Calcium in PDB 8vkh: Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin

Calcium Binding Sites:

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Binding sites:

The binding sites of Calcium atom in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin (pdb code 8vkh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin, PDB code: 8vkh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 8vkh

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Calcium binding site 1 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


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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 Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:115.6
occ:1.00
 O3B A:ADP401 2.4 121.6 1.0
O2A A:ADP401 3.2 121.6 1.0
PB A:ADP401 3.7 121.6 1.0
O1B A:ADP401 4.0 121.6 1.0
CA A:GLY156 4.2 120.5 1.0
OE1 A:GLN137 4.2 119.1 1.0
NE2 A:GLN137 4.3 119.1 1.0
PA A:ADP401 4.3 121.6 1.0
OD1 A:ASP154 4.3 119.2 1.0
OD2 A:ASP11 4.4 133.2 1.0
O3A A:ADP401 4.4 121.6 1.0
CD A:GLN137 4.4 119.1 1.0
CA A:GLY13 4.5 132.5 1.0
NZ A:LYS18 4.5 125.2 1.0
OD2 A:ASP154 4.8 119.2 1.0
N A:GLY156 4.8 120.5 1.0
CA A:GLY301 4.9 119.2 1.0
O2B A:ADP401 4.9 121.6 1.0
OD1 A:ASP11 4.9 133.2 1.0
O1A A:ADP401 4.9 121.6 1.0
CG A:ASP154 5.0 119.2 1.0

Calcium binding site 2 out of 14 in 8vkh

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Calcium binding site 2 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:113.9
occ:1.00
 O3B B:ADP401 2.6 121.0 1.0
O2A B:ADP401 3.3 121.0 1.0
PB B:ADP401 3.7 121.0 1.0
O1B B:ADP401 3.7 121.0 1.0
CA B:GLY156 4.0 117.6 1.0
OE1 B:GLN137 4.1 123.3 1.0
OD2 B:ASP154 4.3 118.3 1.0
OD1 B:ASP154 4.4 118.3 1.0
PA B:ADP401 4.5 121.0 1.0
O3A B:ADP401 4.5 121.0 1.0
OD2 B:ASP11 4.5 130.5 1.0
CD B:GLN137 4.6 123.3 1.0
CA B:GLY301 4.7 119.5 1.0
N B:GLY156 4.7 117.6 1.0
NE2 B:GLN137 4.7 123.3 1.0
CG2 B:VAL339 4.8 120.3 1.0
CG B:ASP154 4.8 118.3 1.0
NZ B:LYS18 4.9 121.6 1.0
O2B B:ADP401 4.9 121.0 1.0
OD1 B:ASP11 5.0 130.5 1.0

Calcium binding site 3 out of 14 in 8vkh

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Calcium binding site 3 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:114.4
occ:1.00
 O3B C:ADP401 2.5 120.6 1.0
O2A C:ADP401 2.5 120.6 1.0
O1B C:ADP401 3.3 120.6 1.0
PB C:ADP401 3.3 120.6 1.0
CA C:GLY156 3.4 116.1 1.0
PA C:ADP401 3.7 120.6 1.0
NE2 C:GLN137 3.8 120.5 1.0
O3A C:ADP401 4.0 120.6 1.0
OD2 C:ASP154 4.1 113.2 1.0
N C:GLY156 4.2 116.1 1.0
O1A C:ADP401 4.6 120.6 1.0
C C:GLY156 4.6 116.1 1.0
O2B C:ADP401 4.7 120.6 1.0
OD1 C:ASP154 4.7 113.2 1.0
N C:ASP157 4.8 125.7 1.0
CG C:ASP154 4.8 113.2 1.0
CA C:GLY301 4.9 112.7 1.0
O5' C:ADP401 4.9 120.6 1.0
NZ C:LYS18 4.9 108.1 1.0
C C:SER155 5.0 111.0 1.0
N C:GLY302 5.0 112.0 1.0

Calcium binding site 4 out of 14 in 8vkh

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Calcium binding site 4 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:105.1
occ:1.00
 O3B D:ADP401 2.6 123.5 1.0
OE1 D:GLN137 2.8 130.4 1.0
CD D:GLN137 3.4 130.4 1.0
NE2 D:GLN137 3.5 130.4 1.0
PB D:ADP401 3.7 123.5 1.0
O2A D:ADP401 3.8 123.5 1.0
O1B D:ADP401 3.8 123.5 1.0
CA D:GLY156 3.9 121.6 1.0
OD1 D:ASP154 4.2 129.4 1.0
CA D:GLY13 4.4 125.6 1.0
N D:GLY156 4.5 121.6 1.0
OD2 D:ASP11 4.6 131.8 1.0
OD1 D:ASP11 4.6 131.8 1.0
CG D:GLN137 4.7 130.4 1.0
O3A D:ADP401 4.8 123.5 1.0
O2B D:ADP401 4.8 123.5 1.0
PA D:ADP401 4.9 123.5 1.0

