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Calcium in PDB 7yne: Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form Actin

Protein crystallography data

The structure of Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form Actin, PDB code: 7yne was solved by S.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.21 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.898, 97.999, 420.812, 90, 90, 90
R / Rfree (%) 27.3 / 30.8

Other elements in 7yne:

The structure of Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form Actin also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form Actin (pdb code 7yne). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form Actin, PDB code: 7yne:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 7yne

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Calcium binding site 1 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:59.4
occ:1.00
 O A:HOH506 2.4 35.5 1.0
O A:HOH503 2.4 39.6 1.0
O1B A:ADP401 2.4 44.0 1.0
OE1 A:GLN137 3.1 50.1 1.0
PB A:ADP401 3.6 34.8 1.0
O3B A:ADP401 3.7 47.2 1.0
CD A:GLN137 3.9 43.7 1.0
O A:HOH529 3.9 39.8 1.0
OD2 A:ASP154 4.1 47.6 1.0
CA A:GLY13 4.4 48.1 1.0
OD2 A:ASP11 4.4 34.4 1.0
NE2 A:GLN137 4.4 41.0 1.0
OD1 A:ASP11 4.4 52.0 1.0
O2A A:ADP401 4.5 42.9 1.0
OD1 A:ASP154 4.5 35.4 1.0
O3A A:ADP401 4.5 42.4 1.0
O2B A:ADP401 4.6 38.6 1.0
CG A:ASP154 4.7 34.4 1.0
CG A:GLN137 4.7 43.7 1.0
NZ A:LYS18 4.8 33.5 1.0
CG A:ASP11 4.8 35.5 1.0
CG2 A:VAL339 4.9 43.3 1.0

Calcium binding site 2 out of 12 in 7yne

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Calcium binding site 2 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:48.3
occ:1.00
 OD2 B:ASP115 2.3 35.2 1.0
O B:PRO122 2.4 35.5 1.0
O B:GLY120 2.4 38.9 1.0
OD1 B:ASP115 2.5 35.5 1.0
CG B:ASP115 2.7 32.2 1.0
OE1 A:GLU167 3.1 50.3 1.0
O A:HOH548 3.2 43.0 1.0
C B:GLY120 3.3 42.5 1.0
C B:PRO122 3.6 40.0 1.0
CA B:GLY120 3.7 39.2 1.0
CD A:GLU167 4.2 43.7 1.0
N B:PRO122 4.2 38.1 1.0
CB B:ASP115 4.2 35.1 1.0
C B:LEU121 4.3 41.3 1.0
O B:HOH316 4.4 51.3 1.0
N B:LEU121 4.4 51.4 1.0
CA B:PRO122 4.4 35.5 1.0
OE2 A:GLU167 4.5 41.1 1.0
O B:LEU121 4.6 45.6 1.0
N B:VAL123 4.6 39.4 1.0
NE2 B:GLN124 4.7 31.1 1.0
CD B:PRO122 4.7 36.5 1.0
CA B:VAL123 4.8 31.3 1.0
CA B:LEU121 4.8 52.4 1.0
CB B:PRO122 4.9 39.5 1.0
CG B:GLN124 4.9 36.5 1.0
N B:GLY120 5.0 38.8 1.0

