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Zinc in PDB 3rfr: Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M

Protein crystallography data

The structure of Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M, PDB code: 3rfr was solved by S.M.Smith, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.79 / 2.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 107.718, 178.310, 183.147, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.1

Other elements in 3rfr:

The structure of Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M also contains other interesting chemical elements:

Copper (Cu) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M (pdb code 3rfr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M, PDB code: 3rfr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3rfr

Go back to Zinc Binding Sites List in 3rfr
Zinc binding site 1 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn421

b:88.3
occ:1.00
ND2 A:ASN178 2.9 68.7 1.0
OD1 A:ASN178 3.7 67.0 1.0
CG A:ASN178 3.7 66.5 1.0
O A:PHE162 3.8 76.8 1.0
OD2 A:ASP175 4.0 74.7 1.0
O A:LYS160 4.2 82.7 1.0
CG A:GLU177 4.8 63.3 1.0
C A:PHE162 5.0 76.8 1.0

Zinc binding site 2 out of 9 in 3rfr

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Zinc binding site 2 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn257

b:57.9
occ:1.00
OD2 C:ASP129 1.9 57.8 1.0
NE2 C:HIS133 1.9 59.8 1.0
NE2 C:HIS146 2.0 56.7 1.0
O C:HOH259 2.3 34.0 1.0
CG C:ASP129 2.7 57.2 1.0
CE1 C:HIS133 2.9 59.6 1.0
OD1 C:ASP129 2.9 58.5 1.0
CE1 C:HIS146 2.9 57.7 1.0
CD2 C:HIS133 3.0 60.0 1.0
CD2 C:HIS146 3.1 58.1 1.0
ND1 C:HIS133 4.0 59.5 1.0
ND1 C:HIS146 4.1 57.2 1.0
CG C:HIS133 4.1 59.6 1.0
CB C:ASP129 4.1 55.2 1.0
CG C:HIS146 4.2 58.4 1.0
CE1 C:PHE150 4.6 60.9 1.0
OE1 C:GLU149 4.6 63.4 1.0
O C:ASP129 4.8 56.6 1.0

Zinc binding site 3 out of 9 in 3rfr

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Zinc binding site 3 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn258

b:87.8
occ:1.00
OD2 C:ASP93 2.3 89.5 1.0
CE1 C:HIS177 2.4 77.2 1.0
ND1 C:HIS177 2.6 76.4 1.0
OD1 C:ASP93 2.7 88.5 1.0
CG C:ASP93 2.8 88.3 1.0
NE2 C:HIS177 3.7 78.0 1.0
CG C:HIS177 4.0 75.0 1.0
CB C:ASP93 4.3 87.6 1.0
CD2 C:HIS177 4.5 76.4 1.0
CG1 C:VAL92 4.8 86.2 1.0

Zinc binding site 4 out of 9 in 3rfr

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Zinc binding site 4 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn257

b:64.1
occ:1.00
OD2 G:ASP129 1.8 58.4 1.0
NE2 G:HIS146 2.0 58.3 1.0
NE2 G:HIS133 2.0 60.1 1.0
O G:HOH259 2.6 18.1 1.0
CG G:ASP129 2.7 58.0 1.0
CE1 G:HIS146 2.9 59.3 1.0
CE1 G:HIS133 2.9 60.3 1.0
OD1 G:ASP129 3.0 59.2 1.0
CD2 G:HIS146 3.1 60.1 1.0
CD2 G:HIS133 3.1 60.7 1.0
ND1 G:HIS146 4.0 59.6 1.0
ND1 G:HIS133 4.1 60.3 1.0
CB G:ASP129 4.1 56.1 1.0
CG G:HIS146 4.2 60.9 1.0
CG G:HIS133 4.2 60.5 1.0
CE1 G:PHE150 4.4 62.0 1.0
OE1 G:GLU149 4.6 65.5 1.0
O G:ASP129 5.0 57.4 1.0
CZ G:PHE150 5.0 61.9 1.0

