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Calcium in PDB 7b07: TGOT_6G12 Apo

Enzymatic activity of TGOT_6G12 Apo

All present enzymatic activity of TGOT_6G12 Apo:
2.7.7.7;

Protein crystallography data

The structure of TGOT_6G12 Apo, PDB code: 7b07 was solved by C.Samson, P.Legrand, M.Tekpinar, J.Rozenski, M.Abramov, P.Holliger, V.Pinheiro, P.Herdewijn, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.53 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.89, 110.49, 111.77, 90, 90, 90
R / Rfree (%) 26.2 / 26.5

Calcium Binding Sites:

The binding sites of Calcium atom in the TGOT_6G12 Apo (pdb code 7b07). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the TGOT_6G12 Apo, PDB code: 7b07:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7b07

Go back to Calcium Binding Sites List in 7b07
Calcium binding site 1 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TGOT_6G12 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:85.5
occ:1.00
O A:THR5 2.5 96.4 1.0
OD1 A:ASP4 2.6 102.4 1.0
CG A:ASP4 3.4 102.2 1.0
OD2 A:ASP4 3.6 104.7 1.0
C A:THR5 3.7 96.2 1.0
OD2 A:ASP343 4.0 109.0 1.0
N A:THR5 4.2 95.9 1.0
CB A:ALA117 4.4 95.9 1.0
CA A:THR5 4.6 96.1 1.0
OG A:SER340 4.6 103.8 1.0
OG1 A:THR5 4.6 98.3 1.0
N A:ASP6 4.6 95.7 1.0
CB A:ASP6 4.7 98.0 1.0
CA A:ASP6 4.7 95.8 1.0
CB A:ASP4 4.8 97.9 1.0
OE1 A:GLU251 4.9 128.2 1.0

Calcium binding site 2 out of 4 in 7b07

Go back to Calcium Binding Sites List in 7b07
Calcium binding site 2 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TGOT_6G12 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:105.4
occ:1.00
OD1 A:ASP404 2.9 141.8 1.0
OD2 A:ASP404 3.0 143.0 1.0
CG A:ASP404 3.3 141.0 1.0
OE1 A:GLU578 3.6 148.8 1.0
O A:ASP404 4.6 133.3 1.0
O A:PHE405 4.6 128.5 1.0
CG A:GLU580 4.6 148.5 1.0
CB A:ASP404 4.7 136.6 1.0
CB A:GLU578 4.7 138.3 1.0
CD A:GLU578 4.7 147.9 1.0
CB A:GLU580 4.8 143.2 1.0

Calcium binding site 3 out of 4 in 7b07

Go back to Calcium Binding Sites List in 7b07
Calcium binding site 3 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TGOT_6G12 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:124.0
occ:1.00
OD1 A:ASP455 2.5 114.7 1.0
OE1 A:GLU458 3.5 128.4 1.0
CG A:ASP455 3.7 114.0 1.0
OD2 A:ASP455 4.4 115.9 1.0
N A:ASP455 4.5 107.8 1.0
CA A:ASP455 4.6 108.5 1.0
C A:GLY454 4.7 107.7 1.0
CD A:GLU458 4.7 126.9 1.0
CB A:ASP455 4.7 110.0 1.0
O A:SER451 4.9 108.2 1.0
O A:GLY454 4.9 107.7 1.0

Calcium binding site 4 out of 4 in 7b07

Go back to Calcium Binding Sites List in 7b07
Calcium binding site 4 out of 4 in the TGOT_6G12 Apo


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TGOT_6G12 Apo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:123.3
occ:1.00
O A:ASN568 2.5 138.2 1.0
O A:LEU571 2.9 134.8 1.0
C A:ASN568 3.8 138.1 1.0
C A:LEU571 4.0 134.7 1.0
O A:ALA569 4.2 137.2 1.0
C A:ALA569 4.3 137.0 1.0
CA A:ALA569 4.3 137.4 1.0
N A:LEU571 4.4 135.1 1.0
N A:ALA569 4.5 137.5 1.0
O A:GLY573 4.5 133.6 1.0
CA A:LEU571 4.6 134.9 1.0
CB A:LEU571 4.7 135.2 1.0
CA A:ASN568 4.8 138.4 1.0
O A:LEU575 4.8 132.8 1.0
N A:LYS570 4.9 136.3 1.0

Reference:

C.Samson, P.Legrand, M.Tekpinar, J.Rozenski, M.Abramov, P.Holliger, V.B.Pinheiro, P.Herdwijn, M.Delarue. Structural Studies of Hna Substrate Specificity in Mutants of An Archaeal Dna Polymerase Obtained By Directed Evolution. Biomolecules V. 10 2020.
ISSN: ESSN 2218-273X
PubMed: 33302546
DOI: 10.3390/BIOM10121647
Page generated: Wed Jul 9 20:54:17 2025

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