Calcium in PDB 6dec: Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90

Protein crystallography data

The structure of Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90, PDB code: 6dec was solved by B.J.Nolen, Q.Luan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 4.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 179.840, 197.381, 202.067, 90.00, 90.00, 90.00
R / Rfree (%) 27.5 / 31.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90 (pdb code 6dec). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90, PDB code: 6dec:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6dec

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Calcium binding site 1 out of 4 in the Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90


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 Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:87.5
occ:1.00
O2G A:ATP502 2.6 0.1 1.0
O2B A:ATP502 2.9 0.3 1.0
O1G A:ATP502 3.4 0.3 1.0
PG A:ATP502 3.5 0.3 1.0
PB A:ATP502 4.1 0.0 1.0
OD2 A:ASP11 4.2 0.8 1.0
O3B A:ATP502 4.3 0.7 1.0
O2A A:ATP502 4.4 0.6 1.0
O3A A:ATP502 4.6 0.7 1.0
OD1 A:ASP11 4.6 0.4 1.0
CB A:VAL377 4.7 0.4 1.0
O3G A:ATP502 4.8 0.2 1.0
CG A:ASP11 4.9 0.2 1.0
CA A:GLY13 4.9 0.3 1.0

Calcium binding site 2 out of 4 in 6dec

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Calcium binding site 2 out of 4 in the Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90


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 Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:0.3
occ:1.00
O2G B:ATP502 2.4 0.5 1.0
O2B B:ATP502 2.5 0.5 1.0
PB B:ATP502 3.5 0.8 1.0
O3A B:ATP502 3.6 1.0 1.0
PG B:ATP502 3.8 1.0 1.0
O3B B:ATP502 4.0 0.8 1.0
O2A B:ATP502 4.2 0.6 1.0
PA B:ATP502 4.4 0.2 1.0
O1G B:ATP502 4.5 0.2 1.0
O1A B:ATP502 4.8 0.9 1.0
O3G B:ATP502 4.9 0.8 1.0
O1B B:ATP502 4.9 0.9 1.0
CB B:VAL354 5.0 0.1 1.0

Calcium binding site 3 out of 4 in 6dec

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Calcium binding site 3 out of 4 in the Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90


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 Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca501

b:0.2
occ:1.00
O1G H:ATP502 2.5 0.4 1.0
O1B H:ATP502 2.7 0.3 1.0
CA H:GLY13 3.5 0.9 1.0
PG H:ATP502 3.8 0.1 1.0
PB H:ATP502 3.8 0.8 1.0
O3B H:ATP502 4.0 0.9 1.0
N H:GLY13 4.2 0.9 1.0
O3A H:ATP502 4.2 0.7 1.0
O3G H:ATP502 4.5 0.3 1.0
C H:GLY13 4.7 0.0 1.0
O H:CYS12 4.7 0.2 1.0
C H:CYS12 4.8 0.8 1.0
CB H:VAL377 4.8 1.0 1.0
N H:THR14 4.8 0.0 1.0
O2A H:ATP502 4.9 0.4 1.0
PA H:ATP502 4.9 0.3 1.0
O2G H:ATP502 4.9 0.3 1.0
O1A H:ATP502 5.0 0.4 1.0

Calcium binding site 4 out of 4 in 6dec

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Calcium binding site 4 out of 4 in the Crystal Structure of Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90


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 Bos Taurus ARP2/3 Complex Binding with C-Terminus of Homo Sapiens SPIN90 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca501

b:0.8
occ:1.00
O2G I:ATP502 2.7 1.0 1.0
O1B I:ATP502 3.2 0.5 1.0
PG I:ATP502 4.1 0.9 1.0
CB I:VAL354 4.2 0.5 1.0
PB I:ATP502 4.4 0.3 1.0
O3B I:ATP502 4.6 0.9 1.0
O3A I:ATP502 4.7 0.2 1.0
O1A I:ATP502 4.7 0.7 1.0
O3G I:ATP502 5.0 0.3 1.0

Reference:

Q.Luan, S.L.Liu, L.A.Helgeson, B.J.Nolen. Structure of the Nucleation-Promoting Factor SPIN90 Bound to the Actin Filament Nucleator ARP2/3 Complex. Embo J. V. 37 2018.
ISSN: ESSN 1460-2075
PubMed: 30322896
DOI: 10.15252/EMBJ.2018100005
Page generated: Sat Dec 12 06:03:21 2020

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