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Calcium in PDB 5nbm: Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody

Protein crystallography data

The structure of Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody, PDB code: 5nbm was solved by K.R.Knoll, S.Eustermann, K.P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.74 / 3.40
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 190.581, 190.581, 220.616, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 19.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody (pdb code 5nbm). 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 the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody, PDB code: 5nbm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5nbm

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Calcium binding site 1 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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 ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:86.3
occ:1.00
O1G A:ATP502 2.1 68.0 1.0
O2B A:ATP502 2.3 90.7 1.0
OD2 A:ASP159 3.4 0.6 1.0
PG A:ATP502 3.5 74.8 1.0
PB A:ATP502 3.7 85.7 1.0
OD1 A:ASP159 3.7 1.0 1.0
CG A:ASP159 3.9 0.8 1.0
O2A A:ATP502 4.0 58.7 1.0
O3B A:ATP502 4.0 71.7 1.0
O2G A:ATP502 4.4 55.2 1.0
O3G A:ATP502 4.5 70.5 1.0
OG A:SER452 4.6 0.3 1.0
O3A A:ATP502 4.6 75.6 1.0
O1B A:ATP502 4.7 90.3 1.0
PA A:ATP502 4.9 76.5 1.0

Calcium binding site 2 out of 4 in 5nbm

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Calcium binding site 2 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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 ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:85.2
occ:1.00
O2G B:ATP502 2.3 92.2 1.0
O1B B:ATP502 2.5 96.2 1.0
OD2 B:ASP159 3.4 0.3 1.0
PG B:ATP502 3.5 71.4 1.0
OD1 B:ASP159 3.7 0.8 1.0
O3G B:ATP502 3.7 67.6 1.0
PB B:ATP502 3.8 86.1 1.0
CG B:ASP159 3.9 0.7 1.0
O1A B:ATP502 4.0 72.3 1.0
O3B B:ATP502 4.1 60.8 1.0
OG B:SER452 4.7 0.7 1.0
O3A B:ATP502 4.7 77.3 1.0
O1G B:ATP502 4.8 50.0 1.0
O2B B:ATP502 5.0 93.4 1.0
PA B:ATP502 5.0 78.1 1.0

Calcium binding site 3 out of 4 in 5nbm

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Calcium binding site 3 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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 ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:87.9
occ:1.00
O2B C:ATP502 2.5 0.5 1.0
O3G C:ATP502 2.7 0.3 1.0
OE1 C:GLN137 3.5 0.7 1.0
O2G C:ATP502 3.6 0.1 1.0
PG C:ATP502 3.7 99.1 1.0
PB C:ATP502 3.8 93.9 1.0
OD2 C:ASP11 4.0 91.9 1.0
OD2 C:ASP154 4.2 0.9 1.0
O3B C:ATP502 4.2 94.5 1.0
O3A C:ATP502 4.2 95.3 1.0
OD1 C:ASP11 4.3 0.2 1.0
OD1 C:ASP154 4.3 0.3 1.0
O1A C:ATP502 4.4 0.5 1.0
NZ C:LYS18 4.4 0.3 1.0
CD C:GLN137 4.4 0.2 1.0
CG2 C:VAL339 4.4 95.6 1.0
CA C:GLY13 4.5 0.4 1.0
CG C:ASP11 4.6 97.7 1.0
CG C:ASP154 4.7 0.7 1.0
PA C:ATP502 4.8 87.5 1.0
CB C:VAL339 4.9 76.5 1.0

Calcium binding site 4 out of 4 in 5nbm

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Calcium binding site 4 out of 4 in the Crystal Structure of the ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody


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 ARP4-N-Actin(Atp-State) Heterodimer Bound By A Nanobody within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:85.3
occ:1.00
O1G D:ATP502 2.4 0.6 1.0
O2B D:ATP502 2.5 0.8 1.0
OE1 D:GLN137 3.3 1.0 1.0
PB D:ATP502 3.8 0.8 1.0
PG D:ATP502 3.9 0.7 1.0
OD2 D:ASP11 4.0 86.4 1.0
OD2 D:ASP154 4.1 0.2 1.0
O2A D:ATP502 4.1 79.0 1.0
OD1 D:ASP11 4.2 99.2 1.0
CD D:GLN137 4.2 0.8 1.0
O3A D:ATP502 4.3 0.2 1.0
CG2 D:VAL339 4.3 0.2 1.0
NZ D:LYS18 4.3 0.3 1.0
O3B D:ATP502 4.3 0.8 1.0
OD1 D:ASP154 4.4 0.2 1.0
CA D:GLY13 4.5 0.3 1.0
CG D:ASP11 4.6 98.9 1.0
CG D:ASP154 4.7 0.3 1.0
PA D:ATP502 4.7 89.2 1.0
O2G D:ATP502 4.8 0.7 1.0
CB D:VAL339 4.8 84.2 1.0
O3G D:ATP502 4.8 98.6 1.0
NE2 D:GLN137 4.8 0.4 1.0

Reference:

K.R.Knoll, S.Eustermann, V.Niebauer, E.Oberbeckmann, G.Stoehr, K.Schall, A.Tosi, M.Schwarz, A.Buchfellner, P.Korber, K.P.Hopfner. The Nuclear Actin-Containing ARP8 Module Is A Linker Dna Sensor Driving INO80 Chromatin Remodeling. Nat. Struct. Mol. Biol. V. 25 823 2018.
ISSN: ESSN 1545-9985
PubMed: 30177756
DOI: 10.1038/S41594-018-0115-8
Page generated: Sat Dec 12 05:39:46 2020

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