Zinc in PDB 1yhu: Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.

The structure of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits., PDB code: 1yhu was solved by J.F.Flores, C.R.Fisher, S.L.Carney, B.N.Green, J.K.Freytag, S.W.Schaeffer, W.E.Royer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	195.840, 195.840, 308.820, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 27.1

The structure of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. also contains other interesting chemical elements:

Iron

(Fe)

24 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. (pdb code 1yhu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits., PDB code: 1yhu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn190 b:22.1 occ:1.00 NE2 B:HIS57 2.0 31.4 1.0 NE2 B:HIS31 2.1 29.5 1.0 OE2 J:GLU118 2.2 17.1 1.0 OE1 J:GLU118 2.5 17.1 1.0 CD J:GLU118 2.7 17.1 1.0 CE1 B:HIS57 2.7 31.4 1.0 CE1 B:HIS31 2.9 29.5 1.0 CD2 B:HIS57 3.2 31.4 1.0 CD2 B:HIS31 3.3 29.5 1.0 ND1 B:HIS57 4.0 31.4 1.0 ND1 B:HIS31 4.1 29.5 1.0 CG B:HIS57 4.2 31.4 1.0 CG J:GLU118 4.2 17.1 1.0 CG B:HIS31 4.3 29.5 1.0 CD1 B:ILE56 4.3 35.9 1.0 CB J:SER123 4.6 47.1 1.0 OG B:SER35 4.7 70.4 1.0 CG1 B:ILE56 4.8 32.3 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn191 b:37.7 occ:1.00 NE2 B:HIS40 2.2 53.2 1.0 NE2 B:HIS111 2.2 51.8 1.0 NE2 B:HIS36 2.3 48.3 1.0 CE1 B:HIS36 2.7 48.3 1.0 CE1 B:HIS40 2.8 53.2 1.0 CE1 B:HIS111 3.0 51.8 1.0 CD2 B:HIS111 3.4 51.8 1.0 CD2 B:HIS40 3.4 53.2 1.0 CD2 B:HIS36 3.5 48.3 1.0 ND1 B:HIS36 4.0 48.3 1.0 ND1 B:HIS40 4.1 53.2 1.0 ND1 B:HIS111 4.2 51.8 1.0 CG B:HIS40 4.4 53.2 1.0 CE B:MET115 4.4 52.2 1.0 CG B:HIS36 4.4 48.3 1.0 CG B:HIS111 4.4 51.8 1.0 CG B:MET115 4.5 52.2 1.0 SD B:MET115 4.8 52.2 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn190 b:27.5 occ:1.00 NE2 F:HIS57 2.0 16.6 1.0 NE2 F:HIS31 2.2 46.0 1.0 OE2 B:GLU118 2.3 33.8 1.0 OE1 B:GLU118 2.4 33.8 1.0 CE1 F:HIS57 2.7 16.6 1.0 CD B:GLU118 2.7 33.8 1.0 CE1 F:HIS31 2.9 46.0 1.0 CD2 F:HIS57 3.2 16.6 1.0 CD2 F:HIS31 3.3 46.0 1.0 ND1 F:HIS57 3.9 16.6 1.0 ND1 F:HIS31 4.1 46.0 1.0 CG F:HIS57 4.2 16.6 1.0 CG B:GLU118 4.2 33.8 1.0 CD1 F:ILE56 4.3 30.2 1.0 CG F:HIS31 4.3 46.0 1.0 CB B:SER123 4.7 51.6 1.0 OG F:SER35 4.7 74.8 1.0 CG1 F:ILE56 4.7 26.6 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn191 b:36.0 occ:1.00 NE2 F:HIS111 2.2 37.3 1.0 NE2 F:HIS40 2.2 43.2 1.0 NE2 F:HIS36 2.2 33.9 1.0 CE1 F:HIS36 2.7 33.9 1.0 CE1 F:HIS40 2.9 43.2 1.0 CE1 F:HIS111 2.9 37.3 1.0 CD2 F:HIS111 3.3 37.3 1.0 CD2 F:HIS40 3.4 43.2 1.0 CD2 F:HIS36 3.5 33.9 1.0 ND1 F:HIS36 4.0 33.9 1.0 ND1 F:HIS111 4.1 37.3 1.0 ND1 F:HIS40 4.1 43.2 1.0 CG F:HIS111 4.4 37.3 1.0 CE F:MET115 4.4 65.1 1.0 CG F:HIS36 4.4 33.9 1.0 CG F:HIS40 4.4 43.2 1.0 CG F:MET115 4.4 65.1 1.0 SD F:MET115 4.8 65.1 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn190 b:28.4 occ:1.00 NE2 J:HIS57 1.9 24.5 1.0 OE2 F:GLU118 2.1 29.5 1.0 NE2 J:HIS31 2.1 33.3 1.0 OE1 F:GLU118 2.5 29.5 1.0 CD F:GLU118 2.6 29.5 1.0 CE1 J:HIS57 2.7 24.5 1.0 CE1 J:HIS31 2.9 33.3 1.0 CD2 J:HIS57 3.1 24.5 1.0 CD2 J:HIS31 3.3 33.3 1.0 ND1 J:HIS57 3.9 24.5 1.0 ND1 J:HIS31 4.1 33.3 1.0 CG J:HIS57 4.1 24.5 1.0 CG F:GLU118 4.1 29.5 1.0 CG J:HIS31 4.3 33.3 1.0 CB F:SER123 4.3 51.5 1.0 CD1 J:ILE56 4.3 34.5 1.0 CG1 J:ILE56 4.8 30.9 1.0 OG J:SER35 4.8 34.0 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn191 b:29.5 occ:1.00 NE2 J:HIS111 2.3 43.3 1.0 NE2 J:HIS36 2.3 34.8 1.0 NE2 J:HIS40 2.3 41.2 1.0 CE1 J:HIS36 2.7 34.8 1.0 CE1 J:HIS40 2.9 41.2 1.0 CE1 J:HIS111 3.0 43.3 1.0 CD2 J:HIS111 3.4 43.3 1.0 CD2 J:HIS40 3.5 41.2 1.0 CD2 J:HIS36 3.6 34.8 1.0 ND1 J:HIS36 4.0 34.8 1.0 ND1 J:HIS40 4.2 41.2 1.0 ND1 J:HIS111 4.2 43.3 1.0 CE J:MET115 4.4 51.7 1.0 CG J:HIS36 4.4 34.8 1.0 CG J:HIS111 4.5 43.3 1.0 CG J:MET115 4.5 51.7 1.0 CG J:HIS40 4.5 41.2 1.0 SD J:MET115 4.8 51.7 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn190 b:45.7 occ:1.00 NE2 N:HIS57 2.1 38.8 1.0 NE2 N:HIS31 2.3 64.0 1.0 OE2 V:GLU118 2.3 46.6 1.0 OE1 V:GLU118 2.5 46.6 1.0 CD V:GLU118 2.7 46.6 1.0 CE1 N:HIS57 2.8 38.8 1.0 CE1 N:HIS31 2.9 64.0 1.0 CD2 N:HIS57 3.3 38.8 1.0 CD2 N:HIS31 3.4 64.0 1.0 ND1 N:HIS57 4.0 38.8 1.0 ND1 N:HIS31 4.2 64.0 1.0 CG V:GLU118 4.2 46.6 1.0 CG N:HIS57 4.3 38.8 1.0 CD1 N:ILE56 4.3 51.4 1.0 CG N:HIS31 4.4 64.0 1.0 CB V:SER123 4.6 75.3 1.0 OG N:SER35 4.6 88.7 1.0 CG1 N:ILE56 4.8 47.8 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


