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Magnesium in PDB 3mp3: Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa

Enzymatic activity of Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa

All present enzymatic activity of Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa:
4.1.3.4;

Protein crystallography data

The structure of Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa, PDB code: 3mp3 was solved by Z.Fu, J.A.Runquist, C.Montgomery, H.M.Miziorko, J.-J.P.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.70 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 197.370, 117.000, 86.870, 90.00, 112.31, 90.00
R / Rfree (%) 21.2 / 28.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa (pdb code 3mp3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa, PDB code: 3mp3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3mp3

Go back to Magnesium Binding Sites List in 3mp3
Magnesium binding site 1 out of 6 in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa


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 Human Lyase in Complex with Inhibitor Hg-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:16.9
occ:1.00
 NE2 A:HIS235 2.3 15.6 1.0
NE2 A:HIS233 2.4 12.9 1.0
O4 A:3HG400 2.4 65.9 1.0
OD1 A:ASP42 2.5 20.0 1.0
CE1 A:HIS235 2.8 19.7 1.0
O5 A:3HG400 2.9 67.2 1.0
C5 A:3HG400 3.0 66.0 1.0
CD2 A:HIS233 3.1 13.6 1.0
OD2 A:ASP42 3.1 20.4 1.0
CG A:ASP42 3.2 19.6 1.0
CD2 A:HIS235 3.5 15.9 1.0
CE1 A:HIS233 3.6 11.8 1.0
OD1 A:ASN275 3.7 32.1 1.0
ND1 A:HIS235 4.0 18.3 1.0
CG A:HIS233 4.3 12.2 1.0
CG A:HIS235 4.4 19.2 1.0
ND1 A:HIS233 4.5 11.7 1.0
C4 A:3HG400 4.5 64.5 1.0
CB A:ASP42 4.6 16.1 1.0
CG A:ASN275 4.7 28.4 1.0
ND2 A:ASN275 4.9 29.2 1.0

Magnesium binding site 2 out of 6 in 3mp3

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa


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 Human Lyase in Complex with Inhibitor Hg-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:17.1
occ:1.00
 NE2 B:HIS235 2.3 19.9 1.0
OD1 B:ASP42 2.4 27.9 1.0
O5' B:HGG399 2.5 59.3 1.0
NE2 B:HIS233 2.6 19.9 1.0
O B:HOH992 2.8 32.2 1.0
O3' B:HGG399 2.8 58.9 1.0
CG B:ASP42 3.0 29.7 1.0
CD2 B:HIS233 3.1 21.2 1.0
OD2 B:ASP42 3.1 30.8 1.0
CE1 B:HIS235 3.2 19.4 1.0
C5' B:HGG399 3.4 60.0 1.0
CD2 B:HIS235 3.4 18.5 1.0
CE1 B:HIS233 3.7 20.8 1.0
C3' B:HGG399 3.8 59.8 1.0
OD1 B:ASN275 3.9 28.5 1.0
C4' B:HGG399 3.9 59.6 1.0
CG B:HIS233 4.3 20.4 1.0
O4' B:HGG399 4.3 59.5 1.0
ND1 B:HIS235 4.3 19.9 1.0
C2' B:HGG399 4.4 60.8 1.0
CB B:ASP42 4.4 28.1 1.0
CG B:HIS235 4.5 17.9 1.0
ND1 B:HIS233 4.5 17.8 1.0
O1' B:HGG399 4.7 61.6 1.0
CG B:ASN275 4.8 28.9 1.0
ND2 B:ASN275 4.8 30.3 1.0
C1' B:HGG399 5.0 61.0 1.0

Magnesium binding site 3 out of 6 in 3mp3

Go back to Magnesium Binding Sites List in 3mp3
Magnesium binding site 3 out of 6 in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa


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 Human Lyase in Complex with Inhibitor Hg-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:15.8
occ:1.00
 OD1 C:ASP42 2.3 30.5 1.0
NE2 C:HIS235 2.3 28.3 1.0
NE2 C:HIS233 2.5 25.4 1.0
CE1 C:HIS235 2.8 30.9 1.0
CG C:ASP42 3.1 29.7 1.0
OD1 C:ASN275 3.1 41.1 1.0
CE1 C:HIS233 3.2 24.6 1.0
OD2 C:ASP42 3.2 29.4 1.0
CD2 C:HIS233 3.5 24.5 1.0
CD2 C:HIS235 3.6 28.5 1.0
ND1 C:HIS235 4.0 30.5 1.0
CG C:ASN275 4.1 39.9 1.0
ND1 C:HIS233 4.3 23.2 1.0
ND2 C:ASN275 4.4 41.1 1.0
CG C:HIS235 4.4 27.2 1.0
CB C:ASP42 4.5 29.7 1.0
CG C:HIS233 4.5 22.9 1.0

