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Calcium in PDB 1mdu: Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)

Protein crystallography data

The structure of Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1), PDB code: 1mdu was solved by J.F.Dawson, E.P.Sablin, J.A.Spudich, R.J.Fletterick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.187, 75.942, 96.747, 90.00, 91.87, 90.00
R / Rfree (%) 19.3 / 23.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) (pdb code 1mdu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1), PDB code: 1mdu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 1mdu

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Calcium binding site 1 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:43.4
occ:1.00
 O A:GLY41 2.3 35.9 1.0
OE2 A:GLU73 2.4 27.9 1.0
O A:VAL121 2.4 52.0 1.0
O A:HOH513 2.4 60.1 1.0
OD2 A:ASP42 2.5 45.9 1.0
OE1 A:GLU73 2.7 35.5 1.0
CD A:GLU73 2.9 35.0 1.0
C A:GLY41 3.5 34.8 1.0
C A:VAL121 3.6 50.2 1.0
CG A:ASP42 3.7 44.1 1.0
CA A:ASP42 4.1 35.6 1.0
N A:VAL121 4.1 49.9 1.0
N A:ASP42 4.2 36.2 1.0
O A:HOH476 4.3 34.8 1.0
CG A:GLU73 4.3 34.3 1.0
CA A:VAL121 4.4 50.1 1.0
CB A:ASP42 4.5 39.7 1.0
CA A:GLY41 4.5 34.3 1.0
OG A:SER70 4.6 32.2 1.0
C A:GLY120 4.6 50.0 1.0
N A:ALA122 4.6 50.0 1.0
OD1 A:ASP42 4.6 46.7 1.0
C A:ALA122 4.7 43.8 1.0
N A:SER70 4.7 38.0 1.0
N A:SER123 4.8 42.9 1.0
CA A:ALA122 4.8 47.3 1.0
CA A:CYS69 4.8 42.8 1.0
CA A:GLY120 5.0 50.3 1.0
CB A:VAL121 5.0 49.1 1.0

Calcium binding site 2 out of 7 in 1mdu

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Calcium binding site 2 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:25.6
occ:1.00
 O A:ALA92 2.2 31.3 1.0
OE1 B:GLU169 2.3 29.5 1.0
O A:HOH486 2.3 26.8 1.0
OD2 A:ASP85 2.4 29.4 1.0
O A:GLY90 2.5 30.9 1.0
O A:HOH505 2.6 28.6 1.0
O B:HOH413 3.0 46.1 1.0
OD1 A:ASP85 3.1 33.9 1.0
CG A:ASP85 3.1 27.1 1.0
C A:GLY90 3.4 32.1 1.0
C A:ALA92 3.4 28.6 1.0
CD B:GLU169 3.5 31.7 1.0
N A:ALA92 3.9 28.3 1.0
CA A:GLY90 4.0 32.0 1.0
OE2 B:GLU169 4.0 33.5 1.0
CA A:ALA92 4.2 28.6 1.0
C A:ARG91 4.3 31.9 1.0
O B:HOH414 4.3 24.2 1.0
N A:ARG91 4.4 30.1 1.0
N A:VAL93 4.5 27.6 1.0
CB A:ASP85 4.6 28.2 1.0
CA A:ARG91 4.7 32.2 1.0
CG B:GLU169 4.7 27.4 1.0
CA A:VAL93 4.7 26.6 1.0
NE2 A:GLN94 4.7 23.0 1.0
O A:HOH484 4.7 33.7 1.0
O A:ARG91 4.8 32.5 1.0
CB B:GLU169 4.8 24.7 1.0
CB A:ALA92 4.9 23.8 1.0

