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Magnesium in PDB 4gyi: Crystal Structure of the RIO2 Kinase-Adp/MG2+-Phosphoaspartate Complex From Chaetomium Thermophilum

Protein crystallography data

The structure of Crystal Structure of the RIO2 Kinase-Adp/MG2+-Phosphoaspartate Complex From Chaetomium Thermophilum, PDB code: 4gyi was solved by S.Ferreira-Cerca, V.Sagar, T.Schafer, M.Diop, A.M.Wesseling, H.Lu, E.Chai, E.Hurt, N.Laronde-Leblanc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.53 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 119.624, 119.624, 71.783, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the RIO2 Kinase-Adp/MG2+-Phosphoaspartate Complex From Chaetomium Thermophilum (pdb code 4gyi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the RIO2 Kinase-Adp/MG2+-Phosphoaspartate Complex From Chaetomium Thermophilum, PDB code: 4gyi:

Magnesium binding site 1 out of 1 in 4gyi

Go back to Magnesium Binding Sites List in 4gyi
Magnesium binding site 1 out of 1 in the Crystal Structure of the RIO2 Kinase-Adp/MG2+-Phosphoaspartate Complex From Chaetomium Thermophilum


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 the RIO2 Kinase-Adp/MG2+-Phosphoaspartate Complex From Chaetomium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:35.2
occ:1.00
O1A A:ADP401 2.0 31.8 1.0
O A:HOH523 2.1 39.3 1.0
O2B A:ADP401 2.1 27.9 1.0
O A:HOH543 2.1 35.1 1.0
OD1 A:ASN234 2.1 24.7 1.0
OD1 A:PHD257 2.3 30.1 1.0
CG A:ASN234 3.1 24.3 1.0
CG A:PHD257 3.2 30.8 1.0
PB A:ADP401 3.3 31.4 1.0
PA A:ADP401 3.4 31.0 1.0
OP2 A:PHD257 3.4 38.7 0.8
ND2 A:ASN234 3.4 30.4 1.0
P A:PHD257 3.4 55.2 0.8
CB A:PHD257 3.5 23.9 1.0
O3A A:ADP401 3.7 31.5 1.0
O3B A:ADP401 3.9 36.2 1.0
OD2 A:PHD257 4.3 33.2 1.0
O2A A:ADP401 4.3 32.2 1.0
O5' A:ADP401 4.4 34.3 1.0
OP3 A:PHD257 4.4 34.3 0.8
CB A:ASN234 4.4 24.6 1.0
C5' A:ADP401 4.5 27.0 1.0
OD2 A:ASP229 4.5 51.9 1.0
O A:PHE233 4.6 38.0 1.0
OP1 A:PHD257 4.6 44.9 0.8
O1B A:ADP401 4.6 36.0 1.0
CA A:ASN234 4.8 22.0 1.0
C A:PHE233 4.9 32.3 1.0
CA A:PHD257 5.0 22.8 1.0
CB A:PHE233 5.0 37.4 1.0
N A:ASN234 5.0 25.4 1.0

Reference:

S.Ferreira-Cerca, V.Sagar, T.Schafer, M.Diop, A.M.Wesseling, H.Lu, E.Chai, E.Hurt, N.Laronde-Leblanc. Atpase-Dependent Role of the Atypical Kinase RIO2 on the Evolving Pre-40S Ribosomal Subunit. Nat.Struct.Mol.Biol. V. 19 1316 2012.
ISSN: ISSN 1545-9993
PubMed: 23104056
DOI: 10.1038/NSMB.2403
Page generated: Mon Dec 14 16:56:05 2020

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