Zinc in PDB 4ck0: Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2

All present enzymatic activity of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2:
2.7.1.107;

The structure of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2, PDB code: 4ck0 was solved by D.Li, J.A.Lyons, L.Vogeley, D.Aragao, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.006 / 2.92
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.820, 72.820, 195.670, 90.00, 90.00, 120.00
R / Rfree (%)	24.79 / 28.09

The binding sites of Zinc atom in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2 (pdb code 4ck0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2, PDB code: 4ck0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1120 b:0.6 occ:0.70 OE1 C:GLU76 2.0 0.8 1.0 O2G C:ACP1122 2.0 0.0 0.7 OE2 C:GLU28 2.0 0.8 1.0 O1G C:ACP1122 2.1 0.9 0.7 PG C:ACP1122 2.4 0.1 0.7 O1B C:ACP1122 2.5 0.1 0.7 CD C:GLU76 3.0 0.1 1.0 CD C:GLU28 3.0 0.5 1.0 OE2 C:GLU76 3.3 0.4 1.0 PB C:ACP1122 3.3 0.7 0.7 C3B C:ACP1122 3.4 0.7 0.7 OE1 C:GLU28 3.5 0.0 1.0 O3G C:ACP1122 3.8 0.9 0.7 ZN C:ZN1121 4.1 97.1 0.7 CG C:GLU28 4.3 0.1 1.0 CG C:GLU76 4.3 90.6 1.0 O3A C:ACP1122 4.3 0.1 0.7 O2A C:ACP1122 4.4 87.4 0.7 O2B C:ACP1122 4.5 0.4 0.7 OG C:SER73 4.6 77.5 1.0 CB C:GLU76 4.6 67.6 1.0 PA C:ACP1122 4.8 97.6 0.7 O1A C:ACP1122 5.0 0.3 0.7 CA C:SER73 5.0 68.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Integral Membrane Diacylglycerol Kinase - Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1121 b:97.1 occ:0.70 OE2 C:GLU76 2.0 0.4 1.0 O1A C:ACP1122 2.1 0.3 0.7 O1B C:ACP1122 2.4 0.1 0.7 CD C:GLU76 2.8 0.1 1.0 PA C:ACP1122 3.2 97.6 0.7 PB C:ACP1122 3.5 0.7 0.7 CG C:GLU76 3.5 90.6 1.0 OE1 C:GLU76 3.5 0.8 1.0 O2A C:ACP1122 3.6 87.4 0.7 O3A C:ACP1122 3.6 0.1 0.7 ZN C:ZN1120 4.1 0.6 0.7 O C:LYS94 4.1 75.4 1.0 O2B C:ACP1122 4.1 0.4 0.7 ND2 C:ASN72 4.2 75.1 1.0 OD1 C:ASN72 4.3 72.2 1.0 CB C:LYS94 4.3 72.7 1.0 O3' C:ACP1122 4.4 0.2 0.7 O5' C:ACP1122 4.5 96.6 0.7 CG C:ASN72 4.6 66.1 1.0 CB C:SER98 4.7 71.2 1.0 CG C:LYS94 4.7 67.4 1.0 C C:LYS94 4.8 73.2 1.0 CD C:LYS94 4.8 82.6 1.0 CA C:LYS94 4.8 68.8 1.0 CB C:GLU76 4.8 67.6 1.0 C3' C:ACP1122 4.9 98.7 0.7 C5' C:ACP1122 5.0 0.7 0.7

D.Li, A.Others, M.Caffrey. Crystal Structure of the Integral Membrane Diacylglycerol Kinase with Zn-Amppcp Bound and Its Catalytic Mechanism To Be Published.