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Calcium in PDB 4gkb: Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure

Enzymatic activity of Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure

All present enzymatic activity of Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure:
1.1.1.100;

Protein crystallography data

The structure of Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure, PDB code: 4gkb was solved by M.W.Vetting, M.E.Hobbs, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, F.M.Raushel, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.87 / 1.50
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 99.960, 99.960, 205.801, 90.00, 90.00, 120.00
R / Rfree (%) 15.1 / 17.2

Other elements in 4gkb:

The structure of Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure (pdb code 4gkb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure, PDB code: 4gkb:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4gkb

Go back to Calcium Binding Sites List in 4gkb
Calcium binding site 1 out of 3 in the Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure


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 A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:18.8
occ:0.56
 O A:PRO234 2.3 10.3 1.0
O B:HOH478 2.3 19.3 1.0
O A:HOH614 2.4 22.1 1.0
O A:HOH436 2.4 20.3 1.0
OG A:SER237 2.4 8.4 1.0
O B:HOH467 2.5 13.4 1.0
CB A:SER237 3.3 6.8 1.0
C A:PRO234 3.4 11.6 1.0
CA A:ARG235 4.1 7.1 1.0
O B:HOH493 4.1 21.9 1.0
N A:ARG235 4.2 7.9 1.0
CG B:GLU223 4.2 6.3 1.0
N A:SER237 4.2 7.6 1.0
C A:ARG235 4.4 9.1 1.0
O B:HOH633 4.4 36.3 1.0
OD2 B:ASP226 4.4 13.3 1.0
CA A:SER237 4.4 6.4 1.0
OE2 B:GLU223 4.4 9.3 1.0
CA A:PRO234 4.5 9.5 1.0
CB A:PRO234 4.5 10.7 1.0
O B:HOH457 4.5 12.8 1.0
O A:ARG235 4.6 9.8 1.0
O B:HOH559 4.6 39.5 1.0
O A:HOH477 4.8 27.6 1.0
CD B:GLU223 4.9 9.4 1.0
N A:ALA236 5.0 6.9 1.0
O B:HOH476 5.0 17.6 1.0

Calcium binding site 2 out of 3 in 4gkb

Go back to Calcium Binding Sites List in 4gkb
Calcium binding site 2 out of 3 in the Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure


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 A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:7.3
occ:0.79
 O B:HOH439 2.4 14.1 1.0
OG B:SER237 2.4 9.1 1.0
O B:PRO234 2.4 9.3 1.0
O A:HOH610 2.4 10.3 1.0
O B:HOH679 2.5 15.3 1.0
CB B:SER237 3.4 6.8 1.0
C B:PRO234 3.6 6.2 1.0
O B:HOH516 4.2 25.4 1.0
CG A:GLU223 4.2 8.4 1.0
CA B:ARG235 4.2 6.9 1.0
N B:ARG235 4.3 6.3 1.0
OE2 A:GLU223 4.4 9.3 1.0
N B:SER237 4.4 6.1 1.0
OD2 A:ASP226 4.5 12.2 1.0
O B:HOH686 4.5 28.4 1.0
C B:ARG235 4.5 9.3 1.0
CA B:SER237 4.6 5.7 1.0
CA B:PRO234 4.6 6.6 1.0
CB B:PRO234 4.6 9.4 1.0
O A:HOH611 4.7 17.2 1.0
O B:ARG235 4.7 7.8 1.0
O B:HOH527 4.7 18.7 1.0
O B:HOH654 4.7 38.5 1.0
CD A:GLU223 4.8 8.7 1.0

Calcium binding site 3 out of 3 in 4gkb

Go back to Calcium Binding Sites List in 4gkb
Calcium binding site 3 out of 3 in the Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure


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 A Short Chain Dehydrogenase Homolog (Target Efi- 505321) From Burkholderia Multivorans, Unliganded Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:8.9
occ:0.79
 OG C:SER237 2.4 8.2 1.0
O C:HOH456 2.4 18.1 1.0
O C:HOH437 2.4 17.6 1.0
O D:HOH414 2.4 13.4 1.0
O C:PRO234 2.5 10.1 1.0
O D:HOH458 2.5 18.8 1.0
CB C:SER237 3.4 8.0 1.0
C C:PRO234 3.6 8.6 1.0
CG D:GLU223 4.2 8.6 1.0
CA C:ARG235 4.3 9.1 1.0
O C:HOH517 4.3 34.0 1.0
N C:ARG235 4.4 7.3 1.0
OE2 D:GLU223 4.4 9.6 1.0
N C:SER237 4.5 7.8 1.0
OD2 D:ASP226 4.5 12.6 1.0
O C:HOH669 4.5 45.4 1.0
CA C:SER237 4.6 7.2 1.0
C C:ARG235 4.6 10.0 1.0
O D:HOH440 4.6 20.0 1.0
CA C:PRO234 4.6 8.7 1.0
CB C:PRO234 4.6 10.1 1.0
O C:HOH494 4.7 27.8 1.0
O C:ARG235 4.7 9.5 1.0
CD D:GLU223 4.8 9.1 1.0
O D:HOH532 4.9 32.9 1.0

Reference:

M.W.Vetting, M.E.Hobbs, L.L.Morisco, S.R.Wasserman, S.Sojitra, H.J.Imker, F.M.Raushel, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Short Chain Dehydrogenase Homolog (Target Efi-505321) From Burkholderia Multivorans, Unliganded Structure To Be Published.
Page generated: Tue Jul 8 20:21:37 2025

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