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Magnesium in PDB 5d6o: Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum

Enzymatic activity of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum

All present enzymatic activity of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum:
2.3.1.31;

Protein crystallography data

The structure of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum, PDB code: 5d6o was solved by K.Niefind, C.Toelzer, J.Altenbuchner, H.Watzlawick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.141, 89.612, 322.788, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21

Other elements in 5d6o:

The structure of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum (pdb code 5d6o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum, PDB code: 5d6o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5d6o

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Magnesium binding site 1 out of 5 in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:18.6
occ:1.00
O A:HOH540 1.6 22.2 1.0
NE2 A:HIS74 1.9 10.5 1.0
O A:HOH534 2.2 15.6 1.0
O A:HOH672 2.2 11.6 1.0
O A:HOH572 2.3 13.9 1.0
O A:HOH905 2.3 21.9 1.0
CD2 A:HIS74 2.9 10.2 1.0
CE1 A:HIS74 2.9 13.4 1.0
O A:HOH892 3.0 38.6 1.0
OD2 A:ASP73 3.8 19.9 1.0
OD1 A:ASP73 3.9 18.1 1.0
O A:GLN68 3.9 10.8 1.0
ND1 A:HIS74 4.0 12.2 1.0
CG A:HIS74 4.1 10.3 1.0
CG A:ASP73 4.3 19.5 1.0
O A:ILE70 4.4 11.8 1.0
O A:HOH702 4.4 42.3 1.0
O A:GLN67 4.5 12.1 1.0
O A:HOH1043 4.5 34.1 1.0
O A:HOH1012 4.5 44.4 1.0
O A:HOH939 4.6 35.3 1.0
C A:GLN68 4.6 10.5 1.0
O A:HOH727 4.7 38.2 1.0
O A:HOH624 4.8 31.7 1.0

Magnesium binding site 2 out of 5 in 5d6o

Go back to Magnesium Binding Sites List in 5d6o
Magnesium binding site 2 out of 5 in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:11.6
occ:1.00
NE2 B:HIS74 1.9 13.1 1.0
O B:HOH599 2.1 13.7 1.0
O B:HOH580 2.1 11.8 1.0
O B:HOH715 2.1 16.1 1.0
O B:HOH624 2.2 14.4 1.0
O B:HOH894 2.2 25.7 1.0
CE1 B:HIS74 2.9 14.6 1.0
CD2 B:HIS74 2.9 13.9 1.0
O B:GLN68 3.9 7.5 1.0
OD2 B:ASP73 4.0 21.7 1.0
ND1 B:HIS74 4.0 14.0 1.0
CG B:HIS74 4.1 13.3 1.0
OD1 B:ASP73 4.1 17.1 1.0
O B:GLN67 4.2 18.1 1.0
O B:HOH1008 4.3 42.6 1.0
O B:ILE70 4.4 12.1 1.0
C B:GLN68 4.5 7.3 1.0
CG B:ASP73 4.5 19.6 1.0
O B:HOH1112 4.5 37.4 1.0
O B:HOH984 4.5 33.4 1.0
O B:HOH1150 4.6 37.7 1.0
CA B:GLN68 4.9 7.5 1.0
C B:ILE70 5.0 12.1 1.0