Calcium binding site 5 out of 14 in 8vkh

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Calcium binding site 5 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:115.8
occ:1.00
 O1B E:ATP401 2.5 134.2 1.0
O2G E:ATP401 2.5 134.2 1.0
OE1 E:GLN137 2.9 147.8 1.0
PB E:ATP401 3.6 134.2 1.0
PG E:ATP401 3.6 134.2 1.0
O3B E:ATP401 3.7 134.2 1.0
CD E:GLN137 3.8 147.8 1.0
O3G E:ATP401 3.9 134.2 1.0
OD2 E:ASP11 4.0 136.8 1.0
OD2 E:ASP154 4.1 149.9 1.0
OD1 E:ASP154 4.1 149.9 1.0
O3A E:ATP401 4.2 134.2 1.0
OD1 E:ASP11 4.4 136.8 1.0
NE2 E:GLN137 4.4 147.8 1.0
O1A E:ATP401 4.5 134.2 1.0
CG E:ASP154 4.5 149.9 1.0
CG2 E:VAL339 4.6 134.4 1.0
CG E:ASP11 4.6 136.8 1.0
NZ E:LYS18 4.7 125.8 1.0
CG E:GLN137 4.8 147.8 1.0
CA E:GLY13 4.8 132.9 1.0
PA E:ATP401 4.9 134.2 1.0
O2B E:ATP401 4.9 134.2 1.0
O1G E:ATP401 4.9 134.2 1.0

Calcium binding site 6 out of 14 in 8vkh

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Calcium binding site 6 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca402

b:188.5
occ:1.00
 O1B F:ATP401 2.5 208.3 1.0
O2G F:ATP401 2.5 208.3 1.0
OE1 F:GLN137 3.1 230.6 1.0
PB F:ATP401 3.5 208.3 1.0
PG F:ATP401 3.5 208.3 1.0
O3B F:ATP401 3.6 208.3 1.0
O3G F:ATP401 3.8 208.3 1.0
OD1 F:ASP154 3.9 233.0 1.0
CD F:GLN137 4.0 230.6 1.0
O1A F:ATP401 4.0 208.3 1.0
O3A F:ATP401 4.1 208.3 1.0
OD2 F:ASP154 4.1 233.0 1.0
CG F:ASP154 4.5 233.0 1.0
OD2 F:ASP11 4.5 217.5 1.0
PA F:ATP401 4.6 208.3 1.0
NE2 F:GLN137 4.6 230.6 1.0
CG2 F:VAL339 4.8 219.9 1.0
OD1 F:ASP11 4.8 217.5 1.0
CA F:GLY156 4.9 211.1 1.0
O2B F:ATP401 4.9 208.3 1.0
CG F:GLN137 4.9 230.6 1.0
O1G F:ATP401 4.9 208.3 1.0
NZ F:LYS18 4.9 204.3 1.0
CA F:GLY13 5.0 206.7 1.0

Calcium binding site 7 out of 14 in 8vkh

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Calcium binding site 7 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca801

b:287.9
occ:1.00
 OE2 G:GLU97 2.4 280.1 1.0
O G:GLY65 2.5 294.8 1.0
O G:VAL145 2.5 276.8 1.0
OE1 G:GLU97 2.7 280.1 1.0
CD G:GLU97 2.8 280.1 1.0
OD1 G:ASP66 3.3 289.2 1.0
C G:GLY65 3.6 294.8 1.0
C G:VAL145 3.7 276.8 1.0
OG G:SER94 4.3 280.3 1.0
CG G:GLU97 4.3 280.1 1.0
N G:VAL145 4.3 276.8 1.0
N G:SER94 4.4 280.3 1.0
CG G:ASP66 4.5 289.2 1.0
N G:ASP66 4.5 289.2 1.0
CA G:GLY65 4.5 294.8 1.0
CA G:ASP66 4.6 289.2 1.0
C G:ALA146 4.6 270.3 1.0
CA G:VAL145 4.6 276.8 1.0
N G:ALA146 4.6 270.3 1.0
CA G:CYS93 4.7 298.9 1.0
CA G:ALA146 4.7 270.3 1.0
C G:GLY144 4.7 285.3 1.0
CG1 G:VAL145 4.7 276.8 1.0
N G:SER147 4.7 259.9 1.0
O G:ALA146 4.9 270.3 1.0
CA G:GLY144 5.0 285.3 1.0
CB G:SER94 5.0 280.3 1.0

