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Copper in PDB 3chx: Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)

Protein crystallography data

The structure of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo), PDB code: 3chx was solved by A.S.Hakemian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.00 / 3.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.810, 184.070, 203.900, 90.00, 90.00, 90.00
R / Rfree (%) 34.2 / 37.7

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) (pdb code 3chx). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo), PDB code: 3chx:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 3chx

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Copper binding site 1 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu661

b:0.5
occ:1.00
OD2 C:ASP129 2.2 0.8 1.0
CE1 C:HIS133 2.3 0.8 1.0
NE2 C:HIS133 2.7 0.8 1.0
CE1 C:HIS146 3.0 0.8 1.0
CG C:ASP129 3.0 0.8 1.0
NE2 C:HIS146 3.0 0.8 1.0
OD1 C:ASP129 3.2 0.8 1.0
ND1 C:HIS133 3.3 0.8 1.0
ND1 C:HIS146 3.4 0.8 1.0
CD2 C:HIS146 3.5 0.8 1.0
CG C:HIS146 3.7 0.8 1.0
CD2 C:HIS133 3.8 0.8 1.0
OE1 B:GLU200 3.8 0.8 1.0
O C:ASP129 4.0 0.8 1.0
CG C:HIS133 4.1 0.8 1.0
CD B:GLU200 4.2 0.8 1.0
CG B:GLU200 4.2 0.8 1.0
CB C:ASP129 4.3 0.8 1.0
NH2 B:ARG203 4.7 0.8 1.0
CB C:HIS146 4.7 0.8 1.0
NE C:ARG138 4.8 0.8 1.0
C C:ASP129 4.9 0.8 1.0
CD C:ARG138 4.9 0.8 1.0

Copper binding site 2 out of 9 in 3chx

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Copper binding site 2 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu711

b:0.3
occ:1.00
CD2 A:HIS144 2.7 0.8 1.0
CD2 A:HIS146 2.7 0.8 1.0
CB A:HIS40 3.0 0.8 1.0
CU A:CU712 3.1 0.7 1.0
CG A:HIS40 3.1 0.8 1.0
CG A:HIS146 3.3 0.8 1.0
CG A:HIS144 3.4 0.8 1.0
NE2 A:HIS146 3.5 0.8 1.0
CB A:HIS144 3.6 0.8 1.0
CD2 A:HIS40 3.6 0.8 1.0
N A:HIS146 3.6 0.8 1.0
ND1 A:HIS40 3.7 0.8 1.0
CB A:HIS146 3.7 0.8 1.0
NE2 A:HIS144 3.8 0.8 1.0
C A:HIS144 4.0 0.8 1.0
N A:VAL145 4.0 0.8 1.0
O A:HIS144 4.2 0.8 1.0
CA A:HIS146 4.2 0.8 1.0
C A:VAL145 4.3 0.8 1.0
NE2 A:HIS40 4.3 0.8 1.0
ND1 A:HIS146 4.3 0.8 1.0
CA A:VAL145 4.3 0.8 1.0
CA A:HIS40 4.3 0.8 1.0
CE1 A:HIS40 4.4 0.8 1.0
CE1 A:HIS146 4.4 0.8 1.0
CA A:HIS144 4.4 0.8 1.0
O A:HIS40 4.5 0.8 1.0
ND1 A:HIS144 4.7 0.8 1.0
C A:HIS40 4.7 0.8 1.0
OE2 A:GLU42 4.7 0.8 1.0
CE1 A:HIS144 4.8 0.8 1.0
N A:HIS40 4.9 0.8 1.0
O A:GLY99 4.9 0.8 1.0

Copper binding site 3 out of 9 in 3chx

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Copper binding site 3 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu712

b:0.7
occ:1.00
ND1 A:HIS40 2.7 0.8 1.0
OE2 A:GLU42 3.1 0.8 1.0
CU A:CU711 3.1 0.3 1.0
CG A:HIS40 3.3 0.8 1.0
N A:HIS40 3.5 0.8 1.0
CB A:HIS40 3.5 0.8 1.0
CE1 A:HIS40 3.5 0.8 1.0
NE2 A:HIS146 3.5 0.8 1.0
CD2 A:HIS146 3.6 0.8 1.0
CD A:GLU42 3.7 0.8 1.0
CD2 A:HIS144 3.8 0.8 1.0
CA A:HIS40 3.9 0.8 1.0
OE1 A:GLU42 4.1 0.8 1.0
CG A:HIS144 4.3 0.8 1.0
CD2 A:HIS40 4.3 0.8 1.0
C A:HIS40 4.3 0.8 1.0
NE2 A:HIS144 4.4 0.8 1.0
NE2 A:HIS40 4.4 0.8 1.0
CG A:GLU42 4.6 0.8 1.0
N A:GLY41 4.6 0.8 1.0
CB A:HIS144 4.6 0.8 1.0
CE1 A:HIS146 4.8 0.8 1.0
O A:HIS40 4.8 0.8 1.0
CG A:HIS146 4.9 0.8 1.0

