Zinc in PDB 5lzl: Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase

All present enzymatic activity of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase:
4.2.1.24;

The structure of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase, PDB code: 5lzl was solved by N.Azim, P.T.Erskine, J.Guo, J.B.Cooper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	178.02 / 3.47
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	205.561, 205.561, 199.171, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 25

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase (pdb code 5lzl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase, PDB code: 5lzl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:97.8 occ:1.00 SG A:CYS127 2.3 0.8 1.0 SG A:CYS125 2.5 82.7 1.0 SG A:CYS135 2.6 82.9 1.0 CB A:CYS127 3.3 97.5 1.0 CB A:CYS125 3.3 88.6 1.0 OG A:SER174 3.8 75.2 1.0 CB A:CYS135 3.8 88.0 1.0 O A:SER174 4.0 79.0 1.0 N A:CYS127 4.1 93.2 1.0 CA A:CYS127 4.3 95.1 1.0 C A:SER174 4.3 79.8 1.0 CA A:CYS135 4.5 90.8 1.0 CA A:GLY175 4.5 85.3 1.0 N A:GLY175 4.6 82.8 1.0 CB A:SER174 4.6 75.9 1.0 NH1 A:ARG226 4.7 90.9 1.0 CA A:CYS125 4.7 91.2 1.0 N A:LEU126 4.8 99.1 1.0

Zinc binding site 2 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.5 occ:1.00 OE1 A:GLU242 2.1 87.1 1.0 CD A:GLU242 2.9 82.1 1.0 OE2 A:GLU242 3.1 84.8 1.0 OD1 A:ASP246 3.1 89.5 1.0 O A:MET177 3.8 85.9 1.0 CG A:ASP246 4.0 83.0 1.0 OD2 A:ASP246 4.1 87.2 1.0 CA A:ASP178 4.1 94.4 1.0 OD1 A:ASP178 4.3 0.8 1.0 NE2 A:GLN180 4.3 87.9 1.0 CE A:MET176 4.3 94.2 1.0 CG A:GLU242 4.4 74.9 1.0 N A:GLY179 4.4 94.5 1.0 O A:GLU242 4.4 72.0 1.0 C A:MET177 4.6 88.5 1.0 C A:ASP178 4.8 91.7 1.0 N A:ASP178 4.8 91.3 1.0 CB A:GLU242 4.9 71.8 1.0 O A:SER202 4.9 76.0 1.0 CD A:GLN180 5.0 85.7 1.0 CB A:ASP178 5.0 99.1 1.0

Zinc binding site 3 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:83.1 occ:1.00 SG B:CYS127 1.9 0.1 1.0 SG B:CYS135 2.5 91.1 1.0 SG B:CYS125 2.9 87.1 1.0 CB B:CYS127 3.2 0.4 1.0 CB B:CYS125 3.4 90.6 1.0 CB B:CYS135 3.9 91.2 1.0 OG B:SER174 4.0 84.3 1.0 N B:CYS127 4.3 0.4 1.0 CA B:CYS127 4.3 0.6 1.0 CA B:CYS135 4.6 91.6 1.0 NH1 B:ARG226 4.6 0.8 1.0 O B:SER174 4.7 80.6 1.0 CA B:CYS125 4.8 93.3 1.0 NZ B:LYS204 4.9 89.9 1.0 CB B:SER174 4.9 82.2 1.0

Zinc binding site 4 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:0.2 occ:1.00 OE1 B:GLU242 2.3 78.0 1.0 OD1 B:ASP246 3.1 89.5 1.0 CD B:GLU242 3.3 76.0 1.0 OD2 B:ASP246 3.4 79.0 1.0 OE2 B:GLU242 3.5 76.8 1.0 CG B:ASP246 3.7 79.6 1.0 OD1 B:ASP178 4.0 85.8 1.0 O B:MET177 4.1 83.9 1.0 CA B:ASP178 4.3 84.7 1.0 OE1 B:GLN180 4.4 98.3 1.0 CE B:MET176 4.4 76.3 1.0 O B:GLU242 4.7 67.2 1.0 CG B:GLU242 4.7 72.0 1.0 C B:MET177 4.7 83.7 1.0 N B:GLY179 4.8 88.8 1.0 N B:ASP178 4.9 83.2 1.0 CD B:GLN180 4.9 97.0 1.0 CG B:GLN180 4.9 95.4 1.0 CE B:MET245 4.9 87.3 1.0 CG B:ASP178 4.9 86.0 1.0 CB B:ASP178 5.0 86.1 1.0

Zinc binding site 5 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:92.9 occ:1.00 SG C:CYS125 2.2 88.0 1.0 SG C:CYS135 2.4 87.5 1.0 SG C:CYS127 2.4 87.3 1.0 CB C:CYS125 3.0 90.5 1.0 OG C:SER174 3.5 74.7 1.0 CB C:CYS135 3.7 88.2 1.0 CB C:CYS127 3.8 93.1 1.0 O C:SER174 4.1 74.3 1.0 N C:CYS127 4.2 95.1 1.0 C C:SER174 4.3 76.8 1.0 CA C:CYS125 4.4 91.0 1.0 CA C:CYS135 4.4 88.5 1.0 CA C:GLY175 4.5 77.0 1.0 N C:GLY175 4.6 76.8 1.0 CB C:SER174 4.6 74.7 1.0 CA C:CYS127 4.6 95.7 1.0 N C:LEU126 4.7 95.7 1.0 C C:CYS125 4.9 95.3 1.0

