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Calcium in PDB 2afb: Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution

Protein crystallography data

The structure of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution, PDB code: 2afb was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.63 / 2.05
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 120.993, 120.993, 260.300, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 23

Other elements in 2afb:

The structure of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution also contains other interesting chemical elements:

Nickel (Ni) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution (pdb code 2afb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution, PDB code: 2afb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2afb

Go back to Calcium Binding Sites List in 2afb
Calcium binding site 1 out of 4 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca343

b:52.9
occ:0.33
OD1 A:ASP17 2.4 42.5 1.0
O A:HOH350 2.6 44.9 1.0
CG A:ASP17 3.3 43.4 1.0
OD2 A:ASP17 3.4 43.8 1.0
O A:HOH526 3.9 42.2 1.0
O A:HOH403 4.3 30.0 1.0
CB A:ASP17 4.7 33.5 1.0

Calcium binding site 2 out of 4 in 2afb

Go back to Calcium Binding Sites List in 2afb
Calcium binding site 2 out of 4 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca344

b:47.8
occ:1.00
NE2 A:HIS-4 2.2 57.9 1.0
OE2 A:GLU326 2.5 55.6 1.0
OE1 A:GLU326 2.6 43.8 1.0
O A:HOH555 2.9 53.6 1.0
CD A:GLU326 2.9 31.4 1.0
CD2 A:HIS-4 3.0 62.3 1.0
CE1 A:HIS-4 3.2 57.1 1.0
CG A:HIS-4 4.2 68.7 1.0
ND1 A:HIS-4 4.3 63.9 1.0
CG2 A:ILE322 4.3 32.1 1.0
CG A:GLU326 4.4 35.1 1.0
O A:HOH467 4.6 32.6 1.0

Calcium binding site 3 out of 4 in 2afb

Go back to Calcium Binding Sites List in 2afb
Calcium binding site 3 out of 4 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca343

b:56.7
occ:0.33
OD1 B:ASP17 2.7 38.5 1.0
OD2 B:ASP17 3.3 39.7 1.0
CG B:ASP17 3.4 40.1 1.0
O B:HOH450 4.3 40.1 1.0
CB B:ASP17 4.8 34.8 1.0

Calcium binding site 4 out of 4 in 2afb

Go back to Calcium Binding Sites List in 2afb
Calcium binding site 4 out of 4 in the Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of 2-Dehydro-3- Deoxygluconokinase (Ec 2.7.1.45) (TM0067) From Thermotoga Maritima at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca344

b:12.9
occ:0.33
OD1 B:ASP25 1.7 42.4 1.0
O B:HOH368 2.3 31.6 1.0
CG B:ASP25 2.6 39.4 1.0
OD2 B:ASP25 2.9 49.3 1.0
O B:HOH414 3.8 26.1 1.0
O B:HOH441 4.0 40.5 1.0
CB B:ASP25 4.1 28.6 1.0
C B:ASP25 4.5 26.4 1.0
NZ B:LYS19 4.5 47.1 1.0
OG B:SER26 4.6 28.0 1.0
CA B:ASP25 4.6 28.5 1.0
N B:SER26 4.7 26.0 1.0
O B:ASP25 4.7 24.5 1.0
CB B:SER26 4.8 30.3 1.0
N B:ASP25 4.8 27.7 1.0

Reference:

I.I.Mathews, D.Mcmullan, M.D.Miller, J.M.Canaves, M.A.Elsliger, R.Floyd, S.K.Grzechnik, L.Jaroszewski, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, T.M.Mcphillips, A.T.Morse, K.Quijano, C.L.Rife, R.Schwarzenbacher, G.Spraggon, R.C.Stevens, H.Van Den Bedem, D.Weekes, G.Wolf, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Crystal Structure of 2-Keto-3-Deoxygluconate Kinase (TM0067) From Thermotoga Maritima at 2.05 A Resolution. Proteins V. 70 603 2007.
ISSN: ISSN 0887-3585
PubMed: 18004772
DOI: 10.1002/PROT.21842
Page generated: Tue Jul 8 04:17:27 2025

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