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Calcium in PDB 2az1: Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum

Enzymatic activity of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum

All present enzymatic activity of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum:
2.7.4.6;

Protein crystallography data

The structure of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum, PDB code: 2az1 was solved by H.Besir, K.Zeth, A.Bracher, U.Heider, M.Ishibashi, M.Tokunaga, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.280, 108.700, 119.650, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 28.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum (pdb code 2az1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum, PDB code: 2az1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 2az1

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Calcium binding site 1 out of 5 in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:71.1
occ:1.00
 O A:HIS52 2.4 58.3 1.0
O A:HOH222 2.4 60.8 1.0
OE1 A:GLU55 2.6 74.6 1.0
CD A:GLU55 3.5 71.7 1.0
NH2 A:ARG131 3.6 68.7 1.0
C A:HIS52 3.6 58.5 1.0
OE2 A:GLU55 3.8 73.6 1.0
CD2 A:HIS52 4.0 55.9 1.0
NH1 A:ARG131 4.3 68.3 1.0
OE2 A:GLU132 4.4 51.9 1.0
CZ A:ARG131 4.4 68.5 1.0
N A:TYR53 4.5 58.9 1.0
CA A:HIS52 4.5 58.5 1.0
CA A:TYR53 4.5 59.4 1.0
NE2 A:HIS52 4.7 53.4 1.0
O A:GLU51 4.7 58.9 1.0
N A:ALA54 4.8 60.2 1.0
CG A:GLU55 4.9 65.9 1.0
C A:TYR53 4.9 59.8 1.0
CG A:HIS52 4.9 57.9 1.0

Calcium binding site 2 out of 5 in 2az1

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Calcium binding site 2 out of 5 in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:52.4
occ:1.00
 O C:ALA134 2.2 43.6 1.0
OD1 C:ASP138 2.3 55.6 1.0
O C:PHE137 2.3 49.3 1.0
C C:PHE137 3.2 48.8 1.0
C C:ALA134 3.4 43.2 1.0
CG C:ASP138 3.5 54.0 1.0
N C:ASP138 3.7 50.3 1.0
CA C:ASP138 3.7 52.1 1.0
CA C:CA204 3.9 72.4 1.0
CA C:ALA134 4.0 42.6 1.0
CB C:ASP138 4.1 52.2 1.0
O C:LEU135 4.3 46.6 1.0
CA C:PHE137 4.4 46.8 1.0
N C:PHE137 4.4 45.4 1.0
OD2 C:ASP138 4.4 58.6 1.0
N C:LEU135 4.4 43.7 1.0
C C:LEU135 4.5 45.4 1.0
CA C:LEU135 4.7 44.5 1.0
CB C:ALA134 4.7 42.5 1.0
O C:HOH220 4.7 49.7 1.0
O C:ILE133 4.9 40.0 1.0

Calcium binding site 3 out of 5 in 2az1

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Calcium binding site 3 out of 5 in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca204

b:72.4
occ:1.00
 OD2 C:ASP138 2.8 58.6 1.0
OD1 C:ASP138 2.9 55.6 1.0
CG C:ASP138 3.2 54.0 1.0
CA C:CA201 3.9 52.4 1.0
CB C:ASP138 4.6 52.2 1.0
O C:HOH220 4.8 49.7 1.0

Calcium binding site 4 out of 5 in 2az1

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Calcium binding site 4 out of 5 in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:56.7
occ:1.00
 O D:ALA134 2.1 51.0 1.0
OD1 D:ASP138 2.2 49.8 1.0
O D:HOH225 2.4 51.0 1.0
O D:PHE137 2.6 51.5 1.0
C D:ALA134 3.3 51.1 1.0
C D:PHE137 3.5 52.6 1.0
CG D:ASP138 3.5 55.6 1.0
CA D:CA205 4.0 79.0 1.0
CA D:ALA134 4.0 51.3 1.0
N D:ASP138 4.1 53.7 1.0
CA D:ASP138 4.1 55.0 1.0
O D:LEU135 4.1 52.4 1.0
N D:LEU135 4.3 51.0 1.0
C D:LEU135 4.3 52.1 1.0
OD2 D:ASP138 4.3 57.3 1.0
CB D:ASP138 4.4 55.0 1.0
N D:PHE137 4.4 51.9 1.0
CA D:LEU135 4.5 51.6 1.0
CA D:PHE137 4.5 52.5 1.0
CB D:ALA134 4.7 51.5 1.0
N D:PHE136 4.9 51.7 1.0
O D:ILE133 5.0 51.3 1.0

Calcium binding site 5 out of 5 in 2az1

Go back to Calcium Binding Sites List in 2az1
Calcium binding site 5 out of 5 in the Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca205

b:79.0
occ:1.00
 OD2 D:ASP138 2.4 57.3 1.0
OD1 D:ASP138 2.9 49.8 1.0
CG D:ASP138 3.0 55.6 1.0
CA D:CA202 4.0 56.7 1.0
O D:HOH224 4.3 55.9 1.0
CB D:ASP138 4.5 55.0 1.0
O D:HOH225 4.9 51.0 1.0

Reference:

H.Besir, K.Zeth, A.Bracher, U.Heider, M.Ishibashi, M.Tokunaga, D.Oesterhelt. Structure of A Halophilic Nucleoside Diphosphate Kinase From Halobacterium Salinarum Febs Lett. V. 579 6595 2005.
ISSN: ISSN 0014-5793
PubMed: 16293253
DOI: 10.1016/J.FEBSLET.2005.10.052
Page generated: Fri Jul 12 08:53:48 2024

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