Magnesium binding site 3 out of 5 in 5d6o

Go back to Magnesium Binding Sites List in 5d6o
Magnesium binding site 3 out of 5 in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:23.4
occ:1.00
NE2 C:HIS74 1.9 16.7 1.0
O C:HOH556 2.0 26.1 1.0
O C:HOH718 2.1 22.2 1.0
O C:HOH580 2.3 21.4 1.0
O C:HOH519 2.5 21.9 1.0
O C:HOH726 2.7 43.9 1.0
CE1 C:HIS74 2.8 16.4 1.0
CD2 C:HIS74 3.0 16.9 1.0
OD2 C:ASP73 3.4 28.7 1.0
O C:GLN68 3.8 16.5 1.0
ND1 C:HIS74 4.0 16.5 1.0
OD1 C:ASP73 4.0 24.8 1.0
CG C:HIS74 4.1 15.7 1.0
CG C:ASP73 4.1 25.2 1.0
O C:GLN67 4.3 19.3 1.0
O C:HOH696 4.3 44.7 1.0
O C:ILE70 4.4 15.8 1.0
C C:GLN68 4.4 16.3 1.0
O C:HOH934 4.5 34.3 1.0
O C:HOH590 4.6 41.6 1.0
O C:HOH974 4.7 38.2 1.0
O C:HOH661 4.7 35.1 1.0
CA C:GLN68 4.8 15.8 1.0

Magnesium binding site 4 out of 5 in 5d6o

Go back to Magnesium Binding Sites List in 5d6o
Magnesium binding site 4 out of 5 in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:14.9
occ:1.00
NE2 D:HIS74 1.9 15.2 1.0
O D:HOH678 2.0 14.1 1.0
O D:HOH605 2.2 10.4 1.0
O D:HOH684 2.2 11.3 1.0
O D:HOH911 2.2 23.0 1.0
O D:HOH549 2.3 11.7 1.0
CE1 D:HIS74 2.9 14.6 1.0
CD2 D:HIS74 3.0 11.5 1.0
O D:GLN68 3.9 10.3 1.0
OD2 D:ASP73 4.0 20.9 1.0
ND1 D:HIS74 4.0 12.9 1.0
CG D:HIS74 4.1 12.5 1.0
OD1 D:ASP73 4.1 18.1 1.0
O D:ILE70 4.4 13.1 1.0
CG D:ASP73 4.4 18.8 1.0
O D:HOH531 4.5 19.7 1.0
O D:GLN67 4.5 18.0 1.0
O D:HOH868 4.5 42.2 1.0
C D:GLN68 4.5 9.0 1.0
O D:HOH930 4.9 40.4 1.0
O D:HOH1046 4.9 39.6 1.0

Magnesium binding site 5 out of 5 in 5d6o

Go back to Magnesium Binding Sites List in 5d6o
Magnesium binding site 5 out of 5 in the Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Orthorhombic Crystal Structure of An Acetylester Hydrolase From Corynebacterium Glutamicum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:34.4
occ:1.00
O D:HOH810 2.0 41.8 1.0
O D:HOH973 2.4 36.9 1.0
O D:HOH823 2.4 36.9 1.0
O D:VAL11 3.4 20.3 1.0
O D:HOH970 3.4 33.7 1.0
NE2 D:GLN63 3.6 31.0 1.0
CG D:GLN63 3.8 19.6 1.0
N D:GLY13 3.9 17.5 1.0
C D:GLN12 4.0 15.7 1.0
CA D:GLY13 4.1 20.6 1.0
O D:HOH561 4.2 30.0 1.0
O D:GLN12 4.2 15.1 1.0
CD D:GLN63 4.2 25.2 1.0
C D:VAL11 4.2 18.7 1.0
O D:HOH900 4.3 34.4 1.0
OE1 D:GLN67 4.4 42.8 1.0
CA D:GLN12 4.6 13.8 1.0
N D:GLN12 4.7 14.3 1.0
O D:HOH592 4.8 15.5 1.0
O D:GLU10 4.9 24.2 1.0

Reference:

C.Tolzer, S.Pal, H.Watzlawick, J.Altenbuchner, K.Niefind. A Novel Esterase Subfamily with Alpha / Beta-Hydrolase Fold Suggested By Structures of Two Bacterial Enzymes Homologous to L-Homoserine O-Acetyl Transferases. Febs Lett. V. 590 174 2016.
ISSN: ISSN 0014-5793
PubMed: 26787467
DOI: 10.1002/1873-3468.12031
Page generated: Mon Dec 14 20:10:16 2020

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