Zinc in PDB 4o6s: 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)

The structure of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound), PDB code: 4o6s was solved by S.Lovell, R.Kumar, K.P.Battaile, H.Matsumura, H.Yao, J.C.Rodriguez, P.Moenne-Loccoz, M.Rivera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.63 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.898, 66.232, 40.999, 90.00, 97.13, 90.00
R / Rfree (%)	14.3 / 16.8

The structure of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) (pdb code 4o6s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound), PDB code: 4o6s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:9.9 occ:1.00 O A:HOH419 1.7 12.1 1.0 O A:HOH392 1.7 11.4 1.0 O A:HOH375 1.9 20.2 1.0 O A:HOH325 1.9 16.5 1.0 ZN A:ZN207 3.3 8.4 1.0 CE1 A:HIS74 4.4 7.5 1.0 NE2 A:HIS74 4.4 7.8 1.0 OD2 A:ASP72 4.8 9.3 1.0 OD1 A:ASP72 4.8 9.2 1.0

Zinc binding site 2 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:8.4 occ:1.00 O A:HOH392 2.0 11.4 1.0 NE2 A:HIS74 2.0 7.8 1.0 OD2 A:ASP72 2.1 9.3 1.0 CG A:ASP72 2.9 8.9 1.0 CE1 A:HIS74 2.9 7.5 1.0 OD1 A:ASP72 3.0 9.2 1.0 CD2 A:HIS74 3.0 8.1 1.0 ZN A:ZN206 3.3 9.9 1.0 O A:HOH325 3.9 16.5 1.0 ND1 A:HIS74 4.1 8.2 1.0 O A:HOH375 4.1 20.2 1.0 CG A:HIS74 4.2 8.1 1.0 CB A:ASP72 4.3 8.3 1.0 O A:HOH419 4.5 12.1 1.0 O A:HOH309 4.6 12.7 1.0 O A:ASP72 4.7 7.1 1.0 C A:ASP72 4.9 6.2 1.0 CH2 A:TRP86 5.0 8.5 1.0 CZ3 A:TRP86 5.0 8.7 1.0

Zinc binding site 3 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:13.1 occ:1.00 O A:HOH305 2.0 16.3 1.0 ND1 A:HIS179 2.0 10.8 1.0 O A:HOH320 2.1 23.1 1.0 CE1 A:HIS179 2.9 12.6 1.0 CG A:HIS179 3.1 10.8 1.0 CB A:HIS179 3.5 9.8 1.0 O A:HOH331 3.8 11.7 1.0 NE2 A:HIS179 4.1 13.1 1.0 CA A:HIS179 4.2 9.5 1.0 CD2 A:HIS179 4.2 11.7 1.0 O A:HOH422 4.6 28.5 1.0 O A:ALA178 4.6 9.2 1.0 O A:HOH462 4.9 42.5 1.0

Zinc binding site 4 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn209 b:18.2 occ:1.00 O A:HOH429 1.7 16.4 1.0 O A:HOH424 1.8 13.6 1.0 O A:HOH404 1.9 23.8 1.0 O A:HOH472 1.9 24.7 1.0 ZN A:ZN210 3.2 11.9 1.0 O A:HOH393 3.7 13.4 1.0 OG A:SER162 3.8 15.9 1.0 CB A:SER162 3.8 14.3 1.0 OD2 A:ASP160 4.7 9.5 1.0

Zinc binding site 5 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn210 b:11.9 occ:1.00 O A:HOH424 1.9 13.6 1.0 O A:HOH393 1.9 13.4 1.0 OD2 A:ASP160 2.0 9.5 1.0 CG A:ASP160 2.8 9.7 1.0 OD1 A:ASP160 3.1 10.2 1.0 ZN A:ZN209 3.2 18.2 1.0 O A:HOH429 3.4 16.4 1.0 OG A:SER162 3.6 15.9 1.0 CB A:ASP160 4.1 10.1 1.0 O A:HOH404 4.1 23.8 1.0 CD A:PRO161 4.2 13.8 1.0 N A:SER162 4.2 10.1 1.0 CB A:SER162 4.2 14.3 1.0 N A:PRO161 4.4 9.9 1.0 CA A:ASP160 4.4 9.0 1.0 C A:ASP160 4.5 9.7 1.0 O A:HOH472 4.8 24.7 1.0 CA A:SER162 4.9 11.9 1.0 CG A:PRO161 4.9 18.1 1.0

