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Magnesium in PDB 9ob9: Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp

Enzymatic activity of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp

All present enzymatic activity of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp, PDB code: 9ob9 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) 47.98 / 1.60
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.784, 69.784, 315.704, 90, 90, 120
R / Rfree (%) 15 / 17.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp (pdb code 9ob9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp, PDB code: 9ob9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9ob9

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Magnesium binding site 1 out of 3 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp


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 with Adp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:26.7
occ:1.00
 O1A A:ADP202 2.1 24.6 0.5
O1A A:CTP201 2.2 22.5 0.5
O1G A:CTP201 2.3 29.1 0.5
O1B A:CTP201 2.4 24.3 0.5
O2B A:ADP202 2.4 23.9 0.5
O A:HOH389 2.4 22.4 1.0
O A:HOH374 2.4 28.5 1.0
O A:HOH373 2.6 27.7 1.0
PA A:ADP202 3.4 23.3 0.5
PB A:ADP202 3.4 22.6 0.5
PB A:CTP201 3.4 24.4 0.5
PG A:CTP201 3.5 32.2 0.5
PA A:CTP201 3.6 25.0 0.5
O1B A:ADP202 3.6 27.2 0.5
O3A A:ADP202 3.7 23.8 0.5
O3B A:CTP201 3.8 26.7 0.5
O3A A:CTP201 3.9 24.7 0.5
O A:HOH310 4.0 34.8 1.0
O A:HOH318 4.1 16.6 0.5
NH1 A:ARG109 4.1 32.9 1.0
OE2 A:GLU76 4.2 50.4 1.0
O3G A:CTP201 4.2 24.3 0.5
O A:HOH305 4.2 37.2 1.0
O2A A:ADP202 4.3 24.5 0.5
NE2 A:HIS77 4.4 28.0 1.0
C5' A:ADP202 4.4 26.0 0.5
C5' A:CTP201 4.5 26.0 0.5
O A:HOH336 4.5 18.1 1.0
O5' A:ADP202 4.5 24.7 0.5
CE1 A:HIS139 4.5 17.5 1.0
O2A A:CTP201 4.5 24.1 0.5
O5' A:CTP201 4.5 24.9 0.5
ND1 A:HIS139 4.6 17.0 1.0
O2G A:CTP201 4.7 17.8 0.5
NH2 A:ARG109 4.7 36.7 1.0
O A:HOH301 4.7 30.1 1.0
O3B A:ADP202 4.8 21.4 0.5
O2B A:CTP201 4.8 22.2 0.5
OD2 A:ASP142 4.8 31.5 1.0
CZ A:ARG109 4.8 37.9 1.0
CD A:GLU76 4.9 41.0 1.0
O A:HOH320 4.9 23.1 1.0

Magnesium binding site 2 out of 3 in 9ob9

Go back to Magnesium Binding Sites List in 9ob9
Magnesium binding site 2 out of 3 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp


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 with Adp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:56.9
occ:1.00
 O1B B:CTP201 2.4 51.4 0.5
O1A B:ADP202 2.5 58.2 0.5
O2B B:ADP202 2.6 48.3 0.5
O1G B:CTP201 2.7 44.0 0.5
O1A B:CTP201 2.9 58.4 0.5
O B:HOH315 3.6 21.4 1.0
NH1 B:ARG109 3.8 33.0 1.0
PB B:ADP202 3.8 49.4 0.5
PB B:CTP201 3.8 56.1 0.5
PG B:CTP201 3.9 51.1 0.5
PA B:ADP202 3.9 61.2 0.5
O1B B:ADP202 4.0 54.5 0.5
CE1 B:HIS139 4.1 22.4 1.0
O3B B:CTP201 4.2 52.1 0.5
PA B:CTP201 4.2 62.1 0.5
OE2 B:GLU76 4.3 52.5 1.0
OD2 B:ASP142 4.3 34.3 1.0
ND1 B:HIS139 4.3 27.3 1.0
O3A B:ADP202 4.3 57.8 0.5
O3G B:CTP201 4.3 40.0 0.5
O B:HOH378 4.4 18.8 0.5
O3A B:CTP201 4.5 57.8 0.5
CB B:ASP142 4.6 23.6 1.0
O B:GLY140 4.6 18.7 1.0
CZ B:ARG109 4.6 40.5 1.0
CG B:ASP142 4.7 27.8 1.0
NH2 B:ARG109 4.7 38.2 1.0
O B:HOH313 4.8 36.5 1.0
O2A B:ADP202 4.8 59.3 0.5
O2B B:CTP201 4.9 46.8 0.5
C5' B:ADP202 4.9 58.1 0.5
O5' B:ADP202 5.0 59.7 0.5

Magnesium binding site 3 out of 3 in 9ob9

Go back to Magnesium Binding Sites List in 9ob9
Magnesium binding site 3 out of 3 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp


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 Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Adp and Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:33.2
occ:1.00
 O1A C:ADP202 2.0 37.6 0.5
O1B C:CTP201 2.2 31.1 0.5
O1A C:CTP201 2.2 37.1 0.5
O1G C:CTP201 2.3 30.9 0.5
O C:HOH397 2.3 25.2 1.0
O2B C:ADP202 2.4 30.8 0.5
O C:HOH302 2.4 32.3 1.0
O C:HOH391 2.4 35.4 1.0
PB C:CTP201 3.3 35.6 0.5
PA C:ADP202 3.3 36.1 0.5
PB C:ADP202 3.4 32.6 0.5
PG C:CTP201 3.5 36.0 0.5
PA C:CTP201 3.5 36.6 0.5
O3B C:CTP201 3.7 34.0 0.5
O1B C:ADP202 3.7 34.0 0.5
O3A C:ADP202 3.8 34.8 0.5
O3A C:CTP201 3.8 34.9 0.5
NH1 C:ARG109 4.0 32.5 1.0
O3G C:CTP201 4.1 28.1 0.5
O C:HOH308 4.1 22.9 0.5
OD2 C:ASP142 4.2 33.4 1.0
C5' C:ADP202 4.3 40.6 0.5
O2A C:ADP202 4.3 36.4 0.5
O5' C:ADP202 4.4 40.2 0.5
C5' C:CTP201 4.4 40.5 0.5
O C:HOH345 4.4 22.2 1.0
OE2 C:GLU76 4.5 56.8 1.0
CE1 C:HIS139 4.5 21.9 1.0
O5' C:CTP201 4.5 40.2 0.5
O2A C:CTP201 4.5 35.5 0.5
NH2 C:ARG109 4.6 48.4 1.0
ND1 C:HIS139 4.6 24.7 1.0
O2B C:CTP201 4.6 32.2 0.5
O2G C:CTP201 4.7 23.4 0.5
OE1 C:GLU76 4.7 55.4 1.0
CZ C:ARG109 4.7 42.8 1.0
O3B C:ADP202 4.8 30.0 0.5
CD C:GLU76 4.8 58.0 1.0
O C:HOH382 4.9 28.4 1.0
NE2 C:HIS77 4.9 43.8 1.0
CG C:ASP142 4.9 29.1 1.0

Reference:

L.Liu, S.Lovell, K.P.Battaile. Crystal Structure of Nucleoside-Diphosphate Kinase Cryptosporidium Parvum in Complex with Adp and Ctp To Be Published.
Page generated: Sat Aug 16 06:59:48 2025

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