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Magnesium in PDB 3c5e: Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp

Enzymatic activity of Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp

All present enzymatic activity of Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp:
6.2.1.2;

Protein crystallography data

The structure of Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp, PDB code: 3c5e was solved by E.S.Pilka, G.T.Kochan, C.Bhatia, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.700, 98.073, 120.263, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.4

Other elements in 3c5e:

The structure of Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp (pdb code 3c5e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp, PDB code: 3c5e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3c5e

Go back to Magnesium Binding Sites List in 3c5e
Magnesium binding site 1 out of 2 in the Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp


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 Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg701

b:40.4
occ:1.00
 O A:HOH1365 2.2 44.8 1.0
O A:HIS485 2.6 17.7 1.0
O A:MET483 2.7 28.2 1.0
O A:VAL488 2.7 21.4 1.0
O A:HOH1613 3.3 47.8 1.0
C A:HIS485 3.6 18.9 1.0
C A:MET483 3.6 24.2 1.0
C A:VAL488 3.8 20.4 1.0
CA A:PRO486 4.0 21.3 1.0
N A:VAL488 4.2 16.5 1.0
CA A:MET483 4.2 19.6 1.0
N A:HIS485 4.3 19.7 1.0
N A:PRO486 4.3 21.9 1.0
C A:PRO486 4.3 20.9 1.0
C A:GLU484 4.3 23.2 1.0
CA A:VAL488 4.4 17.5 1.0
O A:PRO486 4.4 22.9 1.0
CB A:VAL488 4.5 18.2 1.0
CA A:HIS485 4.6 17.1 1.0
O A:GLU484 4.6 28.2 1.0
N A:GLU484 4.6 23.9 1.0
CA A:GLU484 4.8 24.0 1.0
O A:LEU482 4.9 22.1 1.0
N A:VAL489 5.0 19.4 1.0
N A:ALA487 5.0 18.2 1.0
CB A:MET483 5.0 25.6 1.0

Magnesium binding site 2 out of 2 in 3c5e

Go back to Magnesium Binding Sites List in 3c5e
Magnesium binding site 2 out of 2 in the Crystal Structure of Human Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp


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 Acyl-Coa Synthetase Medium-Chain Family Member 2A (L64P Mutation) in Complex with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:15.2
occ:0.65
 O1G A:ATP801 2.0 9.6 0.7
O A:HOH913 2.0 12.6 1.0
O1B A:ATP801 2.1 14.0 0.7
O A:HOH912 2.1 22.7 1.0
O A:HOH911 2.2 20.6 1.0
O A:HOH915 2.2 21.2 1.0
O A:HOH916 3.0 42.5 0.3
PG A:ATP801 3.1 12.4 0.7
PB A:ATP801 3.2 18.8 0.7
O3B A:ATP801 3.6 15.8 0.7
O2G A:ATP801 3.6 12.7 0.7
O3A A:ATP801 3.7 19.4 1.0
O A:HOH986 4.0 27.2 1.0
NZ A:LYS229 4.1 29.5 1.0
OE2 A:GLU365 4.2 17.3 1.0
NH1 A:ARG461 4.3 21.6 0.7
O1A A:ATP801 4.3 18.2 1.0
OE1 A:GLU365 4.3 15.5 1.0
O A:HOH1684 4.4 24.6 0.7
O3G A:ATP801 4.4 10.1 0.7
O A:HOH914 4.4 19.0 0.3
NE2 A:GLN363 4.5 17.7 1.0
O2B A:ATP801 4.6 11.1 0.7
PA A:ATP801 4.6 24.1 1.0
O A:HOH1148 4.6 25.7 0.7
NH1 A:ARG461 4.7 14.9 0.3
NH2 A:ARG461 4.7 19.0 0.3
CD A:GLU365 4.7 13.8 1.0
C5' A:ATP801 4.8 14.4 1.0
CZ A:ARG461 4.8 21.3 0.3
CB A:THR221 4.9 21.8 1.0
O5' A:ATP801 4.9 17.1 1.0
O3' A:ATP801 4.9 14.0 1.0
CG2 A:THR221 4.9 21.9 1.0
CE A:LYS229 5.0 33.1 1.0

Reference:

G.Kochan, E.S.Pilka, F.Von Delft, U.Oppermann, W.W.Yue. Structural Snapshots For the Conformation-Dependent Catalysis By Human Medium-Chain Acyl-Coenzyme A Synthetase ACSM2A. J.Mol.Biol. V. 388 997 2009.
ISSN: ISSN 0022-2836
PubMed: 19345228
DOI: 10.1016/J.JMB.2009.03.064
Page generated: Wed Aug 14 09:27:29 2024

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