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Magnesium in PDB 1gy3: PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate

Protein crystallography data

The structure of PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate, PDB code: 1gy3 was solved by A.Cook, E.D.Lowe, E.D.Chrysina, V.T.Skamnaki, N.G.Oikonomakos, L.N.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 150.710, 164.100, 72.430, 90.00, 90.00, 90.00
R / Rfree (%) 25 / 31.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate (pdb code 1gy3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate, PDB code: 1gy3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1gy3

Go back to Magnesium Binding Sites List in 1gy3
Magnesium binding site 1 out of 2 in the PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1298

b:44.1
occ:1.00
OD1 A:ASN132 2.0 19.0 1.0
O3B A:ATP1297 2.1 60.7 1.0
O3 A:NO31299 2.3 51.2 1.0
O2A A:ATP1297 2.4 57.6 1.0
OD2 A:ASP145 2.4 35.1 1.0
CG A:ASN132 2.8 22.5 1.0
O1B A:ATP1297 3.0 57.3 1.0
ND2 A:ASN132 3.1 27.4 1.0
PB A:ATP1297 3.1 59.7 1.0
N A:NO31299 3.2 50.7 1.0
CG A:ASP145 3.2 27.4 1.0
CB A:ASP145 3.6 23.4 1.0
PA A:ATP1297 3.6 58.4 1.0
O3A A:ATP1297 3.9 59.2 1.0
O2 A:NO31299 4.0 49.7 1.0
O1 A:NO31299 4.0 50.2 1.0
C5' A:ATP1297 4.1 53.0 1.0
CB A:ASN132 4.2 23.0 1.0
OD1 A:ASP145 4.3 27.9 1.0
O2B A:ATP1297 4.4 59.3 1.0
O5' A:ATP1297 4.4 55.3 1.0
O3' A:ATP1297 4.4 47.6 1.0
O A:GLN131 4.5 25.5 1.0
CA A:ASN132 4.6 22.9 1.0
CE A:LYS129 4.6 26.2 1.0
O1A A:ATP1297 4.8 60.5 1.0
OD2 A:ASP127 4.9 22.3 1.0
OG E:SER5 4.9 52.4 1.0
C3' A:ATP1297 4.9 51.5 1.0
CA A:ASP145 5.0 23.0 1.0

Magnesium binding site 2 out of 2 in 1gy3

Go back to Magnesium Binding Sites List in 1gy3
Magnesium binding site 2 out of 2 in the PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PCDK2/Cyclin A in Complex with Mgadp, Nitrate and Peptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1299

b:49.6
occ:1.00
OD1 C:ASN132 2.0 34.3 1.0
O2A C:ATP1298 2.0 57.8 1.0
OD2 C:ASP145 2.5 45.4 1.0
CG C:ASN132 2.8 28.6 1.0
ND2 C:ASN132 3.1 31.1 1.0
O1B C:ATP1298 3.2 56.6 1.0
O1 C:NO31300 3.2 60.3 1.0
CG C:ASP145 3.3 35.3 1.0
PA C:ATP1298 3.4 54.8 1.0
O3B C:ATP1298 3.6 56.9 1.0
CB C:ASP145 3.6 29.2 1.0
C5' C:ATP1298 3.6 54.8 1.0
PB C:ATP1298 3.8 57.5 1.0
N C:NO31300 4.0 59.9 1.0
O5' C:ATP1298 4.1 52.8 1.0
O3A C:ATP1298 4.1 55.7 1.0
CB C:ASN132 4.1 26.4 1.0
O3 C:NO31300 4.3 58.8 1.0
OD1 C:ASP145 4.4 40.6 1.0
CE C:LYS129 4.4 24.8 1.0
CA C:ASN132 4.4 26.8 1.0
O1A C:ATP1298 4.6 55.7 1.0
O3' C:ATP1298 4.6 57.2 1.0
O C:GLN131 4.6 28.7 1.0
N C:ASN132 4.7 27.6 1.0
C4' C:ATP1298 4.7 56.7 1.0
C C:GLN131 4.8 27.9 1.0
C3' C:ATP1298 4.8 57.2 1.0
CG C:GLN131 4.8 34.5 1.0
O2 C:NO31300 4.9 59.6 1.0
OD2 C:ASP127 5.0 28.6 1.0
CA C:ASP145 5.0 28.5 1.0

Reference:

A.Cook, E.D.Lowe, E.D.Chrysina, V.T.Skamnaki, N.G.Oikonomakos, L.N.Johnson. Structural Studies on Phospho-CDK2/Cyclin A Bound to Nitrate, A Transition State Analogue: Implications For the Protein Kinase Mechanism Biochemistry V. 41 7301 2002.
ISSN: ISSN 0006-2960
PubMed: 12044161
DOI: 10.1021/BI0201724
Page generated: Mon Dec 14 05:58:29 2020

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