Magnesium binding site 4 out of 6 in 3mp3

Go back to Magnesium Binding Sites List in 3mp3
Magnesium binding site 4 out of 6 in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa


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 Human Lyase in Complex with Inhibitor Hg-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg405

b:28.5
occ:1.00
 OD1 D:ASP42 2.4 41.4 1.0
NE2 D:HIS233 2.4 33.1 1.0
NE2 D:HIS235 2.5 23.8 1.0
O D:HOH684 2.7 18.2 1.0
CG D:ASP42 3.0 40.8 1.0
CE1 D:HIS235 3.1 26.0 1.0
CD2 D:HIS233 3.2 34.1 1.0
OD2 D:ASP42 3.2 41.2 1.0
CE1 D:HIS233 3.4 34.1 1.0
CD2 D:HIS235 3.8 26.1 1.0
NH2 D:ARG41 3.9 36.5 1.0
OD1 D:ASN275 4.3 42.0 1.0
CG D:HIS233 4.3 32.0 1.0
ND1 D:HIS235 4.3 26.7 1.0
CB D:ASP42 4.4 38.8 1.0
ND1 D:HIS233 4.4 32.9 1.0
NH1 D:ARG41 4.6 39.9 1.0
CG D:HIS235 4.7 26.0 1.0
CZ D:ARG41 4.7 38.8 1.0
ND2 D:ASN275 4.8 40.2 1.0
CG D:ASN275 5.0 40.3 1.0

Magnesium binding site 5 out of 6 in 3mp3

Go back to Magnesium Binding Sites List in 3mp3
Magnesium binding site 5 out of 6 in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:13.3
occ:1.00
 OD2 E:ASP42 2.3 27.9 1.0
NE2 E:HIS233 2.4 19.8 1.0
NE2 E:HIS235 2.6 22.9 1.0
CG E:ASP42 3.0 29.8 1.0
CE1 E:HIS235 3.0 23.5 1.0
OD1 E:ASP42 3.1 33.0 1.0
OD1 E:ASN275 3.2 24.8 1.0
CE1 E:HIS233 3.2 19.6 1.0
CD2 E:HIS233 3.4 17.4 1.0
CD2 E:HIS235 3.8 22.6 1.0
CG E:ASN275 4.2 23.1 1.0
ND1 E:HIS235 4.3 25.3 1.0
CB E:ASP42 4.3 27.1 1.0
ND1 E:HIS233 4.3 18.3 1.0
CG E:HIS233 4.4 17.4 1.0
ND2 E:ASN275 4.6 23.5 1.0
CG E:HIS235 4.7 21.9 1.0
CE1 E:TYR167 4.8 32.8 1.0

Magnesium binding site 6 out of 6 in 3mp3

Go back to Magnesium Binding Sites List in 3mp3
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Lyase in Complex with Inhibitor Hg-Coa within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg406

b:30.6
occ:1.00
 OD1 F:ASP42 2.7 37.1 1.0
CE1 F:HIS235 2.8 41.0 1.0
NE2 F:HIS235 2.8 40.8 1.0
NE2 F:HIS233 2.9 35.2 1.0
OD2 F:ASP42 3.2 39.1 1.0
CG F:ASP42 3.3 38.0 1.0
CD2 F:HIS233 3.5 34.3 1.0
CE1 F:HIS233 3.9 33.9 1.0
ND1 F:HIS235 4.1 41.4 1.0
CD2 F:HIS235 4.1 40.9 1.0
OD1 F:ASN275 4.4 36.1 1.0
NH2 F:ARG41 4.4 38.6 1.0
CG2 F:THR205 4.5 39.3 1.0
OG1 F:THR205 4.7 37.3 1.0
CB F:ASP42 4.7 38.6 1.0
CG F:HIS233 4.7 33.0 1.0
CG F:HIS235 4.8 40.0 1.0
ND1 F:HIS233 4.9 33.8 1.0
CE1 F:TYR167 5.0 42.3 1.0

Reference:

Z.Fu, J.A.Runquist, C.Montgomery, H.M.Miziorko, J.J.Kim. Functional Insights Into Human Hmg-Coa Lyase From Structures of Acyl-Coa-Containing Ternary Complexes. J.Biol.Chem. V. 285 26341 2010.
ISSN: ISSN 0021-9258
PubMed: 20558737
DOI: 10.1074/JBC.M110.139931
Page generated: Mon Dec 14 08:26:33 2020

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