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Magnesium in PDB 4d5e: Crystal Structure of Recombinant Wildtype Cdh

Enzymatic activity of Crystal Structure of Recombinant Wildtype Cdh

All present enzymatic activity of Crystal Structure of Recombinant Wildtype Cdh:
3.7.1.11;

Protein crystallography data

The structure of Crystal Structure of Recombinant Wildtype Cdh, PDB code: 4d5e was solved by S.Loschonsky, T.Wacker, S.Waltzer, P.P.Giovannini, M.J.Mcleish, S.L.A.Andrade, M.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.68 / 1.43
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.188, 123.188, 143.070, 90.00, 90.00, 90.00
R / Rfree (%) 12.2 / 14.733

Other elements in 4d5e:

The structure of Crystal Structure of Recombinant Wildtype Cdh also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Recombinant Wildtype Cdh (pdb code 4d5e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Recombinant Wildtype Cdh, PDB code: 4d5e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4d5e

Go back to Magnesium Binding Sites List in 4d5e
Magnesium binding site 1 out of 3 in the Crystal Structure of Recombinant Wildtype Cdh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Recombinant Wildtype Cdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1592

b:5.9
occ:1.00
O1A A:TPP1589 2.1 7.5 1.0
OD1 A:ASP451 2.1 7.5 1.0
OD1 A:ASN478 2.1 8.0 1.0
O A:SER480 2.1 7.4 1.0
O1B A:TPP1589 2.1 7.5 1.0
O A:HOH2409 2.2 8.3 1.0
CG A:ASN478 3.1 7.8 1.0
CG A:ASP451 3.3 8.2 1.0
PA A:TPP1589 3.3 7.1 1.0
C A:SER480 3.3 7.9 1.0
ND2 A:ASN478 3.4 8.2 1.0
PB A:TPP1589 3.4 7.3 1.0
O3A A:TPP1589 3.5 6.6 1.0
OD2 A:ASP451 3.9 7.7 1.0
N A:ASP451 4.0 6.8 1.0
N A:GLY482 4.0 6.6 1.0
O7 A:TPP1589 4.1 7.8 1.0
N A:SER480 4.1 8.5 1.0
N A:GLY452 4.2 7.0 1.0
O3B A:TPP1589 4.3 8.0 1.0
CA A:SER480 4.3 8.5 1.0
N A:TYR481 4.3 6.8 1.0
O A:HOH2425 4.4 12.2 1.0
O A:PHE476 4.4 8.4 1.0
N A:ASN478 4.4 7.3 1.0
CB A:ASN478 4.5 8.0 1.0
O2A A:TPP1589 4.5 7.1 1.0
O2B A:TPP1589 4.5 7.0 1.0
CB A:ASP451 4.5 7.7 1.0
CA A:TYR481 4.5 7.4 1.0
CA A:ASP451 4.6 6.7 1.0
CZ A:PHE500 4.7 9.1 1.0
CA A:GLY450 4.7 7.3 1.0
CB A:SER480 4.8 10.1 1.0
CA A:ASN478 4.8 7.6 1.0
C A:TYR481 4.8 7.2 1.0
CA A:GLY482 4.9 7.0 1.0
C A:GLY450 4.9 6.9 1.0
N A:GLU479 4.9 7.6 1.0
C A:ASN478 4.9 8.1 1.0
C A:ASP451 5.0 7.1 1.0

Magnesium binding site 2 out of 3 in 4d5e

Go back to Magnesium Binding Sites List in 4d5e
Magnesium binding site 2 out of 3 in the Crystal Structure of Recombinant Wildtype Cdh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Recombinant Wildtype Cdh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1593

b:38.9
occ:1.00
O B:HOH2428 2.5 29.0 1.0
O B:HOH2142 2.7 27.7 1.0
C1 B:PG41602 3.1 45.0 1.0
N B:ALA184 3.2 21.0 1.0
O B:HOH2120 3.4 36.4 1.0
CA B:ARG183 3.5 25.6 1.0
NH1 B:ARG148 3.7 18.6 1.0
C B:ARG183 3.8 24.4 1.0
CB B:ARG183 3.9 31.4 1.0
CB B:ALA184 4.1 23.4 1.0
CA B:ALA184 4.3 21.5 1.0
C2 B:PG41602 4.6 36.1 1.0
O B:THR182 4.7 28.5 1.0
N B:ARG183 4.7 26.1 1.0
CZ B:ARG148 4.7 17.0 1.0
O B:HOH2040 4.8 39.9 1.0
NH2 B:ARG148 4.9 14.8 1.0

Magnesium binding site 3 out of 3 in 4d5e

Go back to Magnesium Binding Sites List in 4d5e
Magnesium binding site 3 out of 3 in the Crystal Structure of Recombinant Wildtype Cdh


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Recombinant Wildtype Cdh within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1594

b:7.0
occ:1.00
O1A B:TPP1590 2.1 8.2 1.0
OD1 B:ASP451 2.1 8.5 1.0
O B:SER480 2.1 7.6 0.5
OD1 B:ASN478 2.2 10.4 1.0
O1B B:TPP1590 2.2 8.0 1.0
O B:SER480 2.2 9.0 0.5
O B:HOH2328 2.2 9.4 1.0
CG B:ASN478 3.1 9.8 1.0
CG B:ASP451 3.3 8.8 1.0
PA B:TPP1590 3.3 8.1 1.0
C B:SER480 3.4 8.8 0.5
C B:SER480 3.4 7.6 0.5
PB B:TPP1590 3.4 8.4 1.0
ND2 B:ASN478 3.5 9.3 1.0
O3A B:TPP1590 3.5 8.4 1.0
OD2 B:ASP451 3.9 9.2 1.0
N B:GLY482 4.0 7.9 1.0
N B:ASP451 4.0 7.8 1.0
O7 B:TPP1590 4.1 8.0 1.0
N B:SER480 4.1 10.2 0.5
N B:SER480 4.1 8.9 0.5
N B:GLY452 4.2 7.7 1.0
O3B B:TPP1590 4.3 9.1 1.0
CA B:SER480 4.3 10.3 0.5
N B:TYR481 4.3 8.0 1.0
CA B:SER480 4.3 7.8 0.5
O B:PHE476 4.4 9.9 1.0
O B:HOH2337 4.4 12.8 1.0
CA B:TYR481 4.4 7.8 1.0
O2A B:TPP1590 4.5 7.8 1.0
N B:ASN478 4.5 9.2 1.0
O2B B:TPP1590 4.5 8.1 1.0
CB B:ASN478 4.5 9.7 1.0
CB B:ASP451 4.5 8.3 1.0
CB B:SER480 4.6 10.6 0.5
CA B:ASP451 4.7 8.2 1.0
CZ B:PHE500 4.7 9.7 1.0
CA B:GLY450 4.7 8.3 1.0
C B:TYR481 4.8 7.5 1.0
CA B:GLY482 4.8 8.2 1.0
C B:GLY450 4.8 8.6 1.0
CA B:ASN478 4.8 9.4 1.0
CB B:SER480 4.9 7.5 0.5
C B:ASP451 4.9 7.8 1.0
N B:GLU479 5.0 9.6 1.0
C B:ASN478 5.0 9.2 1.0

Reference:

S.Loschonsky, T.Wacker, S.Waltzer, P.P.Giovannini, M.J.Mcleish, S.L.A.Andrade, M.Mueller. Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-Dione Hydrolase: From C- C Bond Cleavage to C-C Bond Ligation To Be Published.
Page generated: Mon Dec 14 11:58:13 2020

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