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Calcium in PDB 1ucn: X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution

Enzymatic activity of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution

All present enzymatic activity of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution:
2.7.4.6;

Protein crystallography data

The structure of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution, PDB code: 1ucn was solved by Y.Chen, S.Gallois-Montbrun, B.Schneider, M.Veron, S.Morera, D.Deville-Bonne, J.Janin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 116.075, 116.075, 91.292, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.2

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution (pdb code 1ucn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution, PDB code: 1ucn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 1ucn

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Calcium binding site 1 out of 5 in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1162

b:60.3
occ:1.00
 O A:HOH1226 2.3 59.9 1.0
O1A A:ADP1160 2.4 49.1 1.0
OD2 A:ASP121 2.5 56.4 1.0
O1B A:ADP1160 2.7 53.0 1.0
O A:HOH1192 2.9 42.1 1.0
O A:GLY119 3.1 53.4 1.0
O3B A:ADP1160 3.5 50.8 1.0
CG A:ASP121 3.5 57.5 1.0
O1 A:PO41161 3.5 45.3 0.5
PB A:ADP1160 3.6 51.2 1.0
NH1 A:ARG88 3.8 64.2 1.0
OD1 A:ASP121 3.8 58.0 1.0
PA A:ADP1160 3.8 50.3 1.0
C A:GLY119 4.1 52.6 1.0
O3A A:ADP1160 4.2 52.0 1.0
O A:HOH1189 4.4 45.8 1.0
N A:GLY119 4.5 47.4 1.0
C5' A:ADP1160 4.5 44.3 1.0
O4 A:PO41161 4.5 44.0 0.5
N A:ASP121 4.6 53.8 1.0
P A:PO41161 4.7 45.5 0.5
O5' A:ADP1160 4.7 45.6 1.0
CZ A:ARG88 4.7 63.9 1.0
CB A:ASP121 4.8 55.8 1.0
O2A A:ADP1160 4.9 49.6 1.0
C A:SER120 4.9 53.6 1.0
CA A:GLY119 4.9 50.6 1.0
N A:SER120 5.0 52.8 1.0

Calcium binding site 2 out of 5 in 1ucn

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Calcium binding site 2 out of 5 in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2162

b:53.0
occ:1.00
 O1B B:ADP2160 2.4 42.5 1.0
O1A B:ADP2160 2.5 43.5 1.0
O B:HOH2261 2.6 28.1 1.0
O B:GLY119 3.0 31.6 1.0
O B:HOH2236 3.0 48.8 1.0
PB B:ADP2160 3.7 42.7 1.0
O B:HOH2237 3.8 30.0 1.0
NH1 B:ARG88 3.9 50.2 1.0
PA B:ADP2160 3.9 44.9 1.0
O B:HOH2318 3.9 45.2 1.0
O2 B:PO42161 4.0 49.3 0.6
O3B B:ADP2160 4.0 41.8 1.0
C B:GLY119 4.1 31.2 1.0
OD1 B:ASP121 4.1 45.9 1.0
O3A B:ADP2160 4.2 43.8 1.0
CG B:ASP121 4.4 41.8 1.0
CB B:ASP121 4.5 40.1 1.0
CZ B:ARG88 4.5 50.2 1.0
N B:ASP121 4.6 33.7 1.0
N B:GLY119 4.6 28.3 1.0
O B:HOH2275 4.6 39.0 1.0
C B:SER120 4.8 32.5 1.0
O2A B:ADP2160 4.8 48.7 1.0
C5' B:ADP2160 4.8 39.7 1.0
CA B:SER120 4.8 32.1 1.0
N B:SER120 4.9 30.5 1.0
O5' B:ADP2160 4.9 41.3 1.0
O2B B:ADP2160 4.9 42.1 1.0
NH2 B:ARG88 4.9 51.9 1.0
CA B:GLY119 5.0 29.8 1.0

Calcium binding site 3 out of 5 in 1ucn

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Calcium binding site 3 out of 5 in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:56.8
occ:0.50
 O B:HOH2314 2.1 61.5 1.0
O B:HOH2241 2.4 47.1 1.0
O B:HOH2313 2.4 53.5 1.0
O B:GLY131 2.6 37.9 1.0
O B:HOH2289 2.7 58.9 1.0
O B:HOH2298 3.4 50.2 1.0
O B:PHE134 3.5 34.2 1.0
O B:HOH2240 3.5 54.2 1.0
C B:GLY131 3.8 36.6 1.0
CA B:GLY131 4.5 36.7 1.0
O B:HOH2316 4.5 52.0 1.0
C B:PHE134 4.5 35.4 1.0
N B:LEU132 4.8 36.4 1.0
CA B:HIS135 4.9 43.8 1.0

Calcium binding site 4 out of 5 in 1ucn

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Calcium binding site 4 out of 5 in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca3162

b:67.9
occ:1.00
 O1A C:ADP3160 2.3 53.7 1.0
O1B C:ADP3160 2.4 56.2 1.0
O C:HOH3224 2.7 61.5 1.0
O C:HOH3223 2.9 41.6 1.0
O C:HOH3222 3.2 69.0 1.0
PB C:ADP3160 3.5 54.3 1.0
O3B C:ADP3160 3.5 53.7 1.0
PA C:ADP3160 3.6 56.0 1.0
NH1 C:ARG88 3.7 52.4 1.0
O C:GLY119 3.9 36.7 1.0
O3A C:ADP3160 3.9 56.2 1.0
O C:HOH3225 4.0 35.9 1.0
OD1 C:ASP121 4.1 48.5 1.0
CG C:ASP121 4.5 46.8 1.0
O2A C:ADP3160 4.5 57.0 1.0
CZ C:ARG88 4.6 51.6 1.0
CB C:ASP121 4.6 44.4 1.0
O1 C:PO43161 4.7 42.2 0.5
O5' C:ADP3160 4.7 55.7 1.0
C5' C:ADP3160 4.7 56.7 1.0
O2B C:ADP3160 4.8 55.7 1.0
C C:GLY119 4.9 35.9 1.0
NH2 C:ARG88 4.9 51.2 1.0

Calcium binding site 5 out of 5 in 1ucn

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Calcium binding site 5 out of 5 in the X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Human Nucleoside Diphosphate Kinase A Complexed with Adp at 2 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:53.1
occ:0.50
 O C:HOH3206 2.2 44.4 1.0
O C:HOH3204 2.3 50.1 1.0
O C:HOH3205 2.7 52.6 1.0
O C:GLY131 2.8 41.1 1.0
O C:HOH3257 3.5 58.0 1.0
C C:GLY131 3.9 40.3 1.0
O C:PHE134 3.9 37.2 1.0
CA C:GLY131 4.4 40.5 1.0
CD C:PRO136 4.9 45.0 1.0

Reference:

Y.Chen, S.Gallois-Montbrun, B.Schneider, M.Veron, S.Morera, D.Deville-Bonne, J.Janin. Nucleotide Binding to Nucleoside Diphosphate Kinases: X-Ray Structure of Human Ndpk-A in Complex with Adp and Comparison to Protein Kinases J.Mol.Biol. V. 332 915 2003.
ISSN: ISSN 0022-2836
PubMed: 12972261
DOI: 10.1016/J.JMB.2003.07.004
Page generated: Thu Jul 11 23:18:31 2024

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