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Magnesium in PDB 1w5m: Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)

Enzymatic activity of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)

All present enzymatic activity of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C):
4.2.1.24;

Protein crystallography data

The structure of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C), PDB code: 1w5m was solved by F.Frere, H.Reents, W.-D.Schubert, D.W.Heinz, D.Jahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.71 / 1.60
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 126.307, 126.307, 85.156, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 16.5

Other elements in 1w5m:

The structure of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) (pdb code 1w5m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C), PDB code: 1w5m:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1w5m

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Magnesium binding site 1 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1340

b:8.9
occ:1.00
 OE1 A:GLU245 2.0 9.3 1.0
O A:HOH2374 2.0 11.8 1.0
O A:HOH2373 2.1 10.0 1.0
O A:HOH2317 2.1 12.7 1.0
O A:HOH2375 2.1 10.1 1.0
O A:HOH2316 2.1 10.7 1.0
CD A:GLU245 3.0 11.1 1.0
OE2 A:GLU245 3.4 11.2 1.0
NH1 A:ARG181 3.8 12.4 1.0
OD1 A:ASP249 3.9 9.8 1.0
O A:HOH2315 4.1 10.4 1.0
O A:HOH2377 4.1 11.2 1.0
OD2 A:ASP249 4.3 10.7 1.0
O A:HOH2376 4.3 9.6 1.0
O A:MET178 4.3 10.2 1.0
CG A:GLU245 4.4 8.3 1.0
O A:SER203 4.4 10.1 1.0
CG A:ASP249 4.4 9.5 1.0
OD1 A:ASP179 4.5 11.8 1.0
O A:GLU245 4.5 8.8 1.0
CB A:GLU245 4.6 9.7 1.0
CA A:GLU245 4.7 8.5 1.0
O B:HOH2028 4.7 17.9 1.0
CA A:ASP179 4.8 9.9 1.0
SD A:MET177 4.8 10.1 1.0
CE A:MET177 4.9 11.0 1.0

Magnesium binding site 2 out of 7 in 1w5m

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Magnesium binding site 2 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1342

b:11.4
occ:1.00
 O A:HOH2067 2.1 11.8 1.0
O A:LEU27 4.0 11.3 1.0
O A:ARG29 4.2 12.1 1.0
O A:ARG26 4.4 11.6 1.0
C A:LEU27 4.9 10.2 1.0

Magnesium binding site 3 out of 7 in 1w5m

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Magnesium binding site 3 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1343

b:8.4
occ:0.25
 O A:HOH2196 2.0 16.9 0.5
O A:HOH2030 2.0 32.8 1.0
O A:HOH2236 2.0 27.3 0.8
O A:HOH2427 2.1 34.3 1.0
O A:HOH2388 3.9 19.9 0.5
O A:HOH2428 4.0 16.9 1.0
O A:HOH2424 4.2 16.6 1.0
O A:HOH2073 4.3 33.0 1.0
OD1 A:ASP319 4.6 18.4 1.0
O A:GLY317 4.7 16.1 1.0
NZ A:LYS273 4.8 25.7 1.0
CD A:LYS273 4.8 20.8 1.0
CE A:LYS273 4.9 23.8 1.0

Magnesium binding site 4 out of 7 in 1w5m

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Magnesium binding site 4 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1338

b:10.2
occ:1.00
 OE1 B:GLU245 2.0 10.5 1.0
O B:HOH2377 2.1 11.4 1.0
O B:HOH2332 2.1 10.2 1.0
O B:HOH2379 2.1 13.7 1.0
O B:HOH2333 2.1 11.8 1.0
O B:HOH2380 2.2 11.0 1.0
CD B:GLU245 3.0 10.2 1.0
OE2 B:GLU245 3.4 11.4 1.0
NH1 B:ARG181 3.8 12.1 1.0
OD1 B:ASP249 3.8 10.7 1.0
O B:HOH2331 4.0 12.5 1.0
O B:HOH2382 4.1 12.9 1.0
O B:HOH2383 4.2 10.2 1.0
O B:MET178 4.3 11.5 1.0
OD2 B:ASP249 4.3 11.4 1.0
CG B:GLU245 4.3 9.2 1.0
CG B:ASP249 4.4 11.0 1.0
O B:SER203 4.5 11.0 1.0
OD1 B:ASP179 4.5 12.3 1.0
CB B:GLU245 4.6 8.5 1.0
O B:GLU245 4.6 10.8 1.0
O A:HOH2029 4.7 19.2 1.0
CA B:GLU245 4.7 9.2 1.0
CA B:ASP179 4.8 9.7 1.0
SD B:MET177 4.8 10.9 1.0
CE B:MET177 4.9 14.3 1.0

Magnesium binding site 5 out of 7 in 1w5m

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Magnesium binding site 5 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1339

b:14.6
occ:0.50
 O B:HOH2129 1.9 32.2 1.0
OD1 B:ASN49 2.1 23.3 1.0
O B:HOH2130 2.1 25.3 1.0
O B:HOH2172 2.1 26.6 1.0
O B:HOH2133 2.1 37.1 1.0
CG B:ASN49 3.2 21.1 1.0
ND2 B:ASN49 3.8 24.0 1.0
NE2 B:GLN67 4.0 16.5 1.0
OD2 B:ASP66 4.1 19.1 1.0
O B:HOH2047 4.3 49.3 1.0
CB B:ASN49 4.4 14.6 1.0
O B:HOH2134 4.6 19.3 0.2
O B:HOH2135 4.7 22.1 0.5
CA B:ASN49 4.9 12.9 1.0

Magnesium binding site 6 out of 7 in 1w5m

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Magnesium binding site 6 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1341

b:10.6
occ:1.00
 O B:HOH2077 2.1 11.4 1.0
O B:LEU27 4.0 11.3 1.0
O B:ARG29 4.2 12.5 1.0
O B:HOH2081 4.2 22.7 1.0
O B:ARG26 4.4 10.1 1.0
C B:LEU27 4.8 10.6 1.0

Magnesium binding site 7 out of 7 in 1w5m

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Magnesium binding site 7 out of 7 in the Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Stepwise Introduction of Zinc Binding Site Into Porphobilinogen Synthase of Pseudomonas Aeruginosa (Mutations A129C and D139C) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1342

b:7.2
occ:0.30
 O B:HOH2205 1.9 25.7 1.0
O B:HOH2032 2.0 36.2 1.0
O B:HOH2031 2.0 37.2 1.0
O B:HOH2247 2.1 33.3 1.0
O B:HOH2429 2.1 31.2 1.0
O B:HOH2392 4.0 30.6 1.0
O B:HOH2430 4.1 16.7 1.0
O B:HOH2085 4.2 35.6 1.0
O B:HOH2424 4.3 15.4 1.0
O B:GLY317 4.5 16.4 1.0
OD1 B:ASP319 4.7 17.7 1.0
CE B:LYS273 4.7 22.7 1.0
NZ B:LYS273 4.8 22.4 1.0
CD B:LYS273 4.8 20.1 1.0

Reference:

F.Frere, H.Reents, W.-D.Schubert, D.W.Heinz, D.Jahn. Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro J.Mol.Biol. V. 345 1059 2005.
ISSN: ISSN 0022-2836
PubMed: 15644204
DOI: 10.1016/J.JMB.2004.10.053
Page generated: Tue Aug 13 17:06:55 2024

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