Zinc binding site 6 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:0.2 occ:1.00 OE1 C:GLU242 2.2 83.2 1.0 OE2 C:GLU242 2.6 90.9 1.0 CD C:GLU242 2.8 82.3 1.0 OD1 C:ASP246 3.5 74.3 1.0 OD2 C:ASP246 3.6 70.1 1.0 CG C:ASP246 3.8 70.7 1.0 CE C:MET176 4.1 73.0 1.0 OD1 C:ASP178 4.2 86.5 1.0 O C:MET177 4.2 70.0 1.0 CG C:GLU242 4.3 74.9 1.0 O C:GLU242 4.4 71.4 1.0 CA C:ASP178 4.4 80.1 1.0 N C:GLY179 4.4 84.7 1.0 NE2 C:GLN180 4.7 90.3 1.0 CE C:MET245 4.8 71.1 1.0 C C:ASP178 4.9 79.8 1.0 C C:MET177 5.0 73.4 1.0

Zinc binding site 7 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:0.1 occ:1.00 SG D:CYS127 2.1 0.3 1.0 SG D:CYS125 2.3 0.9 1.0 SG D:CYS135 2.7 98.8 1.0 CB D:CYS125 3.2 0.7 1.0 CB D:CYS127 3.3 0.9 1.0 CB D:CYS135 3.8 0.7 1.0 OG D:SER174 3.8 72.7 1.0 O D:SER174 4.2 83.3 1.0 N D:CYS127 4.2 0.1 1.0 CA D:CYS135 4.3 0.0 1.0 CA D:CYS127 4.4 0.2 1.0 NZ D:LYS204 4.5 84.2 1.0 C D:SER174 4.6 82.7 1.0 CA D:CYS125 4.6 0.5 1.0 OE1 D:GLU128 4.7 0.1 1.0 CB D:SER174 4.8 76.0 1.0 N D:GLY175 4.9 83.2 1.0 CA D:GLY175 4.9 84.5 1.0

Zinc binding site 8 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:0.7 occ:1.00 OE1 D:GLU242 2.4 95.6 1.0 OE2 D:GLU242 3.1 89.8 1.0 CD D:GLU242 3.1 89.6 1.0 OD1 D:ASP246 3.5 82.2 1.0 OD2 D:ASP246 4.0 80.2 1.0 CE D:MET176 4.0 89.2 1.0 O D:MET177 4.1 81.0 1.0 CG D:ASP246 4.2 78.1 1.0 OD1 D:ASP178 4.2 88.7 1.0 CA D:ASP178 4.3 81.8 1.0 C D:MET177 4.5 80.8 1.0 O D:MET176 4.5 81.3 1.0 O D:GLU242 4.6 77.9 1.0 CG D:GLU242 4.6 82.5 1.0 C D:MET176 4.6 81.3 1.0 CD D:GLN180 4.7 88.5 1.0 CG D:GLN180 4.7 85.5 1.0 N D:ASP178 4.8 79.8 1.0 NE2 D:GLN180 4.8 92.4 1.0 N D:GLY179 4.8 79.4 1.0 CA D:MET176 4.9 85.5 1.0 O D:SER202 4.9 81.3 1.0 N D:MET177 5.0 79.9 1.0

Zinc binding site 9 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:75.3 occ:1.00 SG E:CYS127 2.2 87.9 1.0 SG E:CYS135 2.4 66.3 1.0 SG E:CYS125 2.5 77.5 1.0 CB E:CYS127 3.2 84.3 1.0 CB E:CYS125 3.4 75.7 1.0 CB E:CYS135 3.7 68.5 1.0 OG E:SER174 3.9 66.5 1.0 N E:CYS127 4.2 81.1 1.0 CA E:CYS127 4.3 82.2 1.0 O E:SER174 4.3 72.8 1.0 CA E:CYS135 4.4 69.2 1.0 OE2 E:GLU128 4.6 96.3 1.0 C E:SER174 4.8 71.3 1.0 CA E:CYS125 4.8 73.8 1.0 CA E:GLY175 4.9 69.9 1.0 C E:CYS125 4.9 74.6 1.0 CB E:SER174 5.0 67.5 1.0

Zinc binding site 10 out of 24 in the Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Pyrobaculum Calidifontis 5-Aminolaevulinic Acid Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:93.1 occ:1.00 OE1 E:GLU242 2.1 78.2 1.0 CD E:GLU242 3.0 72.7 1.0 OE2 E:GLU242 3.2 77.9 1.0 OD1 E:ASP246 3.5 65.4 1.0 OD2 E:ASP246 3.8 67.1 1.0 CG E:ASP246 4.0 64.1 1.0 CE E:MET176 4.0 64.8 1.0 O E:SER202 4.1 63.8 1.0 O E:MET177 4.2 60.1 1.0 NE2 E:GLN180 4.2 70.8 1.0 OD1 E:ASP178 4.3 71.4 1.0 O E:GLU242 4.5 56.2 1.0 CG E:GLU242 4.5 64.0 1.0 SD E:MET176 4.7 65.6 1.0 CA E:ASP178 4.7 61.5 1.0 CD E:GLN180 4.8 70.4 1.0 CG E:GLN180 4.8 69.7 1.0 C E:MET177 4.9 60.7 1.0 CB E:GLU242 4.9 60.2 1.0

N.Mills-Davies, D.Butler, E.Norton, D.Thompson, M.Sarwar, J.Guo, R.Gill, N.Azim, A.Coker, S.P.Wood, P.T.Erskine, L.Coates, J.B.Cooper, N.Rashid, M.Akhtar, P.M.Shoolingin-Jordan. Structural Studies of Substrate and Product Complexes of 5-Aminolaevulinic Acid Dehydratase From Humans, Escherichia Coli and the Hyperthermophile Pyrobaculum Calidifontis. Acta Crystallogr D Struct V. 73 9 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28045381
DOI: 10.1107/S2059798316019525