Magnesium in PDB 8stc: S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate.

Enzymatic activity of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate.

All present enzymatic activity of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate.:
2.5.1.143;

Protein crystallography data

The structure of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate., PDB code: 8stc was solved by S.Chatterjee, J.A.Rankin, J.Hu, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.91 / 2.80
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 120.38, 120.38, 213.159, 90, 90, 90
R / Rfree (%) 23.7 / 27.3

Other elements in 8stc:

The structure of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate. (pdb code 8stc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate., PDB code: 8stc:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8stc

Go back to Magnesium Binding Sites List in 8stc
Magnesium binding site 1 out of 2 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:100.3
occ:1.00
O A:VAL191 2.9 59.5 1.0
O A:SER223 2.9 48.7 0.5
O A:GLY188 3.1 54.2 1.0
O A:SER223 3.1 48.8 0.5
OH B:TYR238 3.2 53.1 1.0
OD1 A:ASP192 3.3 67.2 1.0
C A:SER223 3.9 49.9 0.5
CE1 B:TYR238 4.0 50.8 1.0
C A:SER223 4.0 50.2 0.5
CZ B:TYR238 4.0 51.8 1.0
C A:VAL191 4.1 58.7 1.0
CA A:ASP192 4.3 62.5 1.0
C A:GLY188 4.3 53.4 1.0
O A:ALA222 4.3 54.7 0.5
NH2 B:ARG44 4.5 95.2 1.0
CG A:ASP192 4.5 67.2 1.0
CA A:GLY224 4.6 51.3 1.0
N A:ASP192 4.6 59.8 1.0
N A:GLY224 4.7 51.4 1.0
CA A:SER223 4.7 50.4 0.5
CB A:SER223 4.8 54.8 0.5
CB A:ASP192 4.9 65.1 1.0
CA A:SER223 5.0 51.4 0.5
CA A:GLY189 5.0 53.9 1.0

Magnesium binding site 2 out of 2 in 8stc

Go back to Magnesium Binding Sites List in 8stc
Magnesium binding site 2 out of 2 in the S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:88.2
occ:1.00
O D:SER223 2.7 46.3 0.4
O D:SER223 2.7 45.1 0.6
O D:GLY188 2.8 59.4 1.0
O D:VAL191 3.1 65.1 1.0
CA D:GLY224 3.6 61.0 1.0
C D:SER223 3.7 47.2 0.6
C D:SER223 3.7 48.0 0.4
C D:GLY188 3.8 60.0 1.0
O D:GLY224 4.0 54.5 1.0
C D:GLY224 4.0 55.2 1.0
O D:LYS193 4.1 57.5 1.0
N D:GLY224 4.1 63.3 1.0
CA D:GLY188 4.2 58.7 1.0
CE1 C:TYR238 4.3 51.8 1.0
C D:VAL191 4.3 64.9 1.0
OH C:TYR238 4.4 54.9 1.0
CE C:MET242 4.6 49.8 1.0
CA D:ASP192 4.6 75.0 1.0
OD1 D:ASP192 4.7 79.0 1.0
SD C:MET242 4.7 52.8 1.0
CZ C:TYR238 4.8 52.4 1.0
CG2 D:VAL191 4.8 55.3 1.0
CG2 D:VAL195 4.8 49.2 1.0
N D:LYS193 4.9 65.9 1.0
N D:ASP192 4.9 70.8 1.0
N D:ILE225 5.0 50.8 1.0
CA D:SER223 5.0 47.8 0.6

Reference:

S.Chatterjee, J.A.Rankin, J.Hu, R.P.Hausinger. S127A Variant of Larb, A Carboxylase/Hydrolase Involved in Synthesis of the Cofactor For Lactate Racemase, in Complex with Zinc and Soaked with Bicarbonate. To Be Published.
Page generated: Fri Oct 4 20:09:01 2024

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