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Calcium in PDB 3ffk: Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin

Protein crystallography data

The structure of Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin, PDB code: 3ffk was solved by S.Chumnarnsilpa, R.C.Robinson, L.D.Burtnick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.179, 146.923, 148.301, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.3

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 3ffk

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Calcium binding site 1 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca756

b:3.6
occ:1.00
 O A:GLY186 2.1 28.5 1.0
O A:HOH789 2.2 7.8 1.0
OD2 A:ASP187 2.3 26.9 1.0
OE1 A:GLU209 2.3 28.2 1.0
O A:HOH883 2.4 22.4 1.0
OE2 A:GLU209 2.7 29.6 1.0
OD1 A:ASP259 2.7 45.7 1.0
CD A:GLU209 2.8 29.0 1.0
C A:GLY186 3.3 28.4 1.0
CG A:ASP187 3.4 26.9 1.0
CG A:ASP259 3.6 46.4 1.0
OD2 A:ASP259 3.7 46.5 1.0
CA A:ASP187 3.8 27.6 1.0
N A:ASP187 4.0 28.0 1.0
CB A:ASP187 4.1 27.3 1.0
ND2 A:ASN206 4.2 32.9 1.0
CG A:GLU209 4.3 29.8 1.0
CA A:GLY186 4.3 28.8 1.0
OD1 A:ASP187 4.4 26.4 1.0
CA A:SER205 4.4 31.2 1.0
NZ A:LYS166 4.4 31.9 1.0
N A:ASN206 4.5 32.1 1.0
O A:ASN204 4.7 30.7 1.0
O A:GLY167 4.7 31.2 1.0
CG A:LYS166 4.7 31.4 1.0
CB A:SER205 4.8 31.2 1.0
O A:THR257 4.9 48.6 1.0
CB A:ASP259 5.0 46.6 1.0

Calcium binding site 2 out of 10 in 3ffk

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Calcium binding site 2 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca757

b:8.7
occ:1.00
 OD2 A:ASP66 2.3 22.5 1.0
O A:GLY65 2.4 23.7 1.0
OE1 A:GLU97 2.4 20.0 1.0
O A:VAL145 2.4 28.1 1.0
OE2 A:GLU97 2.8 20.5 1.0
CD A:GLU97 2.9 20.2 1.0
C A:GLY65 3.4 23.6 1.0
CG A:ASP66 3.6 23.1 1.0
C A:VAL145 3.6 28.0 1.0
N A:VAL145 3.9 29.3 1.0
CA A:ASP66 4.1 23.1 1.0
N A:ASP66 4.2 23.3 1.0
CA A:VAL145 4.2 28.5 1.0
CA A:GLY65 4.3 23.8 1.0
O A:HOH788 4.4 35.2 1.0
CG A:GLU97 4.4 18.9 1.0
CB A:ASP66 4.4 23.0 1.0
OD1 A:ASP66 4.4 23.4 1.0
CG1 A:VAL145 4.4 28.6 1.0
O A:HOH872 4.5 20.5 1.0
OG A:SER94 4.5 22.2 1.0
C A:GLY144 4.5 30.2 1.0
N A:ALA146 4.6 27.2 1.0
N A:SER147 4.7 25.8 1.0
C A:ALA146 4.8 26.4 1.0
CA A:GLY144 4.8 31.1 1.0
N A:SER94 4.8 22.9 1.0
CA A:CYS93 4.9 24.2 1.0
CA A:ALA146 4.9 26.7 1.0
CB A:VAL145 4.9 28.5 1.0

