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Zinc in PDB 1yew: Crystal Structure of Particulate Methane Monooxygenase

Protein crystallography data

The structure of Crystal Structure of Particulate Methane Monooxygenase, PDB code: 1yew was solved by R.L.Lieberman, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.55 / 2.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 264.140, 264.140, 150.005, 90.00, 90.00, 90.00
R / Rfree (%) 27.2 / 30.2

Other elements in 1yew:

The structure of Crystal Structure of Particulate Methane Monooxygenase also contains other interesting chemical elements:

Copper (Cu) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Particulate Methane Monooxygenase (pdb code 1yew). 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 Particulate Methane Monooxygenase, PDB code: 1yew:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1yew

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Zinc binding site 1 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:77.4
occ:1.00
OE2 A:GLU57 2.3 75.3 1.0
OE1 A:GLU57 2.7 76.9 1.0
CD A:GLU57 2.8 75.0 1.0
NZ A:LYS155 4.2 66.0 1.0
CG A:GLU57 4.3 72.5 1.0
CE A:LYS155 4.7 66.8 1.0
O A:GLY335 4.9 69.5 1.0
CA A:GLY335 5.0 69.9 1.0

Zinc binding site 2 out of 8 in 1yew

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Zinc binding site 2 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn661

b:73.7
occ:1.00
NE2 C:HIS160 1.7 68.0 1.0
NE2 C:HIS173 2.2 71.1 1.0
OD2 C:ASP156 2.4 69.3 1.0
CE1 C:HIS160 2.7 68.5 1.0
CD2 C:HIS160 2.8 68.5 1.0
OD1 C:ASP156 2.8 71.3 1.0
CG C:ASP156 2.9 69.7 1.0
OE1 B:GLU195 2.9 72.7 1.0
CE1 C:HIS173 3.0 71.5 1.0
CD B:GLU195 3.1 73.6 1.0
CD2 C:HIS173 3.3 71.1 1.0
CG B:GLU195 3.3 75.6 1.0
OE2 B:GLU195 3.7 72.2 1.0
ND1 C:HIS160 3.8 68.1 1.0
CG C:HIS160 3.8 68.4 1.0
CD B:ARG198 4.0 73.8 1.0
ND1 C:HIS173 4.2 71.1 1.0
NH1 B:ARG198 4.3 76.2 1.0
CG C:HIS173 4.3 70.1 1.0
CB C:ASP156 4.4 69.5 1.0
CE1 C:PHE177 4.6 71.8 1.0
OE1 C:GLU176 4.6 70.1 1.0
CZ C:PHE177 4.6 71.7 1.0
CB B:GLU195 4.7 76.0 1.0
O C:ASP156 4.8 68.9 1.0
NE B:ARG198 4.9 76.0 1.0
CG B:ARG198 4.9 72.9 1.0

Zinc binding site 3 out of 8 in 1yew

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Zinc binding site 3 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn700

b:46.1
occ:0.50
NE2 C:HIS231 1.6 69.1 1.0
CE1 C:HIS231 2.6 69.0 1.0
CD2 C:HIS231 2.7 69.3 1.0
CG B:HIS11 3.0 70.1 1.0
ND1 B:HIS11 3.2 69.8 1.0
CD2 B:HIS11 3.3 70.2 1.0
CB B:HIS11 3.4 69.8 1.0
ND1 C:HIS231 3.7 69.0 1.0
CE1 B:HIS11 3.7 69.8 1.0
NE2 B:HIS11 3.7 70.2 1.0
CG C:HIS231 3.8 68.8 1.0
CD1 C:TRP234 3.9 71.6 1.0
NE1 C:TRP234 4.3 71.2 1.0
CB C:PHE233 4.9 70.0 1.0
CA B:HIS11 4.9 70.0 1.0
CG C:TRP234 5.0 71.4 1.0

Zinc binding site 4 out of 8 in 1yew

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Zinc binding site 4 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn900

b:76.9
occ:1.00
OD2 E:ASP328 2.3 77.0 1.0
OD1 E:ASP326 2.4 71.2 1.0
ZN E:ZN702 2.9 0.3 1.0
CG E:ASP326 3.1 69.5 1.0
OD2 E:ASP326 3.3 71.7 1.0
CG E:ASP328 3.4 72.7 1.0
OD1 E:ASP344 3.7 68.2 1.0
CB E:ASP328 3.8 69.8 1.0
N E:ASP328 4.2 68.8 1.0
OD2 E:ASP344 4.2 67.4 1.0
CG E:ASP344 4.4 68.1 1.0
CB E:ASP326 4.4 68.1 1.0
N E:SER327 4.6 68.0 1.0
OD1 E:ASP328 4.6 73.3 1.0
CA E:ASP326 4.6 67.9 1.0
CA E:ASP328 4.6 69.2 1.0
O E:LEU346 4.7 70.0 1.0
C E:ASP326 4.8 67.7 1.0

