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Zinc in PDB 1r79: Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta

Enzymatic activity of Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta

All present enzymatic activity of Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta:
2.7.1.107;

Zinc Binding Sites:

The binding sites of Zinc atom in the Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta (pdb code 1r79). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta, PDB code: 1r79:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1r79

Go back to Zinc Binding Sites List in 1r79
Zinc binding site 1 out of 2 in the Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:0.0
occ:1.00
SG A:CYS78 2.3 0.0 1.0
SG A:CYS62 2.3 0.0 1.0
SG A:CYS59 2.3 0.0 1.0
ND1 A:HIS28 2.3 0.0 1.0
H A:CYS62 2.9 0.0 1.0
HB3 A:HIS28 2.9 0.0 1.0
HB2 A:CYS78 3.0 0.0 1.0
HB3 A:CYS62 3.0 0.0 1.0
HA A:HIS28 3.1 0.0 1.0
CG A:HIS28 3.2 0.0 1.0
CB A:CYS59 3.2 0.0 1.0
CB A:CYS62 3.3 0.0 1.0
CB A:CYS78 3.3 0.0 1.0
HB3 A:CYS59 3.3 0.0 1.0
CE1 A:HIS28 3.3 0.0 1.0
HB2 A:CYS59 3.3 0.0 1.0
CB A:HIS28 3.4 0.0 1.0
HE1 A:HIS28 3.5 0.0 1.0
HB2 A:TRP61 3.6 0.0 1.0
N A:CYS62 3.8 0.0 1.0
HA A:CYS78 3.8 0.0 1.0
CA A:HIS28 3.8 0.0 1.0
HB3 A:CYS78 4.1 0.0 1.0
HB3 A:ALA64 4.1 0.0 1.0
HB2 A:CYS62 4.1 0.0 1.0
CA A:CYS62 4.1 0.0 1.0
CA A:CYS78 4.2 0.0 1.0
H A:GLN29 4.2 0.0 1.0
CD2 A:HIS28 4.3 0.0 1.0
NE2 A:HIS28 4.3 0.0 1.0
HB2 A:HIS28 4.4 0.0 1.0
HE3 A:TRP61 4.5 0.0 1.0
H A:LYS63 4.5 0.0 1.0
H A:SER79 4.5 0.0 1.0
H A:TRP61 4.5 0.0 1.0
H A:ALA64 4.6 0.0 1.0
CB A:TRP61 4.6 0.0 1.0
CA A:CYS59 4.7 0.0 1.0
O A:PRO27 4.7 0.0 1.0
C A:HIS28 4.8 0.0 1.0
N A:GLN29 4.8 0.0 1.0
N A:HIS28 4.8 0.0 1.0
C A:CYS62 4.9 0.0 1.0
C A:TRP61 4.9 0.0 1.0
N A:LYS63 5.0 0.0 1.0
HA A:CYS59 5.0 0.0 1.0
HA A:CYS62 5.0 0.0 1.0

Zinc binding site 2 out of 2 in 1r79

Go back to Zinc Binding Sites List in 1r79
Zinc binding site 2 out of 2 in the Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:0.0
occ:1.00
SG A:CYS70 2.3 0.0 1.0
ND1 A:HIS67 2.3 0.0 1.0
SG A:CYS44 2.3 0.0 1.0
SG A:CYS41 2.3 0.0 1.0
HB2 A:HIS67 2.7 0.0 1.0
HB2 A:CYS70 3.1 0.0 1.0
H A:HIS67 3.2 0.0 1.0
HB3 A:CYS44 3.2 0.0 1.0
HB2 A:CYS41 3.2 0.0 1.0
CG A:HIS67 3.2 0.0 1.0
CB A:CYS41 3.2 0.0 1.0
CB A:CYS70 3.3 0.0 1.0
CE1 A:HIS67 3.3 0.0 1.0
HB3 A:CYS41 3.4 0.0 1.0
CB A:CYS44 3.4 0.0 1.0
H A:CYS44 3.4 0.0 1.0
HB3 A:CYS70 3.5 0.0 1.0
CB A:HIS67 3.5 0.0 1.0
HE1 A:HIS67 3.6 0.0 1.0
HB A:VAL43 3.8 0.0 1.0
HB2 A:LYS46 3.9 0.0 1.0
N A:HIS67 4.0 0.0 1.0
N A:CYS44 4.0 0.0 1.0
HB2 A:CYS44 4.2 0.0 1.0
HB3 A:HIS67 4.3 0.0 1.0
CA A:CYS44 4.3 0.0 1.0
CA A:HIS67 4.4 0.0 1.0
HA A:VAL66 4.4 0.0 1.0
CD2 A:HIS67 4.4 0.0 1.0
NE2 A:HIS67 4.4 0.0 1.0
H A:LYS46 4.5 0.0 1.0
H A:ASP45 4.5 0.0 1.0
H A:VAL43 4.5 0.0 1.0
HG A:CYS48 4.5 0.0 1.0
H A:CYS70 4.5 0.0 1.0
HD2 A:LYS46 4.7 0.0 1.0
HG12 A:VAL43 4.7 0.0 1.0
CA A:CYS70 4.7 0.0 1.0
CA A:CYS41 4.7 0.0 1.0
CB A:VAL43 4.8 0.0 1.0
HA A:CYS41 4.9 0.0 1.0
C A:VAL66 5.0 0.0 1.0
N A:ASP45 5.0 0.0 1.0
CB A:LYS46 5.0 0.0 1.0

Reference:

K.Miyamoto, T.Tomizawa, S.Koshiba, M.Inoue, T.Kigawa, S.Yokoyama. Solution Structure of the C1 Domain of the Human Diacylglycerol Kinase Delta To Be Published.
Page generated: Wed Dec 16 03:02:36 2020

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