.3 123.8 1.0
CG A:ASP131 3.2 128.2 1.0
OD2 A:ASP131 3.3 127.1 1.0
O A:ASP129 3.3 137.2 1.0
O A:ILE126 3.8 133.4 1.0
N A:ASP131 4.5 129.2 1.0
C A:ASP129 4.5 136.9 1.0
CB A:ASP131 4.6 129.3 1.0
C A:ILE126 4.6 125.4 1.0
CG1 A:VAL125 4.9 118.1 1.0
N A:GLY128 4.9 124.7 1.0
CA A:PRO127 4.9 126.8 1.0
N A:ILE126 5.0 119.8 1.0
N A:ASP129 5.0 131.9 1.0

Calcium binding site 4 out of 10 in 9d5b

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Calcium binding site 4 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

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

b:30.0
occ:1.00
 OE2 B:GLU148 2.4 110.8 1.0
O B:LEU142 2.6 104.5 1.0
O B:GLY146 2.6 99.7 1.0
O B:ARG144 2.9 114.5 1.0
CD B:GLU148 3.3 115.7 1.0
CG B:GLU148 3.4 107.0 1.0
C B:LEU142 3.7 105.7 1.0
C B:GLY146 3.8 104.1 1.0
C B:ARG144 4.0 116.4 1.0
O B:ARG89 4.1 103.4 1.0
CA B:LEU142 4.4 100.5 1.0
OE1 B:GLU148 4.4 119.3 1.0
N B:ARG144 4.4 113.9 1.0
N B:GLU148 4.5 100.5 1.0
O A:ASP85 4.5 103.2 1.0
CA B:VAL147 4.5 94.0 1.0
N B:GLY146 4.5 112.3 1.0
N B:VAL147 4.6 100.9 1.0
C B:ALA143 4.6 119.6 1.0
CB B:LEU142 4.6 92.7 1.0
N B:ALA143 4.7 112.4 1.0
CA B:ARG144 4.8 112.1 1.0
CA B:GLY146 4.8 107.8 1.0
CB A:ASP85 4.8 112.0 1.0
C B:VAL147 4.8 99.8 1.0
CB B:GLU148 4.9 95.4 1.0
C B:LYS145 4.9 115.5 1.0
OD2 A:ASP85 4.9 119.4 1.0
CA B:ALA143 4.9 117.1 1.0
CB B:TYR88 4.9 79.9 1.0
CD1 B:TYR88 4.9 85.4 1.0

Calcium binding site 5 out of 10 in 9d5b

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Calcium binding site 5 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

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

b:30.0
occ:1.00
 O B:VAL31 2.3 126.9 1.0
OD2 B:ASP29 2.3 124.1 1.0
OD1 B:ASP29 2.6 129.8 1.0
CG B:ASP29 2.8 128.9 1.0
C B:VAL31 3.3 130.3 1.0
CA B:VAL31 4.1 129.6 1.0
N B:PRO32 4.1 126.3 1.0
NE2 B:GLN36 4.2 122.9 1.0
CB B:VAL31 4.2 130.6 1.0
CA B:PRO32 4.2 126.5 1.0
N B:VAL31 4.3 131.8 1.0
CB B:ASP29 4.3 130.4 1.0
OE1 B:GLN36 4.9 126.0 1.0
CG1 B:VAL31 4.9 135.2 1.0
CD B:GLN36 5.0 121.4 1.0

Calcium binding site 6 out of 10 in 9d5b

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Calcium binding site 6 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:30.0
occ:1.00
 OD1 B:ASP131 2.2 123.8 1.0
OD1 D:ASP131 2.2 123.8 1.0
OD2 B:ASP131 2.9 127.1 1.0
CG B:ASP131 2.9 128.2 1.0
CG D:ASP131 2.9 128.2 1.0
OD2 D:ASP131 2.9 127.1 1.0
O D:ASP129 3.5 137.2 1.0
O B:ASP129 3.6 137.2 1.0
O D:ILE126 3.7 133.4 1.0
O B:ILE126 3.9 133.4 1.0
C D:ILE126 4.3 125.4 1.0
CG1 D:VAL125 4.3 118.1 1.0
CB B:ASP131 4.4 129.3 1.0
CB D:ASP131 4.4 129.3 1.0
CG1 B:VAL125 4.5 118.1 1.0
N B:ASP131 4.5 129.2 1.0
N D:ASP131 4.5 129.2 1.0
N D:ILE126 4.5 119.8 1.0
C B:ILE126 4.6 125.4 1.0
CA D:PRO127 4.7 126.8 1.0
C D:ASP129 4.7 136.9 1.0
N B:ILE126 4.7 119.8 1.0
N D:PRO127 4.8 123.7 1.0
C B:ASP129 4.8 136.9 1.0
CA D:ASP131 4.9 127.8 1.0
CA B:ASP131 4.9 127.8 1.0
CA B:PRO127 4.9 126.8 1.0
N D:GLY128 5.0 124.7 1.0

