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Magnesium in PDB 5gr6: Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142

Enzymatic activity of Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142

All present enzymatic activity of Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142:
2.4.1.18;

Protein crystallography data

The structure of Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142, PDB code: 5gr6 was solved by R.Suzuki, E.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.06 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 133.596, 133.596, 184.227, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142 (pdb code 5gr6). 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 Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142, PDB code: 5gr6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5gr6

Go back to Magnesium Binding Sites List in 5gr6
Magnesium binding site 1 out of 4 in the Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142


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 Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg807

b:60.1
occ:1.00
 O A:HOH936 1.9 63.0 1.0
O A:HOH1331 2.2 29.3 1.0
O A:HOH1574 2.2 42.3 1.0
OE1 A:GLU487 4.0 30.8 1.0
OD1 A:ASP434 4.0 41.2 1.0
O A:HOH1028 4.2 27.7 1.0
O A:HOH1221 4.3 38.8 1.0
OD2 A:ASP555 4.4 32.4 1.0
O A:HOH1067 4.4 33.4 1.0
CD A:GLU487 4.7 27.9 1.0
CB A:ALA435 4.8 31.6 1.0
CG A:ASP434 4.9 41.0 1.0
OE2 A:GLU487 4.9 32.8 1.0
OD2 A:ASP434 5.0 40.5 1.0

Magnesium binding site 2 out of 4 in 5gr6

Go back to Magnesium Binding Sites List in 5gr6
Magnesium binding site 2 out of 4 in the Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142


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 Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:25.1
occ:1.00
 O A:HOH1254 1.9 25.1 1.0
OD1 A:ASP612 2.0 18.2 1.0
O A:HOH1084 2.0 23.9 1.0
O A:HOH1229 2.0 28.8 1.0
O A:HOH1143 2.1 25.1 1.0
CG A:ASP612 3.1 20.7 1.0
OD2 A:ASP612 3.7 20.3 1.0
O A:HOH1264 3.9 42.1 1.0
O A:ASP612 4.0 18.1 1.0
O A:LEU613 4.0 19.5 1.0
N A:ASP612 4.1 20.7 1.0
O A:HOH1177 4.2 28.8 1.0
O A:HOH1138 4.3 26.3 1.0
C A:ASP612 4.3 19.8 1.0
CB A:ASP612 4.3 18.8 1.0
CA A:ASP612 4.4 19.4 1.0
C A:LEU613 4.9 20.3 1.0

Magnesium binding site 3 out of 4 in 5gr6

Go back to Magnesium Binding Sites List in 5gr6
Magnesium binding site 3 out of 4 in the Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142


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 Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg809

b:40.0
occ:1.00
 O A:HOH1528 2.0 32.6 1.0
O A:HOH1102 2.2 38.7 1.0
O A:HOH1293 2.2 35.5 1.0
O A:HOH955 2.3 39.8 1.0
O A:HOH1232 3.9 42.7 1.0
OE1 A:GLU194 4.0 30.6 1.0
O A:TRP163 4.2 26.2 1.0
OE2 A:GLU194 4.4 30.5 1.0
OD1 A:ASP164 4.4 28.6 1.0
CA A:ASP164 4.6 26.7 1.0
O A:HOH1207 4.6 47.0 1.0
CD A:GLU194 4.6 31.9 1.0
O A:HOH1356 4.7 49.8 1.0
N A:GLY165 4.9 28.1 1.0
CG A:ASP164 5.0 30.7 1.0

Magnesium binding site 4 out of 4 in 5gr6

Go back to Magnesium Binding Sites List in 5gr6
Magnesium binding site 4 out of 4 in the Crystal Structure of Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142


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 Branching Enzyme Y500A/D501A Double Mutant From Cyanothece Sp. Atcc 51142 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg810

b:58.5
occ:1.00
 O A:HOH1510 1.8 43.6 1.0
O A:HOH1465 2.1 42.0 1.0
O A:HOH1117 2.3 32.0 1.0
O A:HOH1436 3.7 31.2 1.0
OD1 A:ASN535 4.1 32.8 1.0
ND2 A:ASN534 4.2 31.4 1.0
O A:HOH939 4.3 33.5 1.0
ND1 A:HIS532 4.3 26.6 1.0
OD1 A:ASN534 4.6 30.4 1.0
CE1 A:HIS532 4.8 24.3 1.0
CG A:ASN534 4.8 27.0 1.0

Reference:

M.Hayashi, R.Suzuki, C.Colleoni, S.G.Ball, N.Fujita, E.Suzuki. Structural Basis For Substrate Binding and Catalysis of Branching Enzyme From Cyanothece Sp. Atcc 51142 To Be Published.
Page generated: Sun Sep 29 15:24:12 2024

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