Calcium binding site 3 out of 7 in 1mdu

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Calcium binding site 3 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:29.2
occ:1.00
 O2B B:ATP400 2.4 18.6 1.0
O B:HOH408 2.4 31.6 1.0
O3G B:ATP400 2.4 21.6 1.0
O B:HOH406 2.4 31.5 1.0
O B:HOH409 2.4 25.9 1.0
O B:HOH405 2.5 19.9 1.0
O B:HOH407 2.7 27.7 1.0
PB B:ATP400 3.5 19.1 1.0
PG B:ATP400 3.5 24.9 1.0
O1G B:ATP400 3.8 22.2 1.0
O3B B:ATP400 3.8 25.5 1.0
O B:HOH411 4.2 22.2 1.0
OE1 B:GLN139 4.2 25.2 1.0
O3A B:ATP400 4.3 17.0 1.0
CA B:GLY15 4.4 24.4 1.0
OD1 B:ASP156 4.5 34.5 1.0
CD B:GLN139 4.5 27.2 1.0
O B:HOH478 4.5 30.4 1.0
NZ B:LYS20 4.5 25.5 1.0
O1A B:ATP400 4.6 20.1 1.0
OD2 B:ASP13 4.7 31.8 1.0
PA B:ATP400 4.7 26.5 1.0
OD1 B:ASP13 4.7 33.8 1.0
O1B B:ATP400 4.8 20.1 1.0
O2G B:ATP400 4.8 26.7 1.0
NE2 B:GLN139 4.9 24.0 1.0

Calcium binding site 4 out of 7 in 1mdu

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Calcium binding site 4 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:50.9
occ:1.00
 O B:HOH471 2.2 52.3 1.0
O B:SER325 2.5 35.9 1.0
O B:HOH531 2.5 57.5 1.0
O B:HOH472 2.7 35.3 1.0
O B:HOH572 2.7 58.6 1.0
C B:SER325 3.6 35.8 1.0
O B:MET327 4.2 30.4 1.0
O B:HOH475 4.2 31.1 1.0
CA B:SER325 4.3 36.4 1.0
N B:THR326 4.6 34.7 1.0
CG2 B:THR320 4.7 25.4 1.0
CA B:THR326 4.8 34.9 1.0
N B:MET327 4.9 34.4 1.0
C B:THR326 5.0 34.4 1.0

Calcium binding site 5 out of 7 in 1mdu

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Calcium binding site 5 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:36.5
occ:1.00
 O D:HOH455 2.0 51.3 1.0
O D:HOH418 2.2 30.7 1.0
O D:VAL121 2.3 39.5 1.0
OD2 D:ASP42 2.3 46.0 1.0
O D:GLY41 2.4 30.4 1.0
OE2 D:GLU73 2.4 33.8 1.0
OE1 D:GLU73 2.6 33.5 1.0
CD D:GLU73 2.8 32.7 1.0
C D:VAL121 3.5 39.3 1.0
C D:GLY41 3.5 32.4 1.0
CG D:ASP42 3.5 45.9 1.0
N D:VAL121 3.9 37.8 1.0
CA D:ASP42 4.1 34.8 1.0
O D:HOH456 4.1 58.4 1.0
N D:ASP42 4.2 32.6 1.0
CA D:VAL121 4.3 38.3 1.0
C D:GLY120 4.3 40.2 1.0
O D:HOH410 4.3 19.4 1.0
CG D:GLU73 4.3 31.1 1.0
CG1 D:VAL121 4.4 39.4 1.0
OD1 D:ASP42 4.4 45.8 1.0
CB D:ASP42 4.4 39.7 1.0
N D:ALA122 4.4 38.5 1.0
O D:HOH411 4.5 27.8 1.0
C D:ALA122 4.5 35.5 1.0
CA D:ALA122 4.6 36.9 1.0
O D:HOH445 4.6 34.8 1.0
CA D:GLY120 4.6 41.5 1.0
CA D:GLY41 4.6 32.5 1.0
OG D:SER70 4.6 38.5 1.0
N D:SER123 4.7 35.0 1.0
N D:SER70 4.7 37.8 1.0
O D:ALA122 4.8 35.8 1.0
CA D:CYS69 4.8 37.7 1.0
O D:GLY120 4.9 39.8 1.0
CB D:VAL121 5.0 38.8 1.0

