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Magnesium in PDB 9oan: Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp

Enzymatic activity of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp

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

Protein crystallography data

The structure of Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp, PDB code: 9oan 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) 48.03 / 1.63
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.829, 69.829, 316.142, 90, 90, 120
R / Rfree (%) 15 / 17.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp (pdb code 9oan). 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 Guanosine-5'-Diphosphate and Amp-Pnp, PDB code: 9oan:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 9oan

Go back to Magnesium Binding Sites List in 9oan
Magnesium binding site 1 out of 3 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp


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 Guanosine-5'-Diphosphate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:30.6
occ:1.00
 O1A A:GDP201 2.2 27.4 1.0
O3B A:GDP201 2.3 25.5 1.0
O A:HOH391 2.4 26.0 1.0
O A:HOH365 2.5 29.0 1.0
O A:HOH353 2.5 31.7 1.0
PB A:GDP201 3.4 27.3 1.0
PA A:GDP201 3.4 28.6 1.0
O1B A:GDP201 3.8 31.2 1.0
O3A A:GDP201 3.8 27.7 1.0
NH1 A:ARG109 4.0 28.8 1.0
O A:HOH327 4.0 26.0 1.0
OE2 A:GLU76 4.3 54.8 1.0
NE2 A:HIS77 4.4 30.3 1.0
O A:HOH329 4.4 19.7 1.0
O2A A:GDP201 4.4 28.3 1.0
C5' A:GDP201 4.5 24.8 1.0
O5' A:GDP201 4.5 25.4 1.0
CE1 A:HIS139 4.5 19.3 1.0
O A:HOH333 4.5 26.4 1.0
ND1 A:HIS139 4.6 17.8 1.0
NH2 A:ARG109 4.7 29.6 1.0
OD2 A:ASP142 4.7 29.4 1.0
CZ A:ARG109 4.7 29.0 1.0
O2B A:GDP201 4.8 24.5 1.0
O A:HOH305 4.8 31.4 1.0
CD A:GLU76 4.9 48.9 1.0
OE1 A:GLU76 5.0 38.6 1.0
O A:HOH339 5.0 25.3 1.0
CE1 A:HIS77 5.0 37.6 1.0
O A:GLY140 5.0 16.5 1.0

Magnesium binding site 2 out of 3 in 9oan

Go back to Magnesium Binding Sites List in 9oan
Magnesium binding site 2 out of 3 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp


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 Guanosine-5'-Diphosphate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:60.9
occ:1.00
 O2B B:ANP201 2.5 59.3 1.0
O1A B:ANP201 2.8 65.7 1.0
O2G B:ANP201 2.9 69.2 1.0
O B:HOH314 3.5 21.1 1.0
NH1 B:ARG109 3.8 31.4 1.0
PB B:ANP201 3.9 62.8 1.0
PA B:ANP201 4.0 69.7 1.0
O B:HOH360 4.2 40.2 1.0
OD2 B:ASP142 4.2 33.7 1.0
CE1 B:HIS139 4.2 24.3 1.0
PG B:ANP201 4.3 65.3 1.0
OE2 B:GLU76 4.3 49.9 1.0
O3A B:ANP201 4.4 64.8 1.0
N3B B:ANP201 4.5 58.3 1.0
ND1 B:HIS139 4.5 27.2 1.0
O B:HOH331 4.5 34.0 1.0
CB B:ASP142 4.6 22.0 1.0
CG B:ASP142 4.6 27.8 1.0
CZ B:ARG109 4.7 36.1 1.0
NH2 B:ARG109 4.7 32.4 1.0
O B:HOH315 4.7 39.7 1.0
O B:GLY140 4.8 19.4 1.0
O2A B:ANP201 4.9 78.4 1.0

Magnesium binding site 3 out of 3 in 9oan

Go back to Magnesium Binding Sites List in 9oan
Magnesium binding site 3 out of 3 in the Crystal Structure of Nucleoside-Diphosphate Kinase From Cryptosporidium Parvum in Complex with with Guanosine-5'-Diphosphate and Amp-Pnp


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 Guanosine-5'-Diphosphate and Amp-Pnp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:44.1
occ:1.00
 O1A C:GDP201 2.0 51.2 1.0
O C:HOH401 2.3 28.9 1.0
O3B C:GDP201 2.3 36.6 1.0
O C:HOH387 2.6 40.8 1.0
PA C:GDP201 3.3 46.2 1.0
PB C:GDP201 3.3 41.0 1.0
O1B C:GDP201 3.7 39.4 1.0
O3A C:GDP201 3.7 60.7 1.0
NH1 C:ARG109 4.0 30.1 1.0
O C:HOH348 4.2 27.2 1.0
OD2 C:ASP142 4.2 30.7 1.0
O2A C:GDP201 4.2 49.3 1.0
C5' C:GDP201 4.4 47.2 1.0
O5' C:GDP201 4.4 44.5 1.0
O C:HOH360 4.4 20.8 1.0
O C:HOH344 4.5 30.9 1.0
OE2 C:GLU76 4.6 53.6 1.0
CE1 C:HIS139 4.6 21.6 1.0
O2B C:GDP201 4.6 34.9 1.0
OE1 C:GLU76 4.6 52.4 1.0
NH2 C:ARG109 4.7 38.1 1.0
ND1 C:HIS139 4.7 22.9 1.0
CZ C:ARG109 4.8 38.6 1.0
O C:HOH351 4.8 33.5 1.0
CD C:GLU76 4.9 53.3 1.0
CG C:ASP142 4.9 30.3 1.0
O C:HOH380 4.9 27.5 1.0

Reference:

L.Liu, S.Lovell, K.P.Battaile. Crystal Structure of Nucleoside-Diphosphate Kinase Cryptosporidium Parvum in Complex with Guanosine-5'-Diphosphate and Amp-Pnp To Be Published.
Page generated: Sat Aug 16 06:59:23 2025

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