Calcium binding site 8 out of 14 in 8vkh

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Calcium binding site 8 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca802

b:198.3
occ:1.00
 OD1 G:ASP259 2.4 206.8 1.0
O G:GLY186 2.4 192.9 1.0
OD1 G:ASP187 2.5 190.8 1.0
OD2 G:ASP259 3.0 206.8 1.0
CG G:ASP259 3.0 206.8 1.0
C G:GLY186 3.2 192.9 1.0
CG G:ASP187 3.7 190.8 1.0
NZ G:LYS166 3.7 181.2 1.0
OE1 G:GLU209 3.9 173.7 1.0
O G:THR257 3.9 222.8 1.0
N G:ASP187 3.9 190.8 1.0
OE2 G:GLU209 4.0 173.7 1.0
CA G:GLY186 4.0 192.9 1.0
CA G:ASP187 4.1 190.8 1.0
CB G:ASP259 4.3 206.8 1.0
CG G:LYS166 4.3 181.2 1.0
CD G:GLU209 4.4 173.7 1.0
CB G:ASP187 4.4 190.8 1.0
OD2 G:ASP187 4.6 190.8 1.0
CA G:ASP259 4.7 206.8 1.0
CE G:LYS166 4.8 181.2 1.0
N G:ASP259 4.9 206.8 1.0

Calcium binding site 9 out of 14 in 8vkh

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Calcium binding site 9 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca803

b:250.6
occ:1.00
 O G:GLU302 2.6 251.8 1.0
OE1 G:GLU327 2.6 257.1 1.0
OE2 G:GLU327 2.6 257.1 1.0
CD G:GLU327 2.9 257.1 1.0
OD1 G:ASN324 3.6 253.2 1.0
OD1 G:ASP303 3.7 257.4 1.0
C G:GLU302 3.8 251.8 1.0
O G:GLN322 4.1 245.4 1.0
N G:ASN324 4.3 253.2 1.0
CA G:ALA323 4.3 253.2 1.0
CG G:GLU327 4.4 257.1 1.0
CG G:ASN324 4.5 253.2 1.0
OG G:SER277 4.5 257.1 1.0
CA G:ASP303 4.6 257.4 1.0
N G:ASP303 4.6 257.4 1.0
CB G:GLU302 4.7 251.8 1.0
CA G:GLU302 4.7 251.8 1.0
N G:ASN278 4.7 259.3 1.0
CG G:ASP303 4.9 257.4 1.0
C G:ALA323 4.9 253.2 1.0
CB G:ALA323 5.0 253.2 1.0

Calcium binding site 10 out of 14 in 8vkh

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Calcium binding site 10 out of 14 in the Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Gelsolin Domains G1-G3 Bound to the Barbed End of F-Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca804

b:273.5
occ:1.00
 O G:ALA116 2.5 287.1 1.0
OD1 G:ASP109 2.6 277.8 1.0
O G:GLY114 2.6 282.5 1.0
C G:GLY114 2.8 282.5 1.0
OD2 G:ASP109 3.0 277.8 1.0
N G:ALA116 3.1 287.1 1.0
CA G:GLY114 3.1 282.5 1.0
CG G:ASP109 3.2 277.8 1.0
C G:ALA116 3.4 287.1 1.0
OE2 F:GLU167 3.4 265.8 1.0
N G:ARG115 3.4 295.7 1.0
CA G:ALA116 3.7 287.1 1.0
C G:ARG115 3.9 295.7 1.0
CA G:ARG115 4.1 295.7 1.0
CB G:ALA116 4.2 287.1 1.0
N G:GLY114 4.3 282.5 1.0
CD F:GLU167 4.6 265.8 1.0
N G:VAL117 4.6 283.9 1.0
CB G:ASP109 4.7 277.8 1.0
O G:ARG115 4.9 295.7 1.0

Reference:

K.R.Barrie, G.Rebowski, R.Dominguez. Mechanism of Actin Filament Severing and Capping By Gelsolin. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39345426
DOI: 10.1101/2024.09.10.612341
Page generated: Thu Oct 31 17:15:20 2024

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