Calcium binding site 6 out of 7 in 1mdu

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Calcium binding site 6 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:24.1
occ:1.00
 O D:ALA92 2.2 27.0 1.0
OD2 D:ASP85 2.3 28.3 1.0
OE1 E:GLU169 2.4 29.1 1.0
O D:GLY90 2.4 27.2 1.0
O E:HOH403 2.5 29.4 1.0
O D:HOH425 2.7 24.4 1.0
OD1 D:ASP85 3.0 28.4 1.0
CG D:ASP85 3.0 23.8 1.0
C D:GLY90 3.2 29.3 1.0
C D:ALA92 3.4 26.9 1.0
CD E:GLU169 3.6 31.4 1.0
CA D:GLY90 3.8 31.2 1.0
N D:ALA92 3.8 25.0 1.0
OE2 E:GLU169 4.1 28.4 1.0
C D:ARG91 4.2 28.7 1.0
N D:ARG91 4.2 28.2 1.0
O E:HOH515 4.2 41.2 1.0
CA D:ALA92 4.2 24.9 1.0
O E:HOH404 4.4 27.5 1.0
N D:VAL93 4.5 25.5 1.0
CB D:ASP85 4.5 25.1 1.0
CA D:ARG91 4.5 29.0 1.0
NE2 D:GLN94 4.6 26.5 1.0
O D:ARG91 4.7 28.6 1.0
CA D:VAL93 4.7 25.7 1.0
CG E:GLU169 4.8 26.7 1.0
CB E:GLU169 4.9 26.9 1.0
O D:HOH424 4.9 36.5 1.0
CB D:ALA92 4.9 20.5 1.0

Calcium binding site 7 out of 7 in 1mdu

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Calcium binding site 7 out of 7 in the Crystal Structure of the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1)


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 the Chicken Actin Trimer Complexed with Human Gelsolin Segment 1 (Gs-1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:29.9
occ:1.00
 O E:HOH410 2.3 23.4 1.0
O2B E:ATP400 2.3 22.0 1.0
O E:HOH411 2.4 20.1 1.0
O E:HOH408 2.4 23.7 1.0
O3G E:ATP400 2.5 19.9 1.0
O E:HOH480 2.8 34.3 1.0
PB E:ATP400 3.5 17.9 1.0
PG E:ATP400 3.6 19.6 1.0
O3B E:ATP400 3.9 21.6 1.0
O E:HOH412 3.9 20.6 1.0
O1G E:ATP400 4.0 22.2 1.0
O3A E:ATP400 4.3 18.2 1.0
NZ E:LYS20 4.3 28.5 1.0
OE1 E:GLN139 4.4 28.2 1.0
CA E:GLY15 4.5 27.1 1.0
O E:HOH409 4.5 29.0 1.0
OD1 E:ASP156 4.6 41.9 1.0
CD E:GLN139 4.6 29.0 1.0
OD2 E:ASP156 4.7 39.9 1.0
O1A E:ATP400 4.7 21.7 1.0
PA E:ATP400 4.7 25.5 1.0
O1B E:ATP400 4.8 24.0 1.0
O E:HOH419 4.8 36.3 1.0
OD2 E:ASP13 4.8 33.6 1.0
NE2 E:GLN139 4.9 25.0 1.0
O2G E:ATP400 4.9 26.0 1.0
OD1 E:ASP13 4.9 31.1 1.0
CG E:ASP156 5.0 38.0 1.0

Reference:

J.F.Dawson, E.P.Sablin, J.A.Spudich, R.J.Fletterick. Structure of An F-Actin Trimer Disrupted By Gelsolin and Implications For the Mechanism of Severing J.Biol.Chem. V. 278 1229 2003.
ISSN: ISSN 0021-9258
PubMed: 12356759
DOI: 10.1074/JBC.M209160200
Page generated: Thu Jul 11 12:29:57 2024

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