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Magnesium in PDB 4jhd: Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu

Protein crystallography data

The structure of Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu, PDB code: 4jhd was solved by X.Chen, F.Ni, Q.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.02 / 2.91
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.450, 99.800, 118.270, 65.41, 90.03, 77.77
R / Rfree (%) 20 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu (pdb code 4jhd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu, PDB code: 4jhd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jhd

Go back to Magnesium Binding Sites List in 4jhd
Magnesium binding site 1 out of 4 in the Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:56.4
occ:1.00
O1B A:ANP401 2.4 57.9 1.0
O2G A:ANP401 3.1 76.0 1.0
O1A A:ANP401 3.7 64.2 1.0
PB A:ANP401 3.9 56.6 1.0
OE1 A:GLN137 3.9 45.4 1.0
NZ A:LYS18 4.1 42.0 1.0
OD2 A:ASP11 4.2 47.1 1.0
PG A:ANP401 4.3 76.4 1.0
OD2 A:ASP154 4.3 48.2 1.0
CD A:GLN137 4.3 46.1 1.0
O3G A:ANP401 4.5 64.0 1.0
CA A:GLY13 4.6 48.9 1.0
N3B A:ANP401 4.6 66.5 1.0
OD1 A:ASP11 4.6 42.4 1.0
O3A A:ANP401 4.7 74.5 1.0
PA A:ANP401 4.8 77.5 1.0
NE2 A:GLN137 4.8 49.3 1.0
O2B A:ANP401 4.9 58.3 1.0
CG A:ASP11 4.9 41.9 1.0
CG2 A:VAL339 4.9 36.1 1.0

Magnesium binding site 2 out of 4 in 4jhd

Go back to Magnesium Binding Sites List in 4jhd
Magnesium binding site 2 out of 4 in the Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:53.9
occ:1.00
O1B B:ANP401 2.2 56.0 1.0
O2G B:ANP401 2.3 52.9 1.0
O B:HOH502 2.4 47.8 1.0
PG B:ANP401 3.3 59.6 1.0
PB B:ANP401 3.4 62.7 1.0
O3G B:ANP401 3.5 61.2 1.0
O B:HOH521 3.6 46.1 1.0
O1A B:ANP401 3.8 52.6 1.0
O3A B:ANP401 3.9 57.2 1.0
N3B B:ANP401 4.0 56.2 1.0
OE1 B:GLN137 4.3 51.6 1.0
PA B:ANP401 4.4 57.2 1.0
OD2 B:ASP154 4.4 58.8 1.0
OD1 B:ASP154 4.6 52.2 1.0
NZ B:LYS18 4.6 56.8 1.0
CA B:GLY156 4.6 48.0 1.0
O1G B:ANP401 4.7 56.6 1.0
O2B B:ANP401 4.7 61.3 1.0
CD B:GLN137 4.8 50.9 1.0
OD2 B:ASP11 4.9 51.2 1.0
CA B:GLY13 4.9 58.2 1.0
CG B:ASP154 4.9 56.5 1.0
O2A B:ANP401 4.9 63.1 1.0
CG2 B:VAL339 5.0 44.4 1.0

Magnesium binding site 3 out of 4 in 4jhd

Go back to Magnesium Binding Sites List in 4jhd
Magnesium binding site 3 out of 4 in the Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:69.4
occ:1.00
O D:HOH528 2.0 60.3 1.0
O1B D:ANP401 2.8 81.6 1.0
O2G D:ANP401 3.1 81.1 1.0
O1A D:ANP401 3.6 72.3 1.0
OD1 D:ASP154 3.7 55.1 1.0
OD2 D:ASP154 3.9 63.2 1.0
OE1 D:GLN137 4.1 61.8 1.0
CG D:ASP154 4.3 60.7 1.0
PB D:ANP401 4.3 74.4 1.0
CG2 D:VAL339 4.4 59.0 1.0
OD2 D:ASP11 4.4 70.4 1.0
PG D:ANP401 4.5 1.0 1.0
NZ D:LYS18 4.5 72.2 1.0
CD D:GLN137 4.7 60.7 1.0
PA D:ANP401 4.7 84.3 1.0
O3A D:ANP401 4.8 80.8 1.0
O3G D:ANP401 4.9 82.3 1.0
N3B D:ANP401 5.0 79.7 1.0

Magnesium binding site 4 out of 4 in 4jhd

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Magnesium binding site 4 out of 4 in the Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of An Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:67.6
occ:1.00
O1B E:ANP401 2.0 85.9 1.0
O E:HOH502 2.3 55.5 1.0
O2G E:ANP401 2.6 90.2 1.0
PB E:ANP401 3.4 74.9 1.0
O1A E:ANP401 3.7 69.6 1.0
PG E:ANP401 3.7 90.0 1.0
OE1 E:GLN137 3.9 67.3 1.0
O3G E:ANP401 4.0 75.4 1.0
N3B E:ANP401 4.0 81.8 1.0
O3A E:ANP401 4.1 78.7 1.0
NZ E:LYS18 4.4 70.3 1.0
PA E:ANP401 4.5 81.5 1.0
O2B E:ANP401 4.5 75.6 1.0
OD2 E:ASP154 4.5 73.4 1.0
CD E:GLN137 4.7 65.8 1.0
CA E:GLY13 4.7 76.8 1.0
OD1 E:ASP154 4.7 71.6 1.0
CG2 E:VAL339 4.8 53.9 1.0
OD2 E:ASP11 4.9 56.2 1.0
CA E:GLY156 5.0 69.8 1.0

Reference:

X.Chen, F.Ni, X.Tian, E.Kondrashkina, Q.Wang, J.Ma. Structural Basis of Actin Filament Nucleation By Tandem W Domains. Cell Rep V. 3 1910 2013.
ISSN: ESSN 2211-1247
PubMed: 23727244
DOI: 10.1016/J.CELREP.2013.04.028
Page generated: Fri Aug 16 17:22:20 2024

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