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Magnesium in PDB 1q97: The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp

Protein crystallography data

The structure of The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp, PDB code: 1q97 was solved by B.Nolen, J.Ngo, S.Chakrabarti, D.Vu, J.A.Adams, G.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.823, 88.692, 133.495, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 26.4

Other elements in 1q97:

The structure of The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp (pdb code 1q97). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp, PDB code: 1q97:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1q97

Go back to Magnesium Binding Sites List in 1q97
Magnesium binding site 1 out of 2 in the The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg743

b:46.1
occ:1.00
OD2 A:ASP550 2.1 37.8 1.0
O2G A:ATP485 2.4 66.9 1.0
O1A A:ATP485 2.7 57.4 1.0
PG A:ATP485 2.8 67.7 1.0
O1G A:ATP485 2.8 66.8 1.0
OD1 A:ASN299 3.0 31.2 1.0
O3A A:ATP485 3.1 60.0 1.0
CG A:ASP550 3.2 35.1 1.0
O3B A:ATP485 3.2 65.0 1.0
PA A:ATP485 3.5 56.6 1.0
MG A:MG744 3.5 59.9 1.0
CB A:ASP550 3.8 33.7 1.0
PB A:ATP485 3.9 61.4 1.0
CG A:ASN299 4.1 29.8 1.0
OD1 A:ASP550 4.2 34.3 1.0
O3G A:ATP485 4.3 67.0 1.0
ND2 A:ASN299 4.4 27.1 1.0
O2A A:ATP485 4.5 56.6 1.0
O1B A:ATP485 4.5 63.0 1.0
O5' A:ATP485 4.6 54.7 1.0
C5' A:ATP485 4.7 50.1 1.0

Magnesium binding site 2 out of 2 in 1q97

Go back to Magnesium Binding Sites List in 1q97
Magnesium binding site 2 out of 2 in the The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, with Bound Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg744

b:59.9
occ:1.00
O3B A:ATP485 2.1 65.0 1.0
OD2 A:ASP550 2.6 37.8 1.0
OD1 A:ASP550 2.9 34.3 1.0
O1B A:ATP485 2.9 63.0 1.0
CG A:ASP550 3.1 35.1 1.0
O2G A:ATP485 3.1 66.9 1.0
PB A:ATP485 3.1 61.4 1.0
PG A:ATP485 3.2 67.7 1.0
MG A:MG743 3.5 46.1 1.0
O3A A:ATP485 3.9 60.0 1.0
O3G A:ATP485 4.1 67.0 1.0
ND2 A:ASN553 4.1 38.0 1.0
O2B A:ATP485 4.3 61.1 1.0
O1G A:ATP485 4.3 66.8 1.0
CA A:GLY552 4.4 36.0 1.0
NZ A:LYS187 4.4 45.8 1.0
CB A:PHE169 4.4 42.4 1.0
O2A A:ATP485 4.4 56.6 1.0
PA A:ATP485 4.5 56.6 1.0
CB A:ASP550 4.5 33.7 1.0
O1A A:ATP485 4.6 57.4 1.0
N A:GLY552 4.8 34.3 1.0
CD2 A:PHE169 4.8 41.5 1.0
CG A:PHE169 4.9 42.5 1.0
CE A:LYS187 5.0 41.5 1.0
C A:GLY552 5.0 36.8 1.0

Reference:

B.Nolen, J.Ngo, S.Chakrabarti, D.Vu, J.A.Adams, G.Ghosh. Nucleotide-Induced Conformational Changes in the Saccharomyces Cerevisiae Sr Protein Kinase, SKY1P, Revealed By X-Ray Crystallography Biochemistry V. 42 9575 2003.
ISSN: ISSN 0006-2960
PubMed: 12911299
DOI: 10.1021/BI0344331
Page generated: Mon Dec 14 06:38:21 2020

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