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

Protein crystallography data

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

Other elements in 4u9j:

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:

Zinc (Zn) 2 atoms
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 4u9j

Go back to Manganese Binding Sites List in 4u9j
Manganese 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 Manganese with other atoms in the Mn 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:Mn201

b:40.8
occ:1.00
MN A:MNH201 0.0 40.8 1.0
ND A:MNH201 2.1 41.1 1.0
NA A:MNH201 2.1 40.3 1.0
NB A:MNH201 2.2 40.1 1.0
NE2 A:HIS103 2.2 37.0 1.0
NC A:MNH201 2.2 40.4 1.0
C4D A:MNH201 3.1 41.8 1.0
CE1 A:HIS103 3.1 42.5 1.0
C4A A:MNH201 3.1 39.4 1.0
C1A A:MNH201 3.2 40.4 1.0
C4B A:MNH201 3.2 40.2 1.0
C1B A:MNH201 3.2 39.9 1.0
C1D A:MNH201 3.2 41.3 1.0
C4C A:MNH201 3.2 40.5 1.0
HE1 A:HIS103 3.2 51.0 1.0
CD2 A:HIS103 3.2 42.5 1.0
CHB A:MNH201 3.2 39.8 1.0
CHA A:MNH201 3.2 41.1 1.0
C1C A:MNH201 3.3 40.7 1.0
CHD A:MNH201 3.3 40.5 1.0
CHC A:MNH201 3.4 40.5 1.0
HD2 A:HIS103 3.4 51.0 1.0
HD11 A:LEU145 4.0 47.9 1.0
HD12 A:LEU77 4.1 48.4 1.0
HD23 A:LEU115 4.2 53.1 1.0
HHA A:MNH201 4.2 49.3 1.0
HHB A:MNH201 4.2 47.7 1.0
HHD A:MNH201 4.2 48.7 1.0
ND1 A:HIS103 4.3 39.9 1.0
HHC A:MNH201 4.3 48.6 1.0
C3B A:MNH201 4.4 40.6 1.0
CG A:HIS103 4.4 43.5 1.0
C3D A:MNH201 4.4 42.1 1.0
C2A A:MNH201 4.4 39.3 1.0
C3A A:MNH201 4.4 38.4 1.0
C3C A:MNH201 4.4 40.6 1.0
C2D A:MNH201 4.5 41.7 1.0
C2B A:MNH201 4.5 40.1 1.0
HD13 A:LEU77 4.5 48.4 1.0
C2C A:MNH201 4.6 41.1 1.0
HD22 A:LEU115 4.6 53.1 1.0
HD21 A:LEU115 4.6 53.1 1.0
HG23 A:ILE98 4.6 50.6 1.0
CD2 A:LEU115 4.7 44.2 1.0
CD1 A:LEU77 4.7 40.3 1.0
HG21 A:VAL106 4.8 49.1 1.0
HG22 A:ILE102 4.8 48.2 1.0
HD2 A:PRO116 4.8 47.6 1.0
HD12 A:LEU145 4.8 47.9 1.0
HG23 A:ILE102 4.8 48.2 1.0
CD1 A:LEU145 4.8 39.9 1.0
HD11 A:LEU77 4.9 48.4 1.0

Manganese binding site 2 out of 2 in 4u9j

Go back to Manganese Binding Sites List in 4u9j
Manganese 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 Manganese with other atoms in the Mn 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:Mn201

b:53.7
occ:1.00
MN B:MNH201 0.0 53.7 1.0
ND B:MNH201 2.1 54.0 1.0
NA B:MNH201 2.1 50.9 1.0
NB B:MNH201 2.2 55.3 1.0
NC B:MNH201 2.2 57.6 1.0
NE2 B:HIS103 2.3 59.1 1.0
C4D B:MNH201 3.0 52.4 1.0
C1A B:MNH201 3.1 48.9 1.0
CHA B:MNH201 3.1 50.1 1.0
C1D B:MNH201 3.2 56.9 1.0
C4A B:MNH201 3.2 50.6 1.0
CHD B:MNH201 3.2 58.9 1.0
C1B B:MNH201 3.2 55.3 1.0
C4C B:MNH201 3.2 59.6 1.0
CE1 B:HIS103 3.2 55.8 1.0
C4B B:MNH201 3.3 57.2 1.0
CHB B:MNH201 3.3 53.0 1.0
C1C B:MNH201 3.3 59.1 1.0
HE1 B:HIS103 3.3 66.9 1.0
CD2 B:HIS103 3.4 63.0 1.0
CHC B:MNH201 3.5 58.3 1.0
HD2 B:HIS103 3.6 75.6 1.0
HHA B:MNH201 4.0 60.1 1.0
HD13 B:LEU77 4.0 71.6 1.0
HD13 B:LEU145 4.1 62.5 1.0
HHD B:MNH201 4.1 70.6 1.0
HD23 B:LEU115 4.2 67.2 1.0
HHB B:MNH201 4.2 63.6 1.0
C3D B:MNH201 4.3 53.3 1.0
C2A B:MNH201 4.3 47.3 1.0
C3B B:MNH201 4.4 58.5 1.0
C2D B:MNH201 4.4 57.2 1.0
C3A B:MNH201 4.4 49.0 1.0
HHC B:MNH201 4.4 70.0 1.0
ND1 B:HIS103 4.4 58.0 1.0
HD11 B:LEU77 4.4 71.6 1.0
C3C B:MNH201 4.5 63.0 1.0
CG B:HIS103 4.5 59.2 1.0
C2B B:MNH201 4.5 57.4 1.0
C2C B:MNH201 4.6 62.2 1.0
CD1 B:LEU77 4.7 59.6 1.0
HD2 B:PRO116 4.7 62.3 1.0
HD11 B:LEU145 4.7 62.5 1.0
HD21 B:LEU115 4.8 67.2 1.0
CD2 B:LEU115 4.8 56.0 1.0
HG23 B:ILE98 4.8 69.6 1.0
HD22 B:LEU115 4.9 67.2 1.0
CD1 B:LEU145 4.9 52.1 1.0
HD12 B:LEU77 5.0 71.6 1.0

Reference:

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
Page generated: Tue Dec 15 04:29:22 2020

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