Calcium binding site 3 out of 10 in 3ffk

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Calcium binding site 3 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca758

b:15.2
occ:1.00
 O A:HOH882 2.3 28.2 1.0
OE1 B:GLU167 2.4 14.8 1.0
OD2 A:ASP109 2.6 30.5 1.0
O A:GLY114 2.7 34.7 1.0
O A:ALA116 2.7 33.3 1.0
O A:HOH853 2.7 2.0 1.0
OD1 A:ASP109 3.1 30.9 1.0
CG A:ASP109 3.2 30.1 1.0
CD B:GLU167 3.4 14.8 1.0
C A:GLY114 3.4 34.4 1.0
CG B:GLU167 3.7 14.3 1.0
C A:ALA116 3.8 32.9 1.0
N A:ALA116 3.9 33.5 1.0
CA A:GLY114 4.0 34.1 1.0
N A:ARG115 4.3 34.4 1.0
CA A:ALA116 4.5 33.1 1.0
OE2 B:GLU167 4.5 15.2 1.0
C A:ARG115 4.7 34.1 1.0
CB A:ASP109 4.7 29.0 1.0
CB B:GLU167 4.7 14.3 1.0
CA A:ARG115 4.8 34.7 1.0
N A:VAL117 4.9 32.0 1.0
NE2 A:GLN118 5.0 23.5 1.0

Calcium binding site 4 out of 10 in 3ffk

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Calcium binding site 4 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca759

b:15.9
occ:1.00
 O A:HOH802 2.2 23.6 1.0
OE2 A:GLU327 2.2 31.4 1.0
O A:GLU302 2.3 28.7 1.0
OD1 A:ASP303 2.6 28.8 1.0
OE1 A:GLU327 2.6 30.6 1.0
O A:HOH777 2.7 9.7 1.0
CD A:GLU327 2.8 30.9 1.0
C A:GLU302 3.5 28.3 1.0
CG A:ASP303 3.7 28.4 1.0
ND2 A:ASN324 3.9 29.1 1.0
OG A:SER277 4.0 27.1 1.0
CB A:GLU302 4.2 29.3 1.0
CA A:ASP303 4.3 27.2 1.0
CG A:GLU327 4.3 30.3 1.0
OD1 A:ASN278 4.3 28.3 1.0
N A:ASP303 4.3 27.5 1.0
CA A:GLU302 4.4 28.8 1.0
CA A:ALA323 4.5 28.4 1.0
OD2 A:ASP303 4.6 29.7 1.0
N A:ASN324 4.6 29.1 1.0
CG A:ASN324 4.6 28.8 1.0
CB A:ASP303 4.6 27.5 1.0
N A:GLY279 4.6 30.3 1.0
CA A:GLY279 4.7 31.4 1.0
OD1 A:ASN324 4.9 27.9 1.0
N A:ASN278 4.9 28.5 1.0
O A:GLN322 5.0 27.9 1.0

Calcium binding site 5 out of 10 in 3ffk

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Calcium binding site 5 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:7.3
occ:1.00
 O2B B:ATP380 2.1 7.7 1.0
O3G B:ATP380 2.2 7.8 1.0
O B:HOH470 2.2 20.1 1.0
O B:HOH469 2.3 8.2 1.0
O B:HOH392 2.5 4.1 1.0
O B:HOH398 2.6 24.1 1.0
PG B:ATP380 3.2 8.7 1.0
PB B:ATP380 3.4 7.8 1.0
O1G B:ATP380 3.5 7.9 1.0
O3B B:ATP380 3.7 7.9 1.0
CA B:GLY13 4.1 17.2 1.0
OE1 B:GLN137 4.1 16.8 1.0
O B:HOH379 4.1 5.5 1.0
O3A B:ATP380 4.2 9.6 1.0
NZ B:LYS18 4.3 10.0 1.0
CD B:GLN137 4.4 15.9 1.0
O1A B:ATP380 4.4 10.8 1.0
O2G B:ATP380 4.6 8.9 1.0
O1B B:ATP380 4.6 7.4 1.0
OD1 B:ASP154 4.7 19.2 1.0
NE2 B:GLN137 4.7 15.6 1.0
PA B:ATP380 4.8 10.8 1.0
OD2 B:ASP154 4.8 18.6 1.0
CG B:GLN137 4.9 15.6 1.0
O B:ASN12 5.0 17.6 1.0