Calcium binding site 3 out of 12 in 7yne

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Calcium binding site 3 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:32.2
occ:1.00
 OD1 B:ASP70 2.3 33.4 1.0
OE2 B:GLU103 2.3 26.8 1.0
O B:HOH330 2.4 34.0 1.0
O B:VAL152 2.4 63.4 1.0
O B:HOH319 2.4 34.9 1.0
OE1 B:GLU103 2.4 33.3 1.0
O B:GLY69 2.4 34.9 1.0
CD B:GLU103 2.7 28.9 1.0
C B:GLY69 3.5 33.4 1.0
CG B:ASP70 3.6 30.4 1.0
C B:VAL152 3.6 30.8 1.0
CA B:ASP70 4.0 36.6 1.0
N B:VAL152 4.0 31.6 1.0
CG1 B:VAL152 4.0 31.4 1.0
N B:ASP70 4.1 32.1 1.0
CG B:GLU103 4.2 32.2 1.0
O B:HOH302 4.3 35.4 1.0
CA B:VAL152 4.3 26.2 1.0
CB B:ASP70 4.3 29.0 1.0
O B:HOH342 4.3 30.2 1.0
C B:GLY151 4.4 24.7 1.0
OD2 B:ASP70 4.5 35.5 1.0
C B:GLU153 4.5 38.0 1.0
CA B:GLY69 4.5 32.5 1.0
N B:GLU153 4.6 41.4 1.0
OG1 B:THR100 4.6 32.2 1.0
N B:THR154 4.6 36.8 1.0
O B:HOH313 4.7 35.7 1.0
O B:GLU153 4.7 35.4 1.0
CA B:GLY151 4.7 28.4 1.0
O B:HOH349 4.8 32.6 1.0
CA B:GLU153 4.8 86.2 1.0
OG1 B:THR99 4.8 34.6 1.0
CB B:VAL152 4.8 31.8 1.0
CA B:THR99 4.9 33.9 1.0
N B:THR100 4.9 25.4 1.0
O B:GLY151 4.9 28.6 1.0

Calcium binding site 4 out of 12 in 7yne

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Calcium binding site 4 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:58.0
occ:1.00
 O2B C:ADP401 2.2 53.1 1.0
O C:HOH532 2.4 46.0 1.0
O C:HOH506 2.4 46.8 1.0
O1B C:ADP401 3.1 43.6 1.0
PB C:ADP401 3.1 48.1 1.0
OE1 C:GLN137 3.5 64.0 1.0
O3A C:ADP401 4.1 38.5 1.0
OD2 C:ASP154 4.2 70.7 1.0
CD C:GLN137 4.2 51.0 1.0
O1A C:ADP401 4.3 45.1 1.0
CA C:GLY13 4.3 49.8 1.0
O3B C:ADP401 4.4 45.3 1.0
OD1 C:ASP154 4.4 42.9 1.0
NZ C:LYS18 4.6 37.6 1.0
CG C:ASP154 4.7 51.2 1.0
NE2 C:GLN137 4.7 53.1 1.0
OD2 C:ASP11 4.7 45.6 1.0
PA C:ADP401 4.8 31.0 1.0
OD1 C:ASP11 4.9 53.0 1.0
CA C:GLY156 4.9 38.4 1.0
N C:SER14 4.9 47.0 1.0

Calcium binding site 5 out of 12 in 7yne

Go back to Calcium Binding Sites List in 7yne
Calcium binding site 5 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:44.4
occ:1.00
 OD2 D:ASP115 2.3 57.3 1.0
O C:HOH540 2.4 55.0 1.0
O C:HOH538 2.4 57.1 1.0
OD1 D:ASP115 2.4 53.5 1.0
O D:PRO122 2.4 52.9 1.0
OE1 C:GLU167 2.5 61.7 1.0
O D:GLY120 2.5 63.0 1.0
CG D:ASP115 2.7 53.4 1.0
C D:GLY120 3.3 69.5 1.0
CD C:GLU167 3.5 50.7 1.0
C D:PRO122 3.7 51.7 1.0
CA D:GLY120 3.7 67.8 1.0
OE2 C:GLU167 3.9 50.4 1.0
CB D:ASP115 4.2 50.4 1.0
N D:PRO122 4.3 54.7 1.0
C D:LEU121 4.4 53.9 1.0
N D:LEU121 4.4 59.8 1.0
CA D:PRO122 4.5 54.0 1.0
N D:VAL123 4.6 51.9 1.0
O D:LEU121 4.7 50.5 1.0
NE2 D:GLN124 4.7 42.8 1.0
CA D:VAL123 4.8 47.5 1.0
CD D:PRO122 4.8 56.4 1.0
CG C:GLU167 4.8 46.9 1.0
CG D:GLN124 4.8 47.1 1.0
CA D:LEU121 4.9 61.3 1.0
CB C:GLU167 5.0 46.0 1.0
CB D:PRO122 5.0 52.4 1.0

