Calcium in PDB 7q2a: Crystal Structure of Aphc in Complex with 4-Ethylcatechol

Enzymatic activity of Crystal Structure of Aphc in Complex with 4-Ethylcatechol

All present enzymatic activity of Crystal Structure of Aphc in Complex with 4-Ethylcatechol:
1.13.11.2;

Protein crystallography data

The structure of Crystal Structure of Aphc in Complex with 4-Ethylcatechol, PDB code: 7q2a was solved by M.Zahn, J.C.Grigg, L.D.Eltis, J.E.Mcgeehan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.19 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.58, 119.351, 84.528, 90, 114.56, 90
R / Rfree (%) 17.9 / 20.9

Other elements in 7q2a:

The structure of Crystal Structure of Aphc in Complex with 4-Ethylcatechol also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol (pdb code 7q2a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol, PDB code: 7q2a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7q2a

Go back to Calcium Binding Sites List in 7q2a
Calcium binding site 1 out of 6 in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Aphc in Complex with 4-Ethylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:84.8
occ:1.00
 O A:VAL345 2.3 107.0 1.0
OD1 A:ASP347 2.3 96.6 1.0
O A:GLU342 2.5 96.3 1.0
OE1 A:GLU350 2.7 83.2 1.0
CG A:ASP347 3.5 96.7 1.0
C A:VAL345 3.6 104.1 1.0
C A:GLU342 3.6 98.1 1.0
CD A:GLU350 3.9 83.5 1.0
N A:ASP347 4.0 94.3 1.0
O A:LEU343 4.1 85.3 1.0
C A:PRO346 4.2 98.1 1.0
CA A:LEU343 4.2 94.5 1.0
CA A:ASP347 4.3 92.0 1.0
OD2 A:ASP347 4.3 102.4 1.0
C A:LEU343 4.3 90.7 1.0
N A:LEU343 4.3 96.2 1.0
CA A:PRO346 4.4 100.5 1.0
N A:PRO346 4.4 103.6 1.0
CA A:VAL345 4.5 102.9 1.0
CB A:ASP347 4.5 93.0 1.0
N A:VAL345 4.6 101.8 1.0
CB A:GLU350 4.6 83.4 1.0
OE2 A:GLU350 4.6 80.3 1.0
O A:PRO346 4.7 95.3 1.0
CA A:GLU342 4.7 96.8 1.0
CB A:VAL345 4.7 103.9 1.0
CG A:GLU350 4.8 82.7 1.0

Calcium binding site 2 out of 6 in 7q2a

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Calcium binding site 2 out of 6 in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Aphc in Complex with 4-Ethylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:51.4
occ:1.00
 O B:GLU342 2.3 55.9 1.0
O B:VAL345 2.4 59.0 1.0
OE1 B:GLU350 2.4 49.1 1.0
O B:HOH701 2.5 47.4 1.0
OD1 B:ASP347 2.5 60.1 1.0
C B:GLU342 3.4 60.2 1.0
C B:VAL345 3.6 68.2 1.0
CD B:GLU350 3.7 56.6 1.0
CG B:ASP347 3.7 65.8 1.0
N B:ASP347 4.1 59.6 1.0
CA B:LEU343 4.2 63.3 1.0
N B:LEU343 4.2 60.4 1.0
C B:PRO346 4.2 65.0 1.0
O B:LEU343 4.3 62.6 1.0
C B:LEU343 4.4 63.0 1.0
CA B:ASP347 4.4 60.6 1.0
CA B:GLU342 4.4 59.3 1.0
CB B:GLU350 4.4 50.9 1.0
CA B:VAL345 4.4 72.4 1.0
OE2 B:GLU350 4.5 56.2 1.0
CA B:PRO346 4.5 68.3 1.0
N B:PRO346 4.5 67.6 1.0
N B:VAL345 4.5 73.4 1.0
OD2 B:ASP347 4.5 70.3 1.0
CB B:VAL345 4.6 74.3 1.0
CG B:GLU350 4.6 54.3 1.0
CB B:ASP347 4.7 62.1 1.0
O B:PRO346 4.7 62.3 1.0
CG1 B:VAL345 4.9 73.8 1.0
CB B:GLU342 4.9 60.3 1.0

Calcium binding site 3 out of 6 in 7q2a

Go back to Calcium Binding Sites List in 7q2a
Calcium binding site 3 out of 6 in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Aphc in Complex with 4-Ethylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:85.8
occ:1.00
 O C:VAL345 2.3 83.7 1.0
O C:GLU342 2.4 81.2 1.0
OD1 C:ASP347 2.5 94.6 1.0
OE1 C:GLU350 2.6 91.3 1.0
C C:VAL345 3.5 87.4 1.0
C C:GLU342 3.5 91.0 1.0
CG C:ASP347 3.7 95.7 1.0
CD C:GLU350 3.8 93.4 1.0
N C:ASP347 4.0 94.4 1.0
C C:PRO346 4.1 90.3 1.0
O C:LEU343 4.1 96.6 1.0
CA C:LEU343 4.2 95.0 1.0
N C:LEU343 4.3 93.1 1.0
C C:LEU343 4.3 96.6 1.0
CA C:ASP347 4.3 96.9 1.0
CA C:PRO346 4.3 88.9 1.0
N C:PRO346 4.4 85.7 1.0
CA C:VAL345 4.4 94.1 1.0
OD2 C:ASP347 4.4 97.2 1.0
N C:VAL345 4.5 97.0 1.0
CB C:GLU350 4.5 92.0 1.0
OE2 C:GLU350 4.6 94.3 1.0
CA C:GLU342 4.6 90.7 1.0
CB C:VAL345 4.6 94.9 1.0
CB C:ASP347 4.6 97.2 1.0
O C:PRO346 4.6 87.8 1.0
CG C:GLU350 4.7 92.3 1.0
CG1 C:VAL345 4.9 94.4 1.0

