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Magnesium in PDB 1v5g: Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate

Enzymatic activity of Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate

All present enzymatic activity of Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate:
1.2.3.3;

Protein crystallography data

The structure of Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate, PDB code: 1v5g was solved by M.T.Hossain, K.Suzuki, T.Yamamoto, S.Imamura, T.Sekiguchi, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.96
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 78.010, 105.500, 155.850, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate (pdb code 1v5g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate, PDB code: 1v5g:

Magnesium binding site 1 out of 1 in 1v5g

Go back to Magnesium Binding Sites List in 1v5g
Magnesium binding site 1 out of 1 in the Crystal Structure of the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate


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 the Reaction Intermediate Between Pyruvate Oxidase Containing Fad and Tpp, and Substrate Pyruvate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1603

b:27.9
occ:1.00
 OD1 A:ASP442 2.2 20.1 1.0
OD1 A:ASN469 2.2 20.2 1.0
O A:GLU471 2.3 20.9 1.0
O23 A:HTL1602 2.3 21.4 1.0
O12 A:HTL1602 2.3 18.5 1.0
O A:HOH1604 2.4 15.7 1.0
CG A:ASN469 3.1 21.7 1.0
CG A:ASP442 3.2 19.6 1.0
ND2 A:ASN469 3.3 20.2 1.0
C A:GLU471 3.5 23.9 1.0
P1 A:HTL1602 3.5 19.6 1.0
P2 A:HTL1602 3.5 19.8 1.0
O11 A:HTL1602 3.6 18.7 1.0
OD2 A:ASP442 3.7 20.4 1.0
N A:ASP442 3.9 17.4 1.0
N A:GLU471 4.0 24.1 1.0
O22 A:HTL1602 4.0 19.9 1.0
N A:GLY443 4.1 17.0 1.0
O A:PHE467 4.1 16.3 1.0
O5G A:HTL1602 4.3 20.9 1.0
N A:ALA473 4.3 24.2 1.0
CA A:GLU471 4.3 25.3 1.0
CZ A:PHE491 4.4 26.7 1.0
N A:TYR472 4.4 21.9 1.0
N A:ASN469 4.4 19.6 1.0
CB A:ASP442 4.4 17.1 1.0
CB A:ASN469 4.5 20.6 1.0
CA A:TYR472 4.5 23.2 1.0
CA A:ASP442 4.5 17.9 1.0
O13 A:HTL1602 4.6 22.2 1.0
C A:GLY441 4.6 18.4 1.0
N A:THR470 4.7 21.8 1.0
O21 A:HTL1602 4.7 18.5 1.0
CA A:GLY441 4.7 18.5 1.0
C A:ASP442 4.8 17.6 1.0
CB A:ALA473 4.8 26.2 1.0
CA A:ASN469 4.8 20.9 1.0
C A:ASN469 4.9 21.8 1.0
C A:TYR472 5.0 24.0 1.0
CA A:GLY443 5.0 15.6 1.0

Reference:

E.C.Juan, M.M.Hoque, M.T.Hossain, T.Yamamoto, S.Imamura, K.Suzuki, T.Sekiguchi, A.Takenaka. The Structures of Pyruvate Oxidase From Aerococcus Viridans with Cofactors and with A Reaction Intermediate Reveal the Flexibility of the Active-Site Tunnel For Catalysis. Acta Crystallogr.,Sect.F V. 63 900 2007.
ISSN: ESSN 1744-3091
PubMed: 18007037
DOI: 10.1107/S1744309107041012
Page generated: Tue Aug 13 15:01:34 2024

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