Calcium binding site 6 out of 10 in 3ffk

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Calcium binding site 6 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca756

b:22.7
occ:1.00
 O D:GLY186 2.2 11.1 1.0
OE2 D:GLU209 2.3 21.2 1.0
OD1 D:ASP259 2.5 31.7 1.0
OD2 D:ASP187 2.5 12.1 1.0
O D:HOH852 2.5 27.1 1.0
OE1 D:GLU209 2.6 20.0 1.0
O D:HOH784 2.7 17.1 1.0
CD D:GLU209 2.8 21.1 1.0
OD2 D:ASP259 3.1 32.3 1.0
CG D:ASP259 3.2 32.5 1.0
C D:GLY186 3.3 11.2 1.0
CG D:ASP187 3.6 12.3 1.0
CA D:ASP187 4.0 11.5 1.0
N D:ASP187 4.1 11.3 1.0
CA D:SER205 4.3 17.5 1.0
CA D:GLY186 4.3 11.7 1.0
CG D:GLU209 4.3 21.5 1.0
CB D:ASP187 4.4 11.7 1.0
ND2 D:ASN206 4.4 18.8 1.0
O D:ASN204 4.4 16.3 1.0
N D:ASN206 4.5 18.4 1.0
OD1 D:ASP187 4.6 12.9 1.0
CB D:ASP259 4.6 33.0 1.0
C D:SER205 4.9 17.8 1.0
CE D:LYS166 4.9 21.4 1.0
O D:GLY167 4.9 20.7 1.0
CB D:SER205 4.9 17.3 1.0
N D:ASP259 5.0 33.8 1.0

Calcium binding site 7 out of 10 in 3ffk

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Calcium binding site 7 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca757

b:29.0
occ:1.00
 O D:VAL145 2.2 24.4 1.0
OE1 D:GLU97 2.3 15.7 1.0
O D:GLY65 2.4 19.6 1.0
OD2 D:ASP66 2.6 18.8 1.0
CD D:GLU97 3.0 15.7 1.0
OE2 D:GLU97 3.3 15.8 1.0
C D:VAL145 3.4 24.7 1.0
C D:GLY65 3.5 20.1 1.0
CG D:ASP66 3.8 18.9 1.0
N D:VAL145 4.2 25.7 1.0
CA D:ASP66 4.2 19.4 1.0
N D:SER147 4.3 23.0 1.0
OG D:SER94 4.3 18.4 1.0
N D:ALA146 4.3 24.2 1.0
N D:ASP66 4.3 19.9 1.0
C D:ALA146 4.3 23.4 1.0
O D:HOH791 4.3 15.1 1.0
CA D:ALA146 4.3 23.7 1.0
CA D:VAL145 4.4 25.1 1.0
CG D:GLU97 4.4 15.5 1.0
CA D:GLY65 4.5 20.3 1.0
C D:GLY144 4.5 26.3 1.0
CB D:ASP66 4.7 19.3 1.0
OD1 D:ASP66 4.7 18.1 1.0
CG1 D:VAL145 4.7 25.0 1.0
N D:SER94 4.8 17.9 1.0
O D:ALA146 4.9 23.4 1.0
CA D:CYS93 4.9 17.6 1.0
CA D:SER147 4.9 22.4 1.0
CA D:GLY144 5.0 26.6 1.0
O D:GLY144 5.0 26.4 1.0

Calcium binding site 8 out of 10 in 3ffk

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Calcium binding site 8 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca758

b:31.9
occ:1.00
 OE1 E:GLU167 2.3 13.0 1.0
O D:GLY114 2.4 20.7 1.0
OD2 D:ASP109 2.5 15.6 1.0
O D:ALA116 2.6 19.5 1.0
O D:HOH833 2.8 2.0 1.0
OD1 D:ASP109 3.2 15.3 1.0
CG D:ASP109 3.2 15.4 1.0
C D:GLY114 3.5 20.5 1.0
O E:HOH402 3.5 4.1 1.0
CD E:GLU167 3.5 13.2 1.0
C D:ALA116 3.7 19.4 1.0
N D:ALA116 3.9 20.1 1.0
OE2 E:GLU167 4.0 12.1 1.0
CA D:GLY114 4.1 20.4 1.0
CA D:ALA116 4.4 19.6 1.0
N D:ARG115 4.4 20.7 1.0
CG E:GLU167 4.7 13.2 1.0
CB E:GLU167 4.7 13.8 1.0
C D:ARG115 4.7 20.6 1.0
CB D:ASP109 4.7 15.4 1.0
CA D:ARG115 4.7 21.1 1.0
N D:VAL117 4.8 19.1 1.0
NE2 D:GLN118 5.0 15.7 1.0