Calcium binding site 4 out of 6 in 7q2a

Go back to Calcium Binding Sites List in 7q2a
Calcium binding site 4 out of 6 in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Aphc in Complex with 4-Ethylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:35.4
occ:1.00
 O C:HOH621 2.1 33.1 1.0
OD1 C:ASP93 2.1 30.9 1.0
O C:GLY94 2.4 29.4 1.0
O C:HOH665 2.4 28.6 1.0
O C:HOH646 2.5 36.2 1.0
O C:HOH671 2.7 47.7 1.0
CG C:ASP93 3.4 33.4 1.0
C C:GLY94 3.6 34.1 1.0
N C:GLY94 3.6 31.8 1.0
C C:ASP93 4.1 33.2 1.0
O C:HOH557 4.1 40.8 1.0
CA C:ASP93 4.2 32.8 1.0
CA C:GLY94 4.2 30.9 1.0
O C:HOH648 4.2 38.4 1.0
OD2 C:ASP93 4.3 34.2 1.0
CB C:ASP93 4.3 33.8 1.0
O C:HOH679 4.4 37.8 1.0
OG1 C:THR95 4.5 37.5 1.0
N C:THR95 4.6 33.3 1.0
CA C:THR95 5.0 36.2 1.0

Calcium binding site 5 out of 6 in 7q2a

Go back to Calcium Binding Sites List in 7q2a
Calcium binding site 5 out of 6 in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Aphc in Complex with 4-Ethylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:62.9
occ:1.00
 O D:GLU342 2.2 60.6 1.0
OE1 D:GLU350 2.3 60.2 1.0
O D:VAL345 2.4 74.8 1.0
OD1 D:ASP347 2.5 64.3 1.0
C D:GLU342 3.3 64.9 1.0
CD D:GLU350 3.5 64.0 1.0
C D:VAL345 3.6 75.7 1.0
CG D:ASP347 3.8 70.9 1.0
CA D:LEU343 4.1 67.4 1.0
N D:LEU343 4.1 65.0 1.0
N D:ASP347 4.2 68.3 1.0
O D:LEU343 4.3 73.2 1.0
OE2 D:GLU350 4.3 65.7 1.0
CB D:GLU350 4.3 61.6 1.0
CA D:GLU342 4.3 62.7 1.0
C D:PRO346 4.3 74.2 1.0
C D:LEU343 4.3 66.5 1.0
CA D:VAL345 4.4 78.4 1.0
CA D:ASP347 4.4 68.4 1.0
N D:VAL345 4.4 76.3 1.0
CB D:VAL345 4.5 78.9 1.0
CG D:GLU350 4.5 63.1 1.0
OD2 D:ASP347 4.5 69.7 1.0
N D:PRO346 4.5 75.6 1.0
CA D:PRO346 4.6 78.3 1.0
CB D:ASP347 4.7 67.8 1.0
O D:PRO346 4.7 67.6 1.0
CG1 D:VAL345 4.8 80.6 1.0
CB D:GLU342 4.8 61.5 1.0

Calcium binding site 6 out of 6 in 7q2a

Go back to Calcium Binding Sites List in 7q2a
Calcium binding site 6 out of 6 in the Crystal Structure of Aphc in Complex with 4-Ethylcatechol


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Aphc in Complex with 4-Ethylcatechol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca403

b:57.2
occ:1.00
 O D:HOH619 3.1 52.1 1.0
O D:HOH539 3.2 29.9 1.0
NZ D:LYS58 3.7 26.2 1.0
NE2 D:GLN100 3.8 34.5 1.0
OH D:TYR45 4.4 26.6 1.0
OE2 D:GLU40 4.7 44.1 1.0
O D:HOH515 4.7 35.8 1.0
CE D:LYS58 4.7 25.2 1.0
CD D:GLN100 4.8 33.0 1.0
OE1 D:GLN100 4.8 33.2 1.0
O D:ASP99 4.9 35.1 1.0

Reference:

L.E.Navas, M.Zahn, H.Bajwa, J.C.Grigg, M.E.Wolf, A.C.K.Chan, M.E.P.Murphy, J.E.Mcgeehan, L.D.Eltis. Characterization of A Phylogenetically Distinct Extradiol Dioxygenase Involved in the Bacterial Catabolism of Lignin-Derived Aromatic Compounds. J.Biol.Chem. V. 298 01871 2022.
ISSN: ESSN 1083-351X
PubMed: 35346686
DOI: 10.1016/J.JBC.2022.101871
Page generated: Fri Jul 19 03:23:20 2024

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