Zinc binding site 5 out of 8 in 1yew

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Zinc binding site 5 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:56.0
occ:0.50
CE1 E:HIS307 2.7 68.7 1.0
NE2 E:HIS307 2.9 68.8 1.0
ND1 E:HIS307 3.8 67.3 1.0
CD2 E:HIS307 4.0 69.1 1.0
CG E:HIS307 4.5 69.6 1.0
OG1 E:THR305 4.9 68.3 1.0

Zinc binding site 6 out of 8 in 1yew

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Zinc binding site 6 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn702

b:0.3
occ:1.00
ZN E:ZN900 2.9 76.9 1.0
CB E:SER347 3.2 71.1 1.0
CA E:SER347 3.7 70.7 1.0
O E:LEU346 4.3 70.0 1.0
OD2 E:ASP344 4.5 67.4 1.0
OG E:SER347 4.5 72.2 1.0
N E:VAL348 4.6 69.9 1.0
OD2 E:ASP326 4.7 71.7 1.0
C E:SER347 4.7 70.5 1.0
N E:SER347 4.7 70.1 1.0
OD1 E:ASP326 4.8 71.2 1.0
OD1 E:ASP344 4.8 68.2 1.0
C E:LEU346 4.9 69.9 1.0
CG E:ASP326 4.9 69.5 1.0
OD2 E:ASP328 4.9 77.0 1.0

Zinc binding site 7 out of 8 in 1yew

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Zinc binding site 7 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn662

b:46.5
occ:1.00
NE2 G:HIS160 1.8 69.3 1.0
NE2 G:HIS173 1.9 70.7 1.0
OD2 G:ASP156 2.2 69.0 1.0
OD1 G:ASP156 2.6 70.1 1.0
CG G:ASP156 2.7 69.3 1.0
CE1 G:HIS160 2.8 68.9 1.0
CD2 G:HIS160 2.8 69.0 1.0
CD2 G:HIS173 2.8 71.2 1.0
CE1 G:HIS173 2.9 71.3 1.0
OE1 F:GLU195 3.2 72.9 1.0
CD F:GLU195 3.3 73.8 1.0
CG F:GLU195 3.5 75.7 1.0
ND1 G:HIS160 3.8 68.1 1.0
CG G:HIS160 3.9 68.2 1.0
OE2 F:GLU195 3.9 72.4 1.0
ND1 G:HIS173 4.0 71.1 1.0
CG G:HIS173 4.0 70.1 1.0
CB G:ASP156 4.2 69.5 1.0
CD F:ARG198 4.3 73.7 1.0
OE1 G:GLU176 4.3 70.2 1.0
CE1 G:PHE177 4.4 71.8 1.0
CZ G:PHE177 4.5 71.7 1.0
NH1 F:ARG198 4.6 76.2 1.0
O G:ASP156 4.7 69.0 1.0
CB F:GLU195 4.9 76.0 1.0

Zinc binding site 8 out of 8 in 1yew

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Zinc binding site 8 out of 8 in the Crystal Structure of Particulate Methane Monooxygenase


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 Particulate Methane Monooxygenase within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn663

b:60.5
occ:1.00
NE2 K:HIS160 1.7 68.1 1.0
NE2 K:HIS173 2.2 71.1 1.0
OD2 K:ASP156 2.4 69.2 1.0
CE1 K:HIS160 2.6 68.5 1.0
CD2 K:HIS160 2.8 68.5 1.0
OE1 J:GLU195 2.9 72.9 1.0
CE1 K:HIS173 2.9 71.5 1.0
OD1 K:ASP156 2.9 71.1 1.0
CG K:ASP156 3.0 69.7 1.0
CD J:GLU195 3.0 73.6 1.0
CG J:GLU195 3.2 75.4 1.0
CD2 K:HIS173 3.3 71.0 1.0
OE2 J:GLU195 3.7 72.3 1.0
ND1 K:HIS160 3.8 68.2 1.0
CG K:HIS160 3.9 68.3 1.0
ND1 K:HIS173 4.1 71.4 1.0
CD J:ARG198 4.2 73.9 1.0
CG K:HIS173 4.3 70.0 1.0
NH1 J:ARG198 4.4 76.2 1.0
CE1 K:PHE177 4.5 71.8 1.0
CB K:ASP156 4.5 69.5 1.0
CB J:GLU195 4.5 76.0 1.0
CZ K:PHE177 4.6 71.8 1.0
OE1 K:GLU176 4.7 70.2 1.0
O K:ASP156 4.9 69.1 1.0

Reference:

R.L.Lieberman, A.C.Rosenzweig. Crystal Structure of A Membrane-Bound Metalloenzyme That Catalyses the Biological Oxidation of Methane. Nature V. 434 177 2005.
ISSN: ISSN 0028-0836
PubMed: 15674245
DOI: 10.1038/NATURE03311
Page generated: Wed Dec 16 03:14:21 2020

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