Calcium binding site 6 out of 12 in 7yne

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Calcium binding site 6 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:49.4
occ:1.00
 O D:GLY69 2.3 51.7 1.0
OD1 D:ASP70 2.3 40.2 1.0
OE2 D:GLU103 2.3 49.8 1.0
O D:HOH313 2.4 47.5 1.0
OE1 D:GLU103 2.4 44.1 1.0
O D:HOH328 2.4 53.4 1.0
O D:VAL152 2.4 56.9 1.0
CD D:GLU103 2.7 43.9 1.0
C D:GLY69 3.4 44.2 1.0
CG D:ASP70 3.5 49.4 1.0
C D:VAL152 3.6 56.1 1.0
CA D:ASP70 3.8 44.1 1.0
N D:VAL152 3.9 54.4 1.0
CG1 D:VAL152 3.9 48.1 1.0
O D:HOH304 4.0 41.6 1.0
N D:ASP70 4.0 42.7 1.0
CG D:GLU103 4.2 41.3 1.0
CB D:ASP70 4.2 43.3 1.0
CA D:VAL152 4.2 55.4 1.0
C D:GLY151 4.3 53.9 1.0
CA D:GLY69 4.5 45.7 1.0
OD2 D:ASP70 4.5 47.8 1.0
OG1 D:THR100 4.6 44.6 1.0
OG1 D:THR99 4.6 47.9 1.0
CA D:GLY151 4.6 49.8 1.0
O D:HOH320 4.7 49.0 1.0
C D:GLU153 4.7 54.7 1.0
N D:GLU153 4.7 62.8 1.0
CB D:VAL152 4.7 52.5 1.0
O D:GLU153 4.8 61.3 1.0
CA D:THR99 4.8 43.8 1.0
N D:THR154 4.8 58.9 1.0
N D:THR100 4.8 41.2 1.0
O D:GLY151 4.9 59.8 1.0
CA D:GLU153 4.9 64.5 1.0
O D:HOH308 4.9 47.6 1.0

Calcium binding site 7 out of 12 in 7yne

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Calcium binding site 7 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca402

b:81.7
occ:1.00
 O2B E:ADP401 2.2 84.4 1.0
O E:HOH501 2.3 91.5 1.0
PB E:ADP401 3.4 62.0 1.0
OE1 E:GLN137 3.5 101.7 1.0
O1B E:ADP401 3.6 95.9 1.0
O1A E:ADP401 4.0 76.0 1.0
CD E:GLN137 4.2 106.7 1.0
O3A E:ADP401 4.2 70.9 1.0
OD2 E:ASP11 4.2 93.3 1.0
OD2 E:ASP154 4.4 95.5 1.0
OD1 E:ASP154 4.4 85.1 1.0
CA E:GLY13 4.4 99.5 1.0
OD1 E:ASP11 4.5 95.9 1.0
NZ E:LYS18 4.5 79.5 1.0
O3B E:ADP401 4.5 85.3 1.0
PA E:ADP401 4.6 75.6 1.0
NE2 E:GLN137 4.7 110.1 1.0
CG2 E:VAL339 4.8 88.4 1.0
CG E:ASP11 4.8 95.6 1.0
CG E:ASP154 4.8 88.2 1.0

Calcium binding site 8 out of 12 in 7yne

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Calcium binding site 8 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca400

b:121.1
occ:1.00
 OD2 F:ASP115 2.3 124.5 1.0
O F:PRO122 2.4 124.9 1.0
O F:GLY120 2.4 137.9 1.0
OE1 E:GLU167 2.4 129.5 1.0
OD1 F:ASP115 2.4 136.3 1.0
CG F:ASP115 2.7 133.8 1.0
C F:GLY120 3.3 128.2 1.0
CD E:GLU167 3.5 133.6 1.0
C F:PRO122 3.6 127.2 1.0
CA F:GLY120 3.7 123.2 1.0
OE2 E:GLU167 3.9 125.8 1.0
CB F:ASP115 4.2 141.2 1.0
N F:PRO122 4.2 123.7 1.0
C F:LEU121 4.3 123.9 1.0
N F:LEU121 4.4 116.3 1.0
CA F:PRO122 4.5 122.5 1.0
NE2 F:GLN124 4.5 117.5 1.0
N F:VAL123 4.6 133.6 1.0
O F:LEU121 4.6 121.2 1.0
CA F:VAL123 4.7 132.2 1.0
CG E:GLU167 4.8 139.0 1.0
CD F:PRO122 4.8 124.8 1.0
CA F:LEU121 4.8 123.3 1.0
CG F:GLN124 4.8 121.0 1.0
CB E:GLU167 4.9 136.2 1.0
N F:GLY120 5.0 135.2 1.0

