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Holmium in PDB 2olc: Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO

Enzymatic activity of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO

All present enzymatic activity of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO:
2.7.1.100;

Protein crystallography data

The structure of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO, PDB code: 2olc was solved by S.Y.Ku, G.D.Smith, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.83 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 215.200, 83.600, 51.600, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 25

Holmium Binding Sites:

The binding sites of Holmium atom in the Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO (pdb code 2olc). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 4 binding sites of Holmium where determined in the Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO, PDB code: 2olc:
Jump to Holmium binding site number: 1; 2; 3; 4;

Holmium binding site 1 out of 4 in 2olc

Go back to Holmium Binding Sites List in 2olc
Holmium binding site 1 out of 4 in the Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 1 of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho400

b:44.8
occ:1.00
O A:HOH1001 2.0 23.3 1.0
O A:HOH1002 2.2 14.3 1.0
O2A A:ADP999 2.2 29.9 1.0
O3B A:ADP999 2.3 26.1 1.0
OD2 A:ASP250 2.6 17.6 1.0
PB A:ADP999 3.4 25.6 1.0
PA A:ADP999 3.5 28.5 1.0
CG A:ASP250 3.6 20.6 1.0
O2B A:ADP999 3.8 23.9 1.0
O3A A:ADP999 3.9 26.8 1.0
HO A:HO401 4.1 39.2 1.0
CB A:ASP250 4.1 20.3 1.0
OD1 A:ASP40 4.4 45.6 1.0
O A:GLY237 4.5 20.8 1.0
O1A A:ADP999 4.5 29.3 1.0
OD1 A:ASP250 4.6 20.9 1.0
O5' A:ADP999 4.6 27.7 1.0
OG A:SER238 4.7 26.8 1.0
O1B A:ADP999 4.8 26.7 1.0
C5' A:ADP999 4.9 29.2 1.0

Holmium binding site 2 out of 4 in 2olc

Go back to Holmium Binding Sites List in 2olc
Holmium binding site 2 out of 4 in the Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 2 of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ho401

b:39.2
occ:1.00
OE1 A:GLU252 2.3 26.8 1.0
OD2 A:ASP250 2.3 17.6 1.0
O2B A:ADP999 2.3 23.9 1.0
O A:HOH1000 2.4 24.8 1.0
OD1 A:ASP250 2.5 20.9 1.0
CG A:ASP250 2.7 20.6 1.0
O A:HOH1001 2.9 23.3 1.0
CD A:GLU252 3.4 23.4 1.0
PB A:ADP999 3.6 25.6 1.0
CG A:GLU252 3.9 23.7 1.0
O3B A:ADP999 3.9 26.1 1.0
HO A:HO400 4.1 44.8 1.0
CB A:GLU252 4.2 23.2 1.0
ND2 A:ASN44 4.2 33.6 1.0
CB A:ASP250 4.3 20.3 1.0
NZ A:LYS61 4.3 24.9 1.0
OE2 A:GLU252 4.4 26.2 1.0
O3A A:ADP999 4.5 26.8 1.0
O1B A:ADP999 4.5 26.7 1.0
O A:ASP250 4.7 22.6 1.0
O2A A:ADP999 4.9 29.9 1.0
CE1 A:PHE253 4.9 20.3 1.0

Holmium binding site 3 out of 4 in 2olc

Go back to Holmium Binding Sites List in 2olc
Holmium binding site 3 out of 4 in the Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 3 of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ho400

b:41.9
occ:1.00
O2A B:ADP999 2.2 27.3 1.0
O B:HOH1000 2.3 24.5 1.0
O3B B:ADP999 2.4 25.7 1.0
O B:HOH1001 2.5 24.3 1.0
OD2 B:ASP250 2.5 19.5 1.0
PB B:ADP999 3.5 26.2 1.0
CG B:ASP250 3.6 20.0 1.0
PA B:ADP999 3.6 26.8 1.0
O2B B:ADP999 3.7 28.2 1.0
HO B:HO401 3.9 40.0 1.0
O3A B:ADP999 4.0 27.3 1.0
CB B:ASP250 4.2 21.4 1.0
OD1 B:ASP250 4.4 21.0 1.0
O B:GLY237 4.5 20.4 1.0
O1A B:ADP999 4.6 27.7 1.0
O5' B:ADP999 4.6 28.4 1.0
C5' B:ADP999 4.8 29.2 1.0
O1B B:ADP999 4.8 26.4 1.0
OD2 B:ASP40 4.9 45.2 1.0

Holmium binding site 4 out of 4 in 2olc

Go back to Holmium Binding Sites List in 2olc
Holmium binding site 4 out of 4 in the Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 4 of Crystal Structure of 5-Methylthioribose Kinase in Complex with Adp-2HO within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ho401

b:40.0
occ:1.00
O B:HOH1002 2.0 21.9 1.0
O2B B:ADP999 2.3 28.2 1.0
OE1 B:GLU252 2.4 25.8 1.0
OD2 B:ASP250 2.4 19.5 1.0
OD1 B:ASP250 2.4 21.0 1.0
CG B:ASP250 2.8 20.0 1.0
PB B:ADP999 3.5 26.2 1.0
CD B:GLU252 3.6 23.0 1.0
O3B B:ADP999 3.8 25.7 1.0
O B:HOH1001 3.8 24.3 1.0
HO B:HO400 3.9 41.9 1.0
NZ B:LYS61 4.2 26.5 1.0
CB B:ASP250 4.3 21.4 1.0
CG B:GLU252 4.3 22.8 1.0
CB B:GLU252 4.3 23.0 1.0
ND2 B:ASN44 4.3 29.1 1.0
O1B B:ADP999 4.4 26.4 1.0
O3A B:ADP999 4.5 27.3 1.0
OE2 B:GLU252 4.5 23.5 1.0
O B:ASP250 4.6 22.7 1.0
O2A B:ADP999 4.6 27.3 1.0
PA B:ADP999 5.0 26.8 1.0

Reference:

S.Y.Ku, G.D.Smith, P.L.Howell. Adp-2HO As A Phasing Tool For Nucleotide-Containing Proteins. Acta Crystallogr.,Sect.D V. 63 493 2007.
ISSN: ISSN 0907-4449
PubMed: 17372354
DOI: 10.1107/S0907444907006592
Page generated: Sun Dec 13 19:18:53 2020

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