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 Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn191 b:52.5 occ:1.00 NE2 N:HIS111 2.3 49.5 1.0 NE2 N:HIS40 2.3 80.5 1.0 NE2 N:HIS36 2.4 64.9 1.0 CE1 N:HIS36 2.8 64.9 1.0 CE1 N:HIS40 2.9 80.5 1.0 CE1 N:HIS111 2.9 49.5 1.0 CD2 N:HIS111 3.5 49.5 1.0 CD2 N:HIS40 3.5 80.5 1.0 CD2 N:HIS36 3.7 64.9 1.0 ND1 N:HIS36 4.0 64.9 1.0 ND1 N:HIS40 4.2 80.5 1.0 ND1 N:HIS111 4.2 49.5 1.0 CE N:MET115 4.3 66.2 1.0 CG N:HIS111 4.5 49.5 1.0 CG N:HIS40 4.5 80.5 1.0 CG N:MET115 4.5 66.2 1.0 CG N:HIS36 4.5 64.9 1.0 SD N:MET115 4.8 66.2 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn190 b:44.3 occ:1.00 NE2 R:HIS57 2.1 53.5 1.0 NE2 R:HIS31 2.1 34.3 1.0 OE2 N:GLU118 2.3 34.9 1.0 OE1 N:GLU118 2.5 34.9 1.0 CD N:GLU118 2.7 34.9 1.0 CE1 R:HIS57 2.8 53.5 1.0 CE1 R:HIS31 2.8 34.3 1.0 CD2 R:HIS57 3.3 53.5 1.0 CD2 R:HIS31 3.3 34.3 1.0 ND1 R:HIS57 4.0 53.5 1.0 ND1 R:HIS31 4.0 34.3 1.0 CG R:HIS57 4.3 53.5 1.0 CG N:GLU118 4.3 34.9 1.0 CG R:HIS31 4.3 34.3 1.0 CD1 R:ILE56 4.3 50.4 1.0 OG R:SER35 4.6 77.4 1.0 CB N:SER123 4.6 65.1 1.0 CG1 R:ILE56 4.8 46.8 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Riftia Pachyptila C1 Hemoglobin Reveals Novel Assembly of 24 Subunits. within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn191 b:48.4 occ:1.00 NE2 R:HIS36 2.2 66.2 1.0 NE2 R:HIS111 2.2 55.1 1.0 NE2 R:HIS40 2.3 84.1 1.0 CE1 R:HIS36 2.6 66.2 1.0 CE1 R:HIS40 2.9 84.1 1.0 CE1 R:HIS111 3.0 55.1 1.0 CD2 R:HIS111 3.4 55.1 1.0 CD2 R:HIS40 3.5 84.1 1.0 CD2 R:HIS36 3.5 66.2 1.0 ND1 R:HIS36 3.9 66.2 1.0 ND1 R:HIS40 4.2 84.1 1.0 ND1 R:HIS111 4.2 55.1 1.0 CE R:MET115 4.3 61.7 1.0 CG R:HIS36 4.3 66.2 1.0 CG R:MET115 4.4 61.7 1.0 CG R:HIS111 4.4 55.1 1.0 CG R:HIS40 4.5 84.1 1.0 SD R:MET115 4.8 61.7 1.0

J.F.Flores, C.R.Fisher, S.L.Carney, B.N.Green, J.K.Freytag, S.W.Schaeffer, W.E.Royer Jr. Sulfide Binding Is Mediated By Zinc Ions Discovered in the Crystal Structure of A Hydrothermal Vent Tubeworm Hemoglobin. Proc.Natl.Acad.Sci.Usa V. 102 2713 2005.
ISSN: ISSN 0027-8424
PubMed: 15710902
DOI: 10.1073/PNAS.0407455102