Zinc in PDB 3m97: Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans

The structure of Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans, PDB code: 3m97 was solved by C.Rajendran, U.Ermler, B.Ludwig, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.13 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.376, 38.991, 93.014, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.9

The structure of Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans (pdb code 3m97). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans, PDB code: 3m97:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn142 b:15.6 occ:1.00 NE2 X:HIS69 2.0 10.7 1.0 O X:HOH199 2.2 21.3 1.0 O X:HOH334 2.3 22.8 1.0 CE1 X:HIS69 3.0 8.8 1.0 CD2 X:HIS69 3.0 10.2 1.0 NH1 X:ARG76 4.0 10.3 1.0 ND1 X:HIS69 4.1 12.0 1.0 O X:ASN71 4.1 10.9 1.0 CG X:HIS69 4.2 10.4 1.0 O X:HOH323 4.3 25.0 1.0 O X:HOH257 4.3 24.4 1.0 O X:HOH215 4.5 35.5 1.0 CD X:ARG76 4.8 10.8 1.0 O X:HOH197 4.9 31.0 1.0

Zinc binding site 2 out of 4 in the Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn143 b:14.0 occ:1.00 OD2 X:ASP82 1.9 12.1 1.0 CG X:ASP82 2.8 12.5 1.0 OD1 X:ASP82 3.0 13.4 1.0 CB X:ASP82 4.2 10.7 1.0 O X:HOH197 4.8 31.0 1.0

Zinc binding site 3 out of 4 in the Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn144 b:13.1 occ:1.00 OD1 X:ASP88 2.0 12.7 1.0 CG X:ASP88 2.8 13.8 1.0 OD2 X:ASP88 2.9 14.6 1.0 CB X:ASP88 4.2 12.6 1.0 O X:HOH237 4.3 18.8 1.0

Zinc binding site 4 out of 4 in the Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Soluble Domain of Cytochrome C552 with Its Flexible Linker Segment From Paracoccus Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ X:Zn145 b:12.6 occ:1.00 NE2 X:HIS93 2.0 10.5 1.0 O X:HOH244 2.0 13.4 1.0 CD2 X:HIS93 3.0 13.3 1.0 CE1 X:HIS93 3.0 13.2 1.0 O X:HOH191 4.1 31.2 1.0 CG X:HIS93 4.1 9.2 1.0 ND1 X:HIS93 4.1 10.7 1.0 O X:HOH313 4.4 25.5 1.0 O X:VAL112 4.5 11.4 1.0 O X:HOH327 4.7 27.7 1.0

C.Rajendran, U.Ermler, B.Ludwig, H.Michel. Structure at 1.5 A Resolution of Cytochrome C(552) with Its Flexible Linker Segment, A Membrane-Anchored Protein From Paracoccus Denitrificans. Acta Crystallogr.,Sect.D V. 66 850 2010.
ISSN: ISSN 0907-4449
PubMed: 20606266
DOI: 10.1107/S0907444910019396