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Magnesium in PDB 4zp1: Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA

Enzymatic activity of Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA

All present enzymatic activity of Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA:
4.1.1.1;

Protein crystallography data

The structure of Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA, PDB code: 4zp1 was solved by C.Wechsler, P.Neumann, K.Tittmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.55 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.290, 167.640, 110.820, 90.00, 101.66, 90.00
R / Rfree (%) 17 / 21.7

Other elements in 4zp1:

The structure of Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA also contains other interesting chemical elements:

Nickel (Ni) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA (pdb code 4zp1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA, PDB code: 4zp1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4zp1

Go back to Magnesium Binding Sites List in 4zp1
Magnesium binding site 1 out of 4 in the Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA


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 Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:47.9
occ:1.00
 O2A A:TPP603 1.9 52.4 1.0
OD1 A:ASP440 2.0 52.2 1.0
O A:GLY469 2.2 59.5 1.0
O A:HOH795 2.3 47.0 1.0
O3B A:TPP603 2.3 62.4 1.0
OD1 A:ASN467 2.3 43.6 1.0
CG A:ASP440 3.1 49.9 1.0
CG A:ASN467 3.2 45.1 1.0
PA A:TPP603 3.2 51.9 1.0
C A:GLY469 3.3 57.9 1.0
PB A:TPP603 3.4 61.8 1.0
ND2 A:ASN467 3.4 46.5 1.0
OD2 A:ASP440 3.6 52.8 1.0
O3A A:TPP603 3.7 56.7 1.0
N A:GLY441 3.8 41.0 1.0
N A:ASP440 3.8 43.6 1.0
N A:GLY469 3.9 53.8 1.0
O2B A:TPP603 3.9 60.9 1.0
CA A:GLY469 4.2 55.5 1.0
O1A A:TPP603 4.2 52.8 1.0
O7 A:TPP603 4.2 74.1 1.0
N A:TYR470 4.3 57.4 1.0
N A:THR471 4.3 58.2 1.0
CB A:ASP440 4.3 46.7 1.0
O A:ILE465 4.3 40.5 1.0
CA A:TYR470 4.5 59.6 1.0
CA A:ASP440 4.5 44.7 1.0
C A:GLY439 4.5 44.0 1.0
CA A:GLY441 4.5 41.8 1.0
CA A:GLY439 4.6 43.6 1.0
C A:ASP440 4.6 44.4 1.0
CB A:ASN467 4.6 45.7 1.0
OG1 A:THR471 4.7 59.1 1.0
N A:ASN467 4.7 42.5 1.0
O1B A:TPP603 4.7 61.6 1.0
N A:TYR468 4.7 52.1 1.0
C A:TYR470 4.9 59.4 1.0
C A:ASN467 4.9 50.1 1.0
C A:TYR468 5.0 53.2 1.0

Magnesium binding site 2 out of 4 in 4zp1

Go back to Magnesium Binding Sites List in 4zp1
Magnesium binding site 2 out of 4 in the Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA


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 Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:60.8
occ:1.00
 O B:GLY469 2.0 73.6 1.0
OD1 B:ASN467 2.2 67.7 1.0
O2A B:TPP604 2.3 59.2 1.0
O3B B:TPP604 2.3 91.2 1.0
OD1 B:ASP440 2.3 54.0 1.0
O B:HOH713 2.6 53.3 1.0
C B:GLY469 3.2 71.4 1.0
CG B:ASN467 3.2 67.0 1.0
PB B:TPP604 3.3 93.2 1.0
CG B:ASP440 3.4 53.9 1.0
O2B B:TPP604 3.4 94.1 1.0
ND2 B:ASN467 3.5 67.5 1.0
PA B:TPP604 3.5 63.5 1.0
N B:GLY469 3.8 70.3 1.0
O3A B:TPP604 3.8 0.1 1.0
OD2 B:ASP440 3.9 53.6 1.0
CA B:GLY469 4.0 71.6 1.0
N B:GLY441 4.1 49.6 1.0
N B:THR471 4.1 73.9 1.0
N B:TYR470 4.1 71.4 1.0
N B:ASP440 4.2 48.2 1.0
O B:ILE465 4.3 60.0 1.0
CA B:TYR470 4.3 73.9 1.0
O7 B:TPP604 4.5 89.9 1.0
N B:ASN467 4.5 61.3 1.0
CB B:ASN467 4.5 66.4 1.0
O1A B:TPP604 4.6 62.8 1.0
O1B B:TPP604 4.6 93.4 1.0
N B:TYR468 4.6 73.0 1.0
CB B:ASP440 4.7 51.8 1.0
C B:ASN467 4.7 73.0 1.0
C B:TYR470 4.8 74.2 1.0
C B:TYR468 4.8 71.5 1.0
CA B:GLY439 4.8 51.1 1.0
CA B:ASN467 4.8 67.2 1.0
C B:GLY439 4.8 46.5 1.0
CA B:GLY441 4.9 46.1 1.0
CA B:ASP440 4.9 48.9 1.0
CG2 B:THR471 4.9 78.0 1.0
CB B:THR471 5.0 78.2 1.0

