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Magnesium in PDB 2a2z: Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate

Enzymatic activity of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate

All present enzymatic activity of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate:
2.7.1.74;

Protein crystallography data

The structure of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate, PDB code: 2a2z was solved by M.H.Godsey, S.Ort, E.Sabini, M.Konrad, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.66 / 3.02
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.180, 110.850, 155.370, 90.00, 90.00, 90.00
R / Rfree (%) 24.6 / 30

Other elements in 2a2z:

The structure of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate (pdb code 2a2z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate, PDB code: 2a2z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2a2z

Go back to Magnesium Binding Sites List in 2a2z
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:46.8
occ:1.00
 O A:HOH307 2.1 47.2 1.0
O A:HOH305 2.1 45.8 1.0
O A:HOH306 2.1 49.4 1.0
OE1 A:GLU127 2.4 24.5 1.0
O1B A:UDP301 2.6 36.1 1.0
OG A:SER35 2.7 41.1 1.0
O2B A:UDP301 3.1 33.7 1.0
PB A:UDP301 3.3 38.1 1.0
CD A:GLU127 3.5 29.4 1.0
NH2 A:ARG192 3.9 42.9 1.0
CB A:SER35 3.9 43.1 1.0
OE2 A:GLU127 4.0 30.8 1.0
O3A A:UDP301 4.1 39.2 1.0
O A:HOH312 4.2 11.0 1.0
OE2 A:GLU53 4.3 29.7 1.0
CE A:LYS34 4.4 38.0 1.0
N A:SER35 4.5 43.7 1.0
NZ A:LYS34 4.6 36.9 1.0
O3B A:UDP301 4.7 35.2 1.0
CG A:GLU127 4.7 28.8 1.0
CA A:SER35 4.8 44.0 1.0
O1A A:UDP301 4.8 39.9 1.0
O5' A:DCZ304 4.9 13.7 1.0
PA A:UDP301 5.0 41.1 1.0

Magnesium binding site 2 out of 4 in 2a2z

Go back to Magnesium Binding Sites List in 2a2z
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:39.4
occ:1.00
 O B:HOH407 2.1 41.0 1.0
O B:HOH406 2.1 39.9 1.0
O B:HOH405 2.1 38.0 1.0
O1B B:UDP401 2.5 44.4 1.0
OG B:SER35 2.5 40.3 1.0
OE1 B:GLU127 2.5 34.9 1.0
CD B:GLU127 3.5 37.5 1.0
PB B:UDP401 3.8 44.2 1.0
CB B:SER35 3.9 41.8 1.0
OE2 B:GLU127 4.1 40.0 1.0
NH2 B:ARG192 4.1 69.1 1.0
O2B B:UDP401 4.2 45.4 1.0
O B:HOH410 4.2 18.0 1.0
OE1 B:GLU53 4.3 56.2 1.0
NH2 B:ARG194 4.4 72.2 1.0
CG B:GLU127 4.6 36.8 1.0
N B:SER35 4.6 42.0 1.0
O3B B:UDP401 4.7 43.6 1.0
CA B:SER35 4.8 41.5 1.0
CG1 B:VAL55 4.8 57.4 1.0
O1A B:UDP401 4.8 47.5 1.0
O3A B:UDP401 4.8 47.8 1.0
C5' B:DCZ404 4.9 46.8 1.0
O5' B:DCZ404 4.9 51.0 1.0
CB B:GLU53 5.0 48.5 1.0

Magnesium binding site 3 out of 4 in 2a2z

Go back to Magnesium Binding Sites List in 2a2z
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:38.4
occ:1.00
 O C:HOH507 2.1 41.2 1.0
O C:HOH505 2.1 39.7 1.0
O C:HOH506 2.1 42.3 1.0
OE1 C:GLU127 2.4 46.9 1.0
OG C:SER35 2.4 46.2 1.0
O1B C:UDP501 2.5 37.8 1.0
O2B C:UDP501 3.2 40.5 1.0
PB C:UDP501 3.3 40.6 1.0
CD C:GLU127 3.5 45.9 1.0
CB C:SER35 3.8 47.1 1.0
O3A C:UDP501 3.9 42.5 1.0
NH2 C:ARG192 4.1 48.9 1.0
OE2 C:GLU127 4.1 47.2 1.0
O C:HOH514 4.2 5.4 1.0
N C:SER35 4.3 44.7 1.0
CE C:LYS34 4.4 29.4 1.0
OE2 C:GLU53 4.4 31.7 1.0
NZ C:LYS34 4.5 28.1 1.0
O1A C:UDP501 4.5 42.9 1.0
CA C:SER35 4.6 46.1 1.0
O3B C:UDP501 4.6 37.7 1.0
CG C:GLU127 4.7 43.2 1.0
PA C:UDP501 4.7 43.8 1.0
CB C:LYS34 4.9 38.8 1.0

Magnesium binding site 4 out of 4 in 2a2z

Go back to Magnesium Binding Sites List in 2a2z
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Deoxycytidine Kinase in Complex with Deoxycytidine and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:35.6
occ:1.00
 O D:HOH607 2.1 37.5 1.0
O D:HOH606 2.1 33.9 1.0
O D:HOH605 2.1 30.4 1.0
O1B D:UDP601 2.6 55.9 1.0
OG D:SER35 2.6 51.5 1.0
OE1 D:GLU127 2.7 34.0 1.0
CD D:GLU127 3.7 36.5 1.0
PB D:UDP601 3.8 56.7 1.0
NH2 D:ARG192 3.9 58.1 1.0
O2B D:UDP601 3.9 56.6 1.0
CB D:SER35 4.0 49.5 1.0
OE2 D:GLU127 4.3 34.8 1.0
NH2 D:ARG194 4.3 66.1 1.0
O3A D:UDP601 4.5 59.9 1.0
OE1 D:GLU53 4.6 53.7 1.0
CG2 D:VAL55 4.6 65.8 1.0
O1A D:UDP601 4.6 63.4 1.0
O5' D:DCZ604 4.6 46.7 1.0
O D:HOH609 4.7 27.8 1.0
C5' D:DCZ604 4.8 44.5 1.0
N D:SER35 4.8 49.0 1.0
NH1 D:ARG194 4.8 69.4 1.0
CG D:GLU127 4.8 36.6 1.0
CB D:GLU53 4.9 52.5 1.0
CA D:SER35 4.9 49.8 1.0
NZ D:LYS34 4.9 44.8 1.0
O3B D:UDP601 4.9 55.9 1.0
CZ D:ARG192 5.0 57.3 1.0

Reference:

M.H.Godsey, S.Ort, E.Sabini, M.Konrad, A.Lavie. Structural Basis For the Preference of Utp Over Atp in Human Deoxycytidine Kinase: Illuminating the Role of Main-Chain Reorganization. Biochemistry V. 45 452 2006.
ISSN: ISSN 0006-2960
PubMed: 16401075
DOI: 10.1021/BI0518646
Page generated: Tue Aug 13 20:20:57 2024

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