Calcium binding site 9 out of 10 in 3ffk

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Calcium binding site 9 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


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 Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca759

b:26.0
occ:1.00
 OE2 D:GLU327 2.5 19.4 1.0
O D:GLU302 2.5 21.3 1.0
OE1 D:GLU327 2.6 19.8 1.0
OD1 D:ASP303 2.6 21.3 1.0
CD D:GLU327 2.9 19.7 1.0
C D:GLU302 3.5 21.3 1.0
CG D:ASP303 3.8 20.7 1.0
ND2 D:ASN324 4.0 17.6 1.0
O D:HOH810 4.0 31.0 1.0
O D:HOH801 4.1 12.8 1.0
CA D:ASP303 4.1 20.5 1.0
N D:ASP303 4.2 20.9 1.0
CB D:GLU302 4.3 22.0 1.0
OG D:SER277 4.3 16.0 1.0
CG D:GLU327 4.4 19.4 1.0
CA D:GLU302 4.5 21.8 1.0
CB D:ASP303 4.5 20.5 1.0
N D:ASN324 4.6 18.6 1.0
OD1 D:ASN278 4.7 17.3 1.0
CA D:ALA323 4.7 18.7 1.0
N D:GLY279 4.7 16.8 1.0
OD2 D:ASP303 4.7 20.2 1.0
CA D:GLY279 4.8 17.3 1.0
O D:GLN322 4.9 19.4 1.0
CB D:SER277 5.0 15.7 1.0
CG D:ASN324 5.0 18.6 1.0

Calcium binding site 10 out of 10 in 3ffk

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Calcium binding site 10 out of 10 in the Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human Gelsolin Domains G1-G3 Bound to Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:18.2
occ:1.00
 O E:HOH395 2.3 2.0 1.0
O2B E:ATP380 2.3 15.5 1.0
O E:HOH433 2.3 2.0 1.0
O3G E:ATP380 2.5 14.5 1.0
O E:HOH490 2.6 9.6 1.0
O E:HOH441 2.7 2.0 1.0
O1G E:ATP380 3.3 13.4 1.0
PG E:ATP380 3.3 15.2 1.0
PB E:ATP380 3.5 15.8 1.0
O3B E:ATP380 3.8 15.6 1.0
CA E:GLY13 4.0 20.2 1.0
O E:HOH450 4.0 13.6 1.0
OE1 E:GLN137 4.2 12.8 1.0
O3A E:ATP380 4.2 14.6 1.0
CD E:GLN137 4.4 12.8 1.0
NZ E:LYS18 4.5 14.5 1.0
O1A E:ATP380 4.5 15.4 1.0
O2G E:ATP380 4.7 14.3 1.0
NE2 E:GLN137 4.7 13.6 1.0
O1B E:ATP380 4.8 16.2 1.0
N E:GLY13 4.8 20.8 1.0
OD1 E:ASP154 4.8 19.3 1.0
OD2 E:ASP154 4.9 18.1 1.0
OD1 E:ASP11 4.9 25.2 1.0
PA E:ATP380 4.9 14.7 1.0
OD2 E:ASP11 5.0 24.2 1.0
O E:HOH404 5.0 19.9 1.0
N E:SER14 5.0 19.7 1.0

Reference:

S.Nag, Q.Ma, H.Wang, S.Chumnarnsilpa, W.L.Lee, M.Larsson, B.Kannan, M.Hernandez-Valladares, L.D.Burtnick, R.C.Robinson. CA2+ Binding By Domain 2 Plays A Critical Role in the Activation and Stabilization of Gelsolin. Proc.Natl.Acad.Sci.Usa V. 106 13713 2009.
ISSN: ISSN 0027-8424
PubMed: 19666512
DOI: 10.1073/PNAS.0812374106
Page generated: Sat Jul 13 09:49:57 2024

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