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Magnesium in PDB 9oak: Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate

Enzymatic activity of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate

All present enzymatic activity of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate, PDB code: 9oak was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.99 / 1.61
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.734, 69.734, 316.121, 90, 90, 120
R / Rfree (%) 14.5 / 17.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate (pdb code 9oak). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate, PDB code: 9oak:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 9oak

Go back to Magnesium Binding Sites List in 9oak
Magnesium binding site 1 out of 2 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate


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 Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:26.5
occ:0.55
 O A:HOH385 2.2 31.2 1.0
O3G A:CTP201 2.2 20.6 0.6
O2A A:CTP201 2.3 23.8 0.6
O2B A:CTP201 2.3 28.7 0.6
O A:HOH327 2.5 33.1 1.0
O A:HOH376 2.6 36.9 1.0
O1P A:HIS139 2.6 22.4 0.5
PB A:CTP201 3.3 23.5 0.6
PG A:CTP201 3.4 25.4 0.6
O3B A:CTP201 3.4 22.1 0.6
PA A:CTP201 3.6 27.4 0.6
O3A A:CTP201 3.8 24.8 0.6
P A:HIS139 3.8 17.5 0.5
CE1 A:HIS139 4.0 17.7 0.5
NH1 A:ARG109 4.1 27.5 0.5
O2G A:CTP201 4.2 22.7 0.6
ND1 A:HIS139 4.3 18.0 0.5
O A:HOH322 4.3 21.0 1.0
O2P A:HIS139 4.4 20.3 0.5
C5' A:CTP201 4.4 28.1 0.6
CE1 A:HIS139 4.4 16.6 0.6
ND1 A:HIS139 4.4 16.3 0.6
O A:HOH356 4.5 14.9 0.5
OE1 A:GLU76 4.5 55.3 1.0
NH2 A:ARG109 4.5 35.2 0.5
O5' A:CTP201 4.5 29.8 0.6
O1G A:CTP201 4.6 22.7 0.6
O1A A:CTP201 4.6 25.3 0.6
NE2 A:HIS77 4.7 35.7 1.0
O A:HOH302 4.7 31.8 1.0
O1B A:CTP201 4.7 18.4 0.6
OD2 A:ASP142 4.7 42.6 1.0
CZ A:ARG109 4.8 31.8 0.5
O A:HOH339 4.8 24.9 1.0
O A:HOH377 5.0 18.7 0.5

Magnesium binding site 2 out of 2 in 9oak

Go back to Magnesium Binding Sites List in 9oak
Magnesium binding site 2 out of 2 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate


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 Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:38.4
occ:0.66
 O1B C:CDP201 2.2 41.1 0.7
O C:HOH354 2.2 31.6 1.0
O2A C:CDP201 2.4 56.8 0.7
O1P C:HIP139 2.7 31.1 1.0
PB C:CDP201 3.1 42.9 0.7
O3B C:CDP201 3.2 46.5 0.7
PA C:CDP201 3.5 60.8 0.7
O3A C:CDP201 3.5 53.6 0.7
P C:HIP139 4.0 31.1 1.0
NH1 C:ARG109 4.1 23.9 0.6
C5' C:CDP201 4.2 47.9 0.7
OD2 C:ASP142 4.2 33.2 1.0
CE1 C:HIP139 4.3 21.8 1.0
O C:HOH327 4.3 19.2 1.0
O C:HOH321 4.3 21.7 1.0
O5' C:CDP201 4.4 50.8 0.7
O3P C:HIP139 4.4 26.9 1.0
O2B C:CDP201 4.5 29.8 0.7
ND1 C:HIP139 4.5 19.3 1.0
OE2 C:GLU76 4.5 56.5 1.0
O C:HOH382 4.6 28.6 1.0
O1A C:CDP201 4.7 49.6 0.7
NH2 C:ARG109 4.8 36.1 0.6
CZ C:ARG109 4.9 32.6 0.6

Reference:

L.Liu, S.Lovell, K.P.Battaile. Crystal Structure of Nucleoside-Diphosphate Kinase Cryptosporidium Parvum in Complex with Cytidine-5'-Diphosphate and Cytidine-5'-Triphosphate To Be Published.
Page generated: Sat Aug 16 06:59:20 2025

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