Magnesium binding site 3 out of 4 in 4zp1

Go back to Magnesium Binding Sites List in 4zp1
Magnesium binding site 3 out of 4 in the Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA


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 Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:48.9
occ:1.00
 O C:GLY469 2.1 57.6 1.0
OD1 C:ASN467 2.2 47.0 1.0
O1A C:TPP603 2.2 49.4 1.0
O2B C:TPP603 2.2 73.3 1.0
OD1 C:ASP440 2.2 48.9 1.0
O C:HOH751 2.4 41.3 1.0
CG C:ASN467 3.1 49.7 1.0
PB C:TPP603 3.3 74.9 1.0
C C:GLY469 3.3 58.7 1.0
ND2 C:ASN467 3.4 53.6 1.0
CG C:ASP440 3.4 48.8 1.0
PA C:TPP603 3.5 55.2 1.0
O1B C:TPP603 3.6 75.2 1.0
O3A C:TPP603 3.8 45.7 1.0
OD2 C:ASP440 4.0 51.2 1.0
N C:GLY469 4.0 57.2 1.0
N C:THR471 4.1 64.8 1.0
N C:ASP440 4.1 43.5 1.0
N C:GLY441 4.1 43.8 1.0
CA C:GLY469 4.2 58.1 1.0
N C:TYR470 4.2 60.5 1.0
CA C:TYR470 4.3 63.2 1.0
O7 C:TPP603 4.4 67.4 1.0
O C:ILE465 4.4 41.6 1.0
O C:HOH727 4.4 43.3 1.0
OG1 C:THR471 4.5 69.1 1.0
CB C:ASN467 4.5 50.4 1.0
O2A C:TPP603 4.6 52.8 1.0
O3B C:TPP603 4.6 74.4 1.0
N C:ASN467 4.6 50.0 1.0
CB C:ASP440 4.6 45.4 1.0
CA C:GLY439 4.7 40.9 1.0
C C:GLY439 4.7 43.1 1.0
CB C:THR471 4.7 68.0 1.0
C C:TYR470 4.7 63.9 1.0
CA C:ASP440 4.8 42.9 1.0
CA C:GLY441 4.9 42.1 1.0
N C:TYR468 4.9 51.7 1.0
C C:ASN467 4.9 51.5 1.0
CA C:ASN467 4.9 51.3 1.0
C C:ASP440 4.9 45.0 1.0

Magnesium binding site 4 out of 4 in 4zp1

Go back to Magnesium Binding Sites List in 4zp1
Magnesium binding site 4 out of 4 in the Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Zymomonas Mobilis Pyruvate Decarboxylase Variant GLU473ALA within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:58.8
occ:1.00
 O D:GLY469 2.1 70.2 1.0
OD1 D:ASN467 2.1 54.0 1.0
OD1 D:ASP440 2.2 53.7 1.0
O1A D:TPP602 2.3 60.1 1.0
O1B D:TPP602 2.4 71.8 1.0
CG D:ASN467 3.0 55.6 1.0
ND2 D:ASN467 3.2 57.3 1.0
C D:GLY469 3.3 68.4 1.0
PB D:TPP602 3.4 75.0 1.0
CG D:ASP440 3.4 53.8 1.0
O2B D:TPP602 3.4 76.2 1.0
PA D:TPP602 3.6 63.5 1.0
OD2 D:ASP440 3.9 53.8 1.0
O3A D:TPP602 3.9 0.1 1.0
N D:GLY469 4.0 62.6 1.0
N D:GLY441 4.1 49.8 1.0
N D:ASP440 4.1 47.7 1.0
N D:THR471 4.2 74.2 1.0
CA D:GLY469 4.2 65.7 1.0
O D:ILE465 4.3 53.5 1.0
N D:TYR470 4.3 70.2 1.0
CB D:ASN467 4.4 58.3 1.0
CA D:TYR470 4.5 71.8 1.0
O7 D:TPP602 4.5 77.8 1.0
N D:ASN467 4.5 56.7 1.0
CB D:ASP440 4.6 53.2 1.0
O2A D:TPP602 4.6 63.8 1.0
CA D:GLY439 4.6 45.5 1.0
O3B D:TPP602 4.7 73.0 1.0
C D:GLY439 4.7 46.0 1.0
OG1 D:THR471 4.8 75.0 1.0
CA D:ASP440 4.8 49.5 1.0
N D:TYR468 4.8 62.6 1.0
C D:ASN467 4.8 62.2 1.0
CB D:THR471 4.8 75.0 1.0
CA D:ASN467 4.8 59.5 1.0
C D:TYR470 4.8 73.8 1.0
CA D:GLY441 4.9 48.8 1.0
C D:ASP440 5.0 49.9 1.0

Reference:

C.Wechsler, D.Meyer, S.Loschonsky, L.M.Funk, P.Neumann, R.Ficner, F.Brodhun, M.Muller, K.Tittmann. Tuning and Switching Enantioselectivity of Asymmetric Carboligation in An Enzyme Through Mutational Analysis of A Single Hot Spot. Chembiochem V. 16 2580 2015.
ISSN: ESSN 1439-7633
PubMed: 26488818
DOI: 10.1002/CBIC.201500529
Page generated: Mon Dec 14 19:58:13 2020

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