Zinc binding site 6 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn211 b:13.5 occ:1.00 O A:HOH365 1.7 19.5 1.0 OE2 A:GLU113 2.0 10.1 1.0 O A:HOH301 2.3 4.8 1.0 CD A:GLU113 2.8 8.8 1.0 OE1 A:GLU113 2.9 10.5 1.0 O A:HOH480 3.6 19.9 1.0 OD1 A:ASP96 3.8 21.9 1.0 O A:HOH471 3.9 36.8 1.0 O A:HOH358 3.9 17.1 1.0 O A:HOH370 4.2 31.6 1.0 CG A:GLU113 4.2 7.7 1.0 OH A:TYR11 4.4 15.3 1.0 CB A:ASP96 4.4 15.6 1.0 CG A:ASP96 4.6 19.6 1.0 C A:GLY95 4.8 6.9 1.0 N A:ASP96 4.9 8.1 1.0 O A:HOH390 5.0 23.6 1.0 CE2 A:TYR26 5.0 14.2 1.0

Zinc binding site 7 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn212 b:17.4 occ:1.00 O A:HOH446 1.8 19.3 1.0 O2A A:HEM205 2.0 17.0 1.0 CGA A:HEM205 2.8 17.0 1.0 O1A A:HEM205 2.9 17.7 1.0 CBA A:HEM205 4.3 16.6 1.0 O A:HOH332 4.3 13.3 1.0 O1D A:HEM205 4.3 10.7 1.0 O A:HOH506 4.5 31.7 1.0 CB A:PRO34 4.8 14.9 1.0 CGD A:HEM205 5.0 10.0 1.0

Zinc binding site 8 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn213 b:23.8 occ:1.00 OD2 A:ASP29 1.9 14.3 1.0 O A:HOH413 2.2 33.4 1.0 O A:HOH434 2.2 35.0 1.0 O A:HOH409 2.3 25.2 1.0 O A:HOH497 2.3 37.6 1.0 O A:HOH496 2.3 39.4 1.0 CG A:ASP29 3.0 12.7 1.0 OD1 A:ASP29 3.4 11.0 1.0 O A:HOH451 4.1 31.6 1.0 OD1 A:ASN31 4.1 19.8 0.5 CB A:ASP29 4.3 12.7 1.0 NE A:ARG33 4.5 24.1 1.0 OD1 A:ASN31 4.6 16.8 0.5 CD A:ARG33 4.6 23.1 1.0 O A:SER142 4.7 16.7 1.0 CB A:SER142 4.9 17.4 0.5 CB A:SER142 4.9 15.8 0.5

Zinc binding site 9 out of 9 in the 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of 1.32A Resolution Structure of the Hemophore Hasa From Pseudomonas Aeruginosa (H83A Mutant, Zinc Bound) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn214 b:30.1 occ:1.00 OD1 A:ASP122 2.1 22.7 1.0 O A:HOH336 2.1 28.4 1.0 O A:HOH432 2.2 34.1 1.0 O A:HOH499 2.3 42.0 1.0 O A:HOH445 2.3 33.0 1.0 O A:HOH498 2.4 42.7 1.0 CG A:ASP122 3.1 21.8 1.0 OD2 A:ASP122 3.4 24.4 1.0 O A:ASP122 4.0 14.3 1.0 O A:HOH474 4.4 29.8 1.0 CB A:ASP122 4.4 20.4 1.0 C A:ASP122 4.6 11.9 1.0 CD A:PRO124 4.6 12.9 1.0

R.Kumar, H.Matsumura, S.Lovell, H.Yao, J.C.Rodriguez, K.P.Battaile, P.Moenne-Loccoz, M.Rivera. Replacing the Axial Ligand Tyrosine 75 or Its Hydrogen Bond Partner Histidine 83 Minimally Affects Hemin Acquisition By the Hemophore Hasap From Pseudomonas Aeruginosa. Biochemistry V. 53 2112 2014.
ISSN: ISSN 0006-2960
PubMed: 24625274
DOI: 10.1021/BI500030P