Atomistry » Calcium » PDB 2agq-2b03 » 2az1
Atomistry »
  Calcium »
    PDB 2agq-2b03 »
      2az1 »

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

Go back to Calcium Binding Sites List in 2az1
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

Go back to Calcium Binding Sites List in 2az1
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

Go back to Calcium Binding Sites List in 2az1
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

Go back to Calcium Binding Sites List in 2az1
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy