Zinc in PDB 2uyd: Crystal Structure of the Smhasa Mutant H83A

The structure of Crystal Structure of the Smhasa Mutant H83A, PDB code: 2uyd was solved by M.Czjzek, C.Caillet-Saguy, A.Fournelle, B.Guigliarelli, N.Izadi-Pruneyre, A.Lecroisey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.670, 110.670, 52.355, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 27.4

The structure of Crystal Structure of the Smhasa Mutant H83A also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Smhasa Mutant H83A (pdb code 2uyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Smhasa Mutant H83A, PDB code: 2uyd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn201 b:44.9 occ:1.00 OD2 X:ASP8 2.2 26.6 1.0 OD1 X:ASP8 2.2 28.3 1.0 CG X:ASP8 2.6 29.4 1.0 CB X:ASP8 4.1 30.6 1.0 OG X:SER10 4.2 30.3 1.0 CB X:SER10 4.5 30.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn202 b:67.6 occ:1.00 OD2 X:ASP96 2.0 31.1 1.0 CG X:ASP96 3.0 34.2 1.0 ZN X:ZN203 3.3 78.6 1.0 OD1 X:ASP96 3.4 35.8 1.0 ZN X:ZN207 4.1 54.3 1.0 CB X:ASP96 4.3 33.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn203 b:78.6 occ:1.00 ZN X:ZN207 3.1 54.3 1.0 OD2 X:ASP112 3.2 33.0 1.0 ZN X:ZN202 3.3 67.6 1.0 OD2 X:ASP96 3.9 31.1 1.0 CG X:ASP112 4.1 32.5 1.0 OD1 X:ASP112 4.2 30.5 1.0 OD1 X:ASP96 4.4 35.8 1.0 CG X:ASP96 4.5 34.2 1.0 O X:HOH2008 4.9 64.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn204 b:85.2 occ:1.00 OD2 X:ASP29 2.1 48.5 1.0 O X:HOH2066 2.6 49.6 1.0 CG X:ASP29 3.2 45.8 1.0 OD1 X:ASP29 3.6 48.2 1.0 CB X:ASP29 4.5 44.2 1.0 CA X:ASN31 4.8 46.2 1.0 CG2 X:THR33 4.9 49.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn205 b:0.3 occ:1.00 OD1 X:ASP143 2.8 44.7 1.0 OD2 X:ASP143 3.1 44.2 1.0 O X:HOH2067 3.4 67.5 1.0 CG X:ASP143 3.4 42.8 1.0 CA X:GLY145 4.6 39.1 1.0 CB X:ASP143 4.9 41.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn206 b:0.1 occ:1.00 NE2 X:HIS128 1.0 58.7 1.0 CD2 X:HIS128 2.0 57.1 1.0 CE1 X:HIS128 2.2 58.3 1.0 O X:ACT501 2.4 70.1 1.0 OXT X:ACT502 3.0 70.3 1.0 CG X:HIS128 3.1 56.6 1.0 ND1 X:HIS128 3.2 58.4 1.0 C X:ACT501 3.3 69.8 1.0 OXT X:ACT501 3.4 70.3 1.0 C X:ACT502 3.8 69.9 1.0 O X:ACT502 3.9 70.4 1.0 CB X:HIS128 4.5 55.6 1.0 CH3 X:ACT501 4.7 69.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn207 b:54.3 occ:1.00 OD1 X:ASP112 1.9 30.5 1.0 CG X:ASP112 2.7 32.5 1.0 OD2 X:ASP112 2.9 33.0 1.0 ZN X:ZN203 3.1 78.6 1.0 OD2 X:ASP96 3.8 31.1 1.0 CB X:ASP112 4.1 34.3 1.0 ZN X:ZN202 4.1 67.6 1.0 O X:VAL110 4.2 34.5 1.0 CG1 X:VAL110 4.3 34.4 1.0 CZ X:PHE11 4.4 27.8 1.0 CE1 X:PHE11 4.6 28.1 1.0 CA X:ASP112 4.6 34.5 1.0 CG X:ASP96 4.6 34.2 1.0 N X:ASP112 4.8 34.6 1.0 O X:PRO111 4.9 34.7 1.0 CA X:GLY95 5.0 33.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Smhasa Mutant H83A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Smhasa Mutant H83A within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn208 b:0.6 occ:1.00 OD1 X:ASP157 2.0 48.3 1.0 O X:GLY153 2.7 43.7 1.0 OD2 X:ASP156 2.8 50.0 1.0 CG X:ASP157 3.0 48.3 1.0 O X:HOH2049 3.2 72.1 1.0 O X:HOH2068 3.3 55.3 1.0 OD2 X:ASP157 3.4 48.9 1.0 CG X:ASP156 3.7 48.2 1.0 C X:GLY153 3.8 43.2 1.0 N X:ASP157 4.0 46.9 1.0 OD1 X:ASP156 4.1 49.9 1.0 CB X:ASP157 4.2 47.2 1.0 CA X:GLY153 4.3 42.7 1.0 O X:HOH2050 4.3 61.8 1.0 CA X:ASP157 4.6 47.1 1.0 C X:ASP156 4.7 46.9 1.0 CB X:ASP156 4.9 47.4 1.0 N X:ILE154 4.9 43.6 1.0

C.Caillet-Saguy, P.Turano, M.Piccioli, G.S.Lukat-Rodgers, M.Czjzek, B.Guigliarelli, N.Izadi-Pruneyre, K.R.Rodgers, M.Delepierre, A.Lecroisey. Deciphering the Structural Role of Histidine 83 For Heme Binding in Hemophore Hasa. J.Biol.Chem. V. 283 5960 2008.
ISSN: ISSN 0021-9258
PubMed: 18162469
DOI: 10.1074/JBC.M703795200