Zinc in PDB 4u9j: Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant

The structure of Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant, PDB code: 4u9j was solved by M.A.Herzik Jr., R.Jonnalagadda, J.Kuriyan, M.A.Marletta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.03 / 2.10
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	163.801, 163.801, 102.082, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 19.7

The structure of Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant (pdb code 4u9j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant, PDB code: 4u9j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant


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 An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:41.9 occ:1.00 NE2 A:HIS161 2.0 40.8 1.0 SG A:CYS172 2.3 42.3 1.0 SG A:CYS139 2.4 40.6 1.0 SG A:CYS164 2.4 45.0 1.0 CE1 A:HIS161 2.8 42.8 1.0 HE1 A:HIS161 2.8 51.4 1.0 HB2 A:CYS139 2.9 49.5 1.0 HB3 A:CYS172 3.0 48.4 1.0 CB A:CYS139 3.0 41.2 1.0 HA A:CYS164 3.1 53.2 1.0 HB3 A:CYS139 3.1 49.5 1.0 HB2 A:CYS164 3.1 50.9 1.0 CB A:CYS164 3.2 42.4 1.0 CB A:CYS172 3.2 40.3 1.0 CD2 A:HIS161 3.2 43.5 1.0 H A:MET165 3.3 51.6 1.0 HD2 A:HIS161 3.6 52.2 1.0 CA A:CYS164 3.6 44.3 1.0 HD2 A:HIS166 3.6 62.7 1.0 HB2 A:CYS172 3.7 48.4 1.0 O A:HOH366 3.9 39.9 1.0 N A:MET165 4.0 43.0 1.0 ND1 A:HIS161 4.0 44.2 1.0 HB3 A:CYS164 4.1 50.9 1.0 H A:HIS166 4.1 55.2 1.0 CG A:HIS161 4.2 41.4 1.0 C A:CYS164 4.3 43.1 1.0 HE2 A:PHE140 4.4 53.4 1.0 HA A:CYS172 4.4 47.9 1.0 HD12 A:LEU174 4.4 53.4 1.0 O A:THR163 4.5 40.2 1.0 CA A:CYS172 4.5 39.9 1.0 CA A:CYS139 4.5 40.5 1.0 CD2 A:HIS166 4.5 52.3 1.0 HB2 A:MET165 4.6 52.9 1.0 HG3 A:MET165 4.7 51.1 1.0 CE2 A:PHE140 4.7 44.5 1.0 HD1 A:HIS161 4.7 53.0 1.0 H A:CYS139 4.7 49.9 1.0 O B:HOH318 4.8 39.5 1.0 N A:CYS164 4.8 41.2 1.0 HB2 A:HIS166 4.9 61.7 1.0 N A:HIS166 5.0 46.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant


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 An H-Nox Protein From S. Oneidensis in the Mn(II) Ligation State, Q154A/Q155A/K156A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:51.8 occ:1.00 SG B:CYS164 2.1 51.8 1.0 NE2 B:HIS161 2.2 56.2 1.0 SG B:CYS139 2.3 47.9 1.0 SG B:CYS172 2.4 52.3 1.0 HB2 B:CYS139 2.9 54.7 1.0 CB B:CYS139 3.0 45.5 1.0 CE1 B:HIS161 3.0 53.6 1.0 HB3 B:CYS139 3.0 54.7 1.0 HE1 B:HIS161 3.0 64.3 1.0 HA B:CYS164 3.1 65.1 1.0 HB3 B:CYS172 3.1 65.3 1.0 CB B:CYS164 3.2 55.1 1.0 H B:MET165 3.2 64.4 1.0 CD2 B:HIS161 3.3 57.2 1.0 HB2 B:CYS164 3.3 66.1 1.0 CB B:CYS172 3.4 54.4 1.0 HD2 B:HIS166 3.5 64.6 1.0 HD2 B:HIS161 3.6 68.6 1.0 CA B:CYS164 3.6 54.2 1.0 O B:HOH340 3.8 43.6 1.0 N B:MET165 3.9 53.7 1.0 HB2 B:CYS172 4.0 65.3 1.0 H B:HIS166 4.0 59.4 1.0 HB3 B:CYS164 4.0 66.1 1.0 ND1 B:HIS161 4.1 57.0 1.0 CD2 B:HIS166 4.2 53.8 1.0 C B:CYS164 4.2 56.6 1.0 HA B:CYS172 4.3 62.7 1.0 CG B:HIS161 4.3 55.7 1.0 HD11 B:LEU174 4.4 72.6 1.0 CA B:CYS139 4.5 46.5 1.0 CA B:CYS172 4.5 52.2 1.0 O B:THR163 4.7 59.2 1.0 HB2 B:MET165 4.8 57.7 1.0 H B:CYS139 4.8 53.7 1.0 HG3 B:MET165 4.8 61.0 1.0 N B:HIS166 4.8 49.5 1.0 HB2 B:HIS166 4.9 63.1 1.0 N B:CYS164 4.9 64.0 1.0 HE2 B:HIS166 4.9 63.9 1.0 HD1 B:HIS161 4.9 68.5 1.0 NE2 B:HIS166 4.9 53.2 1.0

M.A.Herzik, R.Jonnalagadda, J.Kuriyan, M.A.Marletta. Structural Insights Into the Role of Iron-Histidine Bond Cleavage in Nitric Oxide-Induced Activation of H-Nox Gas Sensor Proteins. Proc.Natl.Acad.Sci.Usa V. 111 E4156 2014.
ISSN: ESSN 1091-6490
PubMed: 25253889
DOI: 10.1073/PNAS.1416936111