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Magnesium in PDB 1xrj: Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative

Enzymatic activity of Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative

All present enzymatic activity of Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative:
2.7.1.48;

Protein crystallography data

The structure of Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative, PDB code: 1xrj was solved by T.C.Appleby, G.Larson, J.Z.Wu, I.W.Cheney, Z.Hong, N.Yao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.630, 109.320, 64.520, 90.00, 94.96, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative (pdb code 1xrj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative, PDB code: 1xrj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1xrj

Go back to Magnesium Binding Sites List in 1xrj
Magnesium binding site 1 out of 2 in the Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg400

b:23.0
occ:1.00
 O2P A:C5P405 2.4 30.8 1.0
OG A:SER34 2.5 28.4 1.0
O A:HOH483 2.6 33.2 1.0
O2B A:ADP410 2.6 33.9 1.0
O A:HOH557 2.7 44.5 1.0
O3B A:ADP410 3.0 34.0 1.0
PB A:ADP410 3.4 31.2 1.0
P A:C5P405 3.5 29.1 1.0
O2A A:ADP410 3.5 40.6 1.0
CB A:SER34 3.5 24.9 1.0
O1P A:C5P405 3.6 30.8 1.0
NH1 A:ARG169 4.0 34.0 1.0
NH2 A:ARG174 4.3 34.6 1.0
OD2 A:ASP62 4.3 38.8 1.0
O3A A:ADP410 4.3 35.4 1.0
OE1 A:GLU135 4.5 27.1 1.0
PA A:ADP410 4.5 41.3 1.0
O3P A:C5P405 4.5 30.1 1.0
O5' A:C5P405 4.5 29.5 1.0
OE2 A:GLU135 4.5 27.9 1.0
N A:SER34 4.6 25.4 1.0
O1B A:ADP410 4.6 33.0 1.0
CA A:SER34 4.6 25.3 1.0
CD A:GLU135 4.9 26.9 1.0
NZ A:LYS33 5.0 25.6 1.0

Magnesium binding site 2 out of 2 in 1xrj

Go back to Magnesium Binding Sites List in 1xrj
Magnesium binding site 2 out of 2 in the Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rapid Structure Determination of Human Uridine-Cytidine Kinase 2 Using A Conventional Laboratory X-Ray Source and A Single Samarium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:29.9
occ:0.50
 O B:HOH603 2.5 41.7 1.0
O B:HOH601 2.6 36.9 1.0
O B:HOH602 2.6 37.9 1.0
OE2 B:GLU135 2.7 27.8 1.0
OD2 B:ASP62 2.7 38.1 1.0
OG B:SER34 2.8 34.7 1.0
O B:HOH599 3.2 29.4 1.0
OG B:SER60 3.4 29.2 1.0
CD B:GLU135 3.7 26.4 1.0
O B:HOH469 3.8 28.6 1.0
CG B:ASP62 3.9 34.5 1.0
O B:HOH565 3.9 46.9 1.0
O B:HOH600 3.9 41.9 1.0
CB B:SER60 3.9 25.9 1.0
CB B:SER34 4.0 26.4 1.0
OE1 B:GLU135 4.1 26.0 1.0
OD1 B:ASP62 4.3 39.0 1.0
O2P B:C5P406 4.5 28.6 1.0
O B:HOH532 4.5 47.2 1.0
CG B:GLU135 4.9 21.5 1.0

Reference:

T.C.Appleby, G.Larson, I.W.Cheney, H.Walker, J.Z.Wu, W.Zhong, Z.Hong, N.Yao. Structure of Human Uridine-Cytidine Kinase 2 Determined By Siras Using A Rotating-Anode X-Ray Generator and A Single Samarium Derivative. Acta Crystallogr.,Sect.D V. 61 278 2005.
ISSN: ISSN 0907-4449
PubMed: 15735337
DOI: 10.1107/S0907444904032937
Page generated: Tue Aug 13 18:22:26 2024

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