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Magnesium in PDB 1pkg: Structure of A C-Kit Kinase Product Complex

Protein crystallography data

The structure of Structure of A C-Kit Kinase Product Complex, PDB code: 1pkg was solved by C.D.Mol, K.B.Lim, V.Sridhar, H.Zou, E.Y.T.Chien, B.-C.Sang, J.Nowakowski, D.B.Kassel, C.N.Cronin, D.E.Mcree, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.667, 116.458, 60.066, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 31.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A C-Kit Kinase Product Complex (pdb code 1pkg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of A C-Kit Kinase Product Complex, PDB code: 1pkg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1pkg

Go back to Magnesium Binding Sites List in 1pkg
Magnesium binding site 1 out of 2 in the Structure of A C-Kit Kinase Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A C-Kit Kinase Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1481

b:5.1
occ:1.00
O2A A:ADP1480 2.0 10.6 1.0
O3B A:ADP1480 2.1 11.5 1.0
OD1 A:ASN797 2.2 9.6 1.0
O2P B:PTR568 2.2 6.4 1.0
OD1 A:ASP810 3.0 13.5 1.0
PA A:ADP1480 3.3 9.7 1.0
CG A:ASN797 3.3 10.0 1.0
PB A:ADP1480 3.4 11.2 1.0
P B:PTR568 3.4 3.8 1.0
O1P B:PTR568 3.5 3.8 1.0
O3A A:ADP1480 3.7 10.5 1.0
C5' A:ADP1480 3.7 7.3 1.0
O3' A:ADP1480 3.8 9.5 1.0
CG A:ARG796 3.8 15.0 1.0
O5' A:ADP1480 3.8 5.0 1.0
ND2 A:ASN797 3.9 8.3 1.0
O A:ARG796 3.9 14.3 1.0
CG A:ASP810 4.0 15.8 1.0
O3P B:PTR568 4.2 6.6 1.0
C3' A:ADP1480 4.3 11.2 1.0
CA A:GLY598 4.3 17.1 1.0
O2B A:ADP1480 4.3 13.2 1.0
CB A:ASP810 4.4 16.2 1.0
CD A:ARG796 4.4 15.8 1.0
C A:ARG796 4.5 13.8 1.0
O1B A:ADP1480 4.5 13.6 1.0
C4' A:ADP1480 4.5 10.3 1.0
CB A:ASN797 4.5 11.3 1.0
O1A A:ADP1480 4.5 8.1 1.0
NE A:ARG796 4.6 16.4 1.0
CA A:ASN797 4.6 11.8 1.0
OH B:PTR568 4.7 3.7 1.0
CB A:ARG796 4.7 14.7 1.0
N A:GLY598 4.8 16.5 1.0
N A:ASN797 4.8 12.6 1.0

Magnesium binding site 2 out of 2 in 1pkg

Go back to Magnesium Binding Sites List in 1pkg
Magnesium binding site 2 out of 2 in the Structure of A C-Kit Kinase Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A C-Kit Kinase Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1485

b:16.1
occ:1.00
O2A B:ADP1486 1.9 9.5 1.0
O3B B:ADP1486 2.0 6.8 1.0
OD1 B:ASN797 2.0 10.9 1.0
OD1 B:ASP810 2.6 24.9 1.0
CG B:ASN797 3.2 12.6 1.0
PA B:ADP1486 3.4 6.2 1.0
PB B:ADP1486 3.4 8.0 1.0
CG B:ASP810 3.6 23.9 1.0
ND2 B:ASN797 3.7 9.1 1.0
C5' B:ADP1486 3.8 9.2 1.0
O3A B:ADP1486 3.9 7.5 1.0
O3' B:ADP1486 3.9 9.3 1.0
CB B:ASP810 4.0 23.0 1.0
O B:ARG796 4.1 14.4 1.0
O5' B:ADP1486 4.1 8.8 1.0
O2B B:ADP1486 4.1 8.9 1.0
CD B:ARG796 4.1 15.5 1.0
NE B:ARG796 4.4 16.3 1.0
O1A B:ADP1486 4.4 8.2 1.0
C B:ARG796 4.4 14.9 1.0
CB B:ASN797 4.4 13.8 1.0
C3' B:ADP1486 4.5 8.8 1.0
O1B B:ADP1486 4.5 8.2 1.0
CG B:ARG796 4.5 16.2 1.0
CA B:ASN797 4.6 14.2 1.0
CB B:ARG796 4.6 15.7 1.0
N B:ASN797 4.7 14.7 1.0
OD2 B:ASP810 4.7 24.9 1.0
C4' B:ADP1486 4.7 9.1 1.0
CA B:GLY598 4.7 15.0 1.0

Reference:

C.D.Mol, K.B.Lim, V.Sridhar, H.Zou, E.Y.T.Chien, B.-C.Sang, J.Nowakowski, D.B.Kassel, C.N.Cronin, D.E.Mcree. Structure of A C-Kit Product Complex Reveals the Basis For Kinase Transactivation. J.Biol.Chem. V. 278 31461 2003.
ISSN: ISSN 0021-9258
PubMed: 12824176
DOI: 10.1074/JBC.C300186200
Page generated: Tue Aug 13 10:53:20 2024

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