Calcium binding site 7 out of 10 in 9d5b

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Calcium binding site 7 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:30.0
occ:1.00
 OE2 C:GLU148 2.4 110.8 1.0
O C:LEU142 2.4 104.5 1.0
O C:GLY146 2.7 99.7 1.0
O C:ARG144 2.8 114.5 1.0
CD C:GLU148 3.3 115.7 1.0
CG C:GLU148 3.5 107.0 1.0
C C:LEU142 3.6 105.7 1.0
C C:GLY146 3.9 104.1 1.0
C C:ARG144 4.0 116.4 1.0
O C:ARG89 4.2 103.4 1.0
CA C:LEU142 4.3 100.5 1.0
N C:ARG144 4.4 113.9 1.0
OE1 C:GLU148 4.4 119.3 1.0
C C:ALA143 4.5 119.6 1.0
CB C:LEU142 4.5 92.7 1.0
O D:ASP85 4.5 103.2 1.0
N C:GLU148 4.5 100.5 1.0
N C:ALA143 4.6 112.4 1.0
N C:GLY146 4.6 112.3 1.0
CA C:VAL147 4.6 94.0 1.0
CA C:ARG144 4.7 112.1 1.0
N C:VAL147 4.7 100.9 1.0
CA C:ALA143 4.8 117.1 1.0
CD1 C:TYR88 4.8 85.4 1.0
CB C:TYR88 4.8 79.9 1.0
CB C:GLU148 4.9 95.4 1.0
CA C:GLY146 4.9 107.8 1.0
C C:VAL147 4.9 99.8 1.0
C C:LYS145 4.9 115.5 1.0
O C:ALA143 5.0 121.2 1.0

Calcium binding site 8 out of 10 in 9d5b

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Calcium binding site 8 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:30.0
occ:1.00
 OD1 C:ASP131 2.3 123.8 1.0
CG C:ASP131 3.2 128.2 1.0
OD2 C:ASP131 3.3 127.1 1.0
O C:ASP129 3.3 137.2 1.0
O C:ILE126 3.9 133.4 1.0
N C:ASP131 4.5 129.2 1.0
C C:ASP129 4.5 136.9 1.0
CB C:ASP131 4.6 129.3 1.0
C C:ILE126 4.6 125.4 1.0
CG1 C:VAL125 4.9 118.1 1.0
N C:GLY128 4.9 124.7 1.0
CA C:PRO127 5.0 126.8 1.0

Calcium binding site 9 out of 10 in 9d5b

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Calcium binding site 9 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:30.0
occ:1.00
 OE2 D:GLU148 2.4 110.8 1.0
O D:LEU142 2.5 104.5 1.0
O D:GLY146 2.6 99.7 1.0
O D:ARG144 2.7 114.5 1.0
CD D:GLU148 3.3 115.7 1.0
CG D:GLU148 3.6 107.0 1.0
C D:LEU142 3.7 105.7 1.0
C D:GLY146 3.8 104.1 1.0
C D:ARG144 3.9 116.4 1.0
O D:ARG89 4.3 103.4 1.0
N D:ARG144 4.3 113.9 1.0
CA D:LEU142 4.4 100.5 1.0
N D:GLY146 4.5 112.3 1.0
C D:ALA143 4.5 119.6 1.0
OE1 D:GLU148 4.5 119.3 1.0
N D:GLU148 4.6 100.5 1.0
CA D:VAL147 4.6 94.0 1.0
CA D:ARG144 4.6 112.1 1.0
N D:ALA143 4.6 112.4 1.0
N D:VAL147 4.7 100.9 1.0
CB D:LEU142 4.7 92.7 1.0
CA D:ALA143 4.8 117.1 1.0
C D:LYS145 4.8 115.5 1.0
CA D:GLY146 4.8 107.8 1.0
O C:ASP85 4.8 103.2 1.0
CD1 D:TYR88 4.9 85.4 1.0
O D:ALA143 4.9 121.2 1.0
C D:VAL147 4.9 99.8 1.0
CB D:TYR88 4.9 79.9 1.0
N D:LYS145 4.9 115.3 1.0
OD2 C:ASP85 5.0 119.4 1.0
CB D:GLU148 5.0 95.4 1.0

Calcium binding site 10 out of 10 in 9d5b

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Calcium binding site 10 out of 10 in the Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Methylobacterium Brachiatum Multi-Ubiquitin Protein Filament within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:30.0
occ:1.00
 OD2 D:ASP29 2.4 124.1 1.0
O D:VAL31 2.4 126.9 1.0
OD1 D:ASP29 2.8 129.8 1.0
CG D:ASP29 2.9 128.9 1.0
C D:VAL31 3.4 130.3 1.0
NE2 D:GLN36 4.0 122.9 1.0
N D:PRO32 4.2 126.3 1.0
CA D:PRO32 4.2 126.5 1.0
CA D:VAL31 4.3 129.6 1.0
CB D:VAL31 4.3 130.6 1.0
CB D:ASP29 4.4 130.4 1.0
N D:VAL31 4.5 131.8 1.0
OE1 D:GLN36 4.8 126.0 1.0
CD D:GLN36 4.9 121.4 1.0

Reference:

M.Gong, Q.Ye, Y.Gu, L.R.Chambers, M.Matyszewski, K.D.Corbett. Structural Diversity and Oligomerization of Bacterial Ubiquitin-Like Proteins To Be Published.
Page generated: Thu Jul 10 09:16:14 2025

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