Zinc binding site 5 out of 9 in 3rfr

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Zinc binding site 5 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn258

b:0.5
occ:1.00
OD2 G:ASP93 2.1 0.3 1.0
CG G:ASP93 2.9 0.7 1.0
OD1 G:ASP93 3.1 0.5 1.0
CE1 G:HIS177 3.1 96.3 1.0
ND1 G:HIS177 3.3 95.6 1.0
CB G:ASP93 4.3 0.4 1.0
NE2 G:HIS177 4.4 96.3 1.0
CG G:HIS177 4.7 93.1 1.0

Zinc binding site 6 out of 9 in 3rfr

Go back to Zinc Binding Sites List in 3rfr
Zinc binding site 6 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn257

b:70.9
occ:1.00
NE2 K:HIS146 1.7 62.4 1.0
O K:HOH259 2.0 22.4 1.0
NE2 K:HIS133 2.1 64.8 1.0
OD2 K:ASP129 2.2 61.4 1.0
CE1 K:HIS146 2.6 63.8 1.0
CD2 K:HIS146 2.7 63.7 1.0
OD1 K:ASP129 2.8 63.0 1.0
CG K:ASP129 2.8 61.1 1.0
CE1 K:HIS133 2.9 64.9 1.0
CD2 K:HIS133 3.3 64.3 1.0
ND1 K:HIS146 3.7 63.1 1.0
CG K:HIS146 3.8 64.4 1.0
ND1 K:HIS133 4.1 65.0 1.0
CB K:ASP129 4.3 58.6 1.0
CG K:HIS133 4.3 64.2 1.0
CE1 K:PHE150 4.5 65.8 1.0
OE1 K:GLU149 4.6 67.0 1.0

Zinc binding site 7 out of 9 in 3rfr

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Zinc binding site 7 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn258

b:0.9
occ:1.00
ND1 K:HIS177 2.7 81.0 1.0
OD2 K:ASP93 2.9 92.9 1.0
CE1 K:HIS177 3.0 81.3 1.0
OD1 K:ASP93 3.7 91.6 1.0
CG K:ASP93 3.7 91.4 1.0
CG K:HIS177 4.1 79.6 1.0
NE2 K:HIS177 4.3 81.8 1.0
CB K:HIS177 4.8 78.4 1.0
CD2 K:HIS177 4.8 80.5 1.0

Zinc binding site 8 out of 9 in 3rfr

Go back to Zinc Binding Sites List in 3rfr
Zinc binding site 8 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn421

b:90.8
occ:1.00
ND2 E:ASN178 3.1 64.2 1.0
OD1 E:ASN178 3.9 63.6 1.0
O E:PHE162 3.9 73.3 1.0
CG E:ASN178 3.9 62.7 1.0
O E:LYS160 4.0 79.9 1.0
OD2 E:ASP175 4.2 70.2 1.0

Zinc binding site 9 out of 9 in 3rfr

Go back to Zinc Binding Sites List in 3rfr
Zinc binding site 9 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn421

b:70.4
occ:1.00
ND2 I:ASN178 3.1 45.1 1.0
O I:PHE162 3.7 53.9 1.0
O I:LYS160 3.8 57.0 1.0
OD1 I:ASN178 3.9 44.6 1.0
CG I:ASN178 3.9 43.3 1.0
OD2 I:ASP175 4.1 51.4 1.0
C I:PHE162 4.9 53.5 1.0
CG I:GLU177 5.0 41.4 1.0

Reference:

S.M.Smith, S.Rawat, J.Telser, B.M.Hoffman, T.L.Stemmler, A.C.Rosenzweig. Crystal Structure and Characterization of Particulate Methane Monooxygenase From Methylocystis Species Strain M. Biochemistry V. 50 10231 2011.
ISSN: ISSN 0006-2960
PubMed: 22013879
DOI: 10.1021/BI200801Z
Page generated: Wed Dec 16 04:47:19 2020

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