Atomistry » Calcium » PDB 7pod-7qfy » 7q2a
Atomistry »
  Calcium »
    PDB 7pod-7qfy »
      7q2a »

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

Go back to Calcium Binding Sites List in 7q2a
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy