Magnesium in PDB 2qrn: Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex

All present enzymatic activity of Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex:
2.7.1.74;

The structure of Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex, PDB code: 2qrn was solved by S.E.Ealick, E.V.Soriano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 3.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.565, 94.565, 335.334, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.9

The binding sites of Magnesium atom in the Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex (pdb code 2qrn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex, PDB code: 2qrn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:56.0 occ:1.00 OG A:SER35 2.3 33.5 1.0 OE1 A:GLU127 2.3 86.3 1.0 O1B A:UDP402 2.5 73.2 1.0 CD A:GLU127 3.3 86.3 1.0 OE2 A:GLU127 3.4 86.3 1.0 O3P A:DCM403 3.6 52.7 1.0 CB A:SER35 3.6 33.5 1.0 NH2 A:ARG194 3.9 67.0 1.0 PB A:UDP402 3.9 73.0 1.0 O1A A:UDP402 4.2 85.1 1.0 O3B A:UDP402 4.3 76.2 1.0 O2B A:UDP402 4.5 69.4 1.0 NH2 A:ARG192 4.6 61.8 1.0 CG A:GLU127 4.7 86.3 1.0 CA A:SER35 4.7 57.6 1.0 N A:SER35 4.9 57.6 1.0 CG1 A:VAL55 4.9 47.7 1.0

Magnesium binding site 2 out of 4 in the Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:56.0 occ:1.00 OG B:SER35 2.4 45.5 1.0 O1B B:UDP402 2.5 73.2 1.0 OE1 B:GLU127 2.7 50.7 1.0 NH2 B:ARG194 3.5 62.2 1.0 CB B:SER35 3.6 45.5 1.0 CD B:GLU127 3.7 50.7 1.0 O1A B:UDP402 3.9 85.1 1.0 O3P B:DCM403 3.9 52.7 1.0 OE2 B:GLU127 3.9 50.7 1.0 PB B:UDP402 4.0 73.0 1.0 NH2 B:ARG192 4.3 68.4 1.0 O3B B:UDP402 4.4 76.2 1.0 O2B B:UDP402 4.7 69.4 1.0 CZ B:ARG194 4.8 62.2 1.0 CA B:SER35 4.9 59.4 1.0 CG1 B:VAL55 4.9 34.4 1.0 PA B:UDP402 4.9 87.4 1.0

Magnesium binding site 3 out of 4 in the Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:56.0 occ:1.00 O1B C:UDP402 2.4 73.2 1.0 OG C:SER35 2.5 35.1 1.0 OE1 C:GLU127 2.7 64.3 1.0 NH2 C:ARG194 3.5 47.6 1.0 CD C:GLU127 3.6 64.3 1.0 CB C:SER35 3.7 35.1 1.0 O3P C:DCM403 3.8 52.7 1.0 OE2 C:GLU127 3.8 64.3 1.0 O1A C:UDP402 3.9 85.1 1.0 PB C:UDP402 3.9 73.0 1.0 NH2 C:ARG192 4.4 59.2 1.0 O3B C:UDP402 4.4 76.2 1.0 O2B C:UDP402 4.6 69.4 1.0 CZ C:ARG194 4.8 47.6 1.0 CG1 C:VAL55 4.8 61.9 1.0 PA C:UDP402 4.9 87.4 1.0 CA C:SER35 4.9 42.2 1.0 O3A C:UDP402 5.0 79.9 1.0

Magnesium binding site 4 out of 4 in the Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Deoxycytidine Kinase Dcmp, Udp, Mg Ion Product Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:56.0 occ:1.00 OG D:SER35 2.4 55.3 1.0 O1B D:UDP402 2.6 73.2 1.0 OE1 D:GLU127 2.7 54.5 1.0 NH2 D:ARG194 3.5 67.2 1.0 CB D:SER35 3.6 55.3 1.0 CD D:GLU127 3.7 54.5 1.0 O3P D:DCM403 3.8 52.7 1.0 O1A D:UDP402 3.8 85.1 1.0 OE2 D:GLU127 3.9 54.5 1.0 PB D:UDP402 4.0 73.0 1.0 NH2 D:ARG192 4.2 66.0 1.0 O3B D:UDP402 4.4 76.2 1.0 CZ D:ARG194 4.8 67.2 1.0 O2B D:UDP402 4.8 69.4 1.0 PA D:UDP402 4.9 87.4 1.0 CA D:SER35 4.9 67.1 1.0 CG1 D:VAL55 4.9 35.8 1.0

E.V.Soriano, V.C.Clark, S.E.Ealick. Structures of Human Deoxycytidine Kinase Product Complexes. Acta Crystallogr.,Sect.D V. 63 1201 2007.
ISSN: ISSN 0907-4449
PubMed: 18084067
DOI: 10.1107/S0907444907048834