Calcium binding site 9 out of 12 in 7yne

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Calcium binding site 9 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:101.9
occ:1.00
 O F:GLY69 2.3 112.1 1.0
OE2 F:GLU103 2.3 105.1 1.0
OD1 F:ASP70 2.4 123.8 1.0
OE1 F:GLU103 2.4 117.0 1.0
O F:VAL152 2.5 122.2 1.0
O F:HOH502 2.6 30.0 1.0
CD F:GLU103 2.7 110.8 1.0
C F:GLY69 3.4 107.8 1.0
CG F:ASP70 3.6 121.8 1.0
C F:VAL152 3.6 107.9 1.0
CA F:ASP70 3.9 109.5 1.0
N F:VAL152 4.0 102.9 1.0
N F:ASP70 4.1 107.8 1.0
CG1 F:VAL152 4.1 113.9 1.0
CG F:GLU103 4.2 103.6 1.0
C F:GLY151 4.3 99.3 1.0
CB F:ASP70 4.3 116.5 1.0
CA F:VAL152 4.4 104.4 1.0
OG1 F:THR100 4.4 131.1 1.0
CA F:GLY69 4.4 103.5 1.0
OD2 F:ASP70 4.5 124.5 1.0
C F:GLU153 4.6 113.7 1.0
CA F:GLY151 4.6 101.6 1.0
N F:GLU153 4.7 100.0 1.0
OG1 F:THR99 4.7 126.2 1.0
N F:THR154 4.8 112.6 1.0
N F:THR100 4.8 131.9 1.0
O F:GLU153 4.8 113.6 1.0
CA F:THR99 4.8 119.4 1.0
O F:GLY151 4.8 102.8 1.0
CA F:GLU153 4.9 123.8 1.0
CB F:VAL152 4.9 108.9 1.0

Calcium binding site 10 out of 12 in 7yne

Go back to Calcium Binding Sites List in 7yne
Calcium binding site 10 out of 12 in the Crystal Structure of Fragmin Domain-1 (1-160) in Complex with G-Form 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 Fragmin Domain-1 (1-160) in Complex with G-Form Actin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca402

b:119.5
occ:1.00
 O1B G:ADP401 2.4 128.2 1.0
OE1 G:GLN137 3.3 135.4 1.0
PB G:ADP401 3.4 120.1 1.0
O3B G:ADP401 3.5 124.3 1.0
CD G:GLN137 4.1 131.6 1.0
OD2 G:ASP154 4.2 225.6 1.0
OD1 G:ASP154 4.3 214.8 1.0
O2A G:ADP401 4.4 106.2 1.0
O3A G:ADP401 4.4 108.3 1.0
OD2 G:ASP11 4.4 122.1 1.0
CA G:GLY13 4.5 183.3 1.0
NZ G:LYS18 4.6 130.2 1.0
O2B G:ADP401 4.6 137.7 1.0
NE2 G:GLN137 4.6 130.3 1.0
CG G:ASP154 4.6 216.8 1.0
OD1 G:ASP11 4.7 115.6 1.0
CA G:GLY156 4.9 123.2 1.0
PA G:ADP401 5.0 111.3 1.0
CG G:ASP11 5.0 116.8 1.0

Reference:

Y.Kanematsu, A.Narita, T.Oda, R.Koike, M.Ota, Y.Takano, K.Moritsugu, I.Fujiwara, K.Tanaka, H.Komatsu, T.Nagae, N.Watanabe, M.Iwasa, Y.Maeda, S.Takeda. Structures and Mechanisms of Actin Atp Hydrolysis. Proc.Natl.Acad.Sci.Usa V. 119 41119 2022.
ISSN: ESSN 1091-6490
PubMed: 36252034
DOI: 10.1073/PNAS.2122641119
Page generated: Fri Jul 19 06:16:12 2024

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