Copper binding site 4 out of 9 in 3chx

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Copper binding site 4 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu662

b:0.5
occ:1.00
OD2 G:ASP129 2.2 0.8 1.0
CE1 G:HIS133 2.3 0.8 1.0
NE2 G:HIS133 2.7 0.8 1.0
CE1 G:HIS146 3.0 0.8 1.0
CG G:ASP129 3.0 0.8 1.0
NE2 G:HIS146 3.0 0.8 1.0
OD1 G:ASP129 3.2 0.8 1.0
ND1 G:HIS133 3.3 0.8 1.0
ND1 G:HIS146 3.4 0.8 1.0
CD2 G:HIS146 3.5 0.8 1.0
CG G:HIS146 3.7 0.8 1.0
CD2 G:HIS133 3.8 0.8 1.0
OE1 F:GLU200 3.8 0.8 1.0
O G:ASP129 4.0 0.8 1.0
CG G:HIS133 4.1 0.8 1.0
CD F:GLU200 4.2 0.8 1.0
CG F:GLU200 4.2 0.8 1.0
CB G:ASP129 4.3 0.8 1.0
NH2 F:ARG203 4.7 0.8 1.0
CB G:HIS146 4.7 0.8 1.0
NE G:ARG138 4.8 0.8 1.0
C G:ASP129 4.9 0.8 1.0
CD G:ARG138 4.9 0.8 1.0

Copper binding site 5 out of 9 in 3chx

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Copper binding site 5 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu721

b:0.3
occ:1.00
CD2 E:HIS144 2.7 0.8 1.0
CD2 E:HIS146 2.7 0.8 1.0
CB E:HIS40 3.0 0.8 1.0
CU E:CU722 3.1 0.7 1.0
CG E:HIS40 3.1 0.8 1.0
CG E:HIS146 3.3 0.8 1.0
CG E:HIS144 3.4 0.8 1.0
NE2 E:HIS146 3.5 0.8 1.0
CB E:HIS144 3.6 0.8 1.0
CD2 E:HIS40 3.6 0.8 1.0
N E:HIS146 3.6 0.8 1.0
ND1 E:HIS40 3.7 0.8 1.0
CB E:HIS146 3.7 0.8 1.0
NE2 E:HIS144 3.8 0.8 1.0
C E:HIS144 4.0 0.8 1.0
N E:VAL145 4.0 0.8 1.0
O E:HIS144 4.2 0.8 1.0
CA E:HIS146 4.2 0.8 1.0
C E:VAL145 4.3 0.8 1.0
NE2 E:HIS40 4.3 0.8 1.0
ND1 E:HIS146 4.3 0.8 1.0
CA E:VAL145 4.3 0.8 1.0
CA E:HIS40 4.3 0.8 1.0
CE1 E:HIS40 4.4 0.8 1.0
CE1 E:HIS146 4.4 0.8 1.0
CA E:HIS144 4.4 0.8 1.0
O E:HIS40 4.5 0.8 1.0
ND1 E:HIS144 4.7 0.8 1.0
C E:HIS40 4.7 0.8 1.0
OE2 E:GLU42 4.7 0.8 1.0
CE1 E:HIS144 4.8 0.8 1.0
N E:HIS40 4.9 0.8 1.0
O E:GLY99 4.9 0.8 1.0

Copper binding site 6 out of 9 in 3chx

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Copper binding site 6 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu722

b:0.7
occ:1.00
ND1 E:HIS40 2.7 0.8 1.0
OE2 E:GLU42 3.1 0.8 1.0
CU E:CU721 3.1 0.3 1.0
CG E:HIS40 3.3 0.8 1.0
N E:HIS40 3.5 0.8 1.0
CB E:HIS40 3.5 0.8 1.0
CE1 E:HIS40 3.5 0.8 1.0
NE2 E:HIS146 3.5 0.8 1.0
CD2 E:HIS146 3.6 0.8 1.0
CD E:GLU42 3.7 0.8 1.0
CD2 E:HIS144 3.8 0.8 1.0
CA E:HIS40 3.9 0.8 1.0
OE1 E:GLU42 4.1 0.8 1.0
CG E:HIS144 4.3 0.8 1.0
CD2 E:HIS40 4.3 0.8 1.0
C E:HIS40 4.3 0.8 1.0
NE2 E:HIS144 4.4 0.8 1.0
NE2 E:HIS40 4.4 0.8 1.0
CG E:GLU42 4.6 0.8 1.0
N E:GLY41 4.6 0.8 1.0
CB E:HIS144 4.6 0.8 1.0
CE1 E:HIS146 4.8 0.8 1.0
O E:HIS40 4.8 0.8 1.0
CG E:HIS146 4.9 0.8 1.0

Copper binding site 7 out of 9 in 3chx

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Copper binding site 7 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu663

b:0.5
occ:1.00
OD2 K:ASP129 2.2 0.8 1.0
CE1 K:HIS133 2.3 0.8 1.0
NE2 K:HIS133 2.7 0.8 1.0
CE1 K:HIS146 3.0 0.8 1.0
CG K:ASP129 3.0 0.8 1.0
NE2 K:HIS146 3.0 0.8 1.0
OD1 K:ASP129 3.2 0.8 1.0
ND1 K:HIS133 3.3 0.8 1.0
ND1 K:HIS146 3.4 0.8 1.0
CD2 K:HIS146 3.5 0.8 1.0
CG K:HIS146 3.7 0.8 1.0
CD2 K:HIS133 3.8 0.8 1.0
OE1 J:GLU200 3.8 0.8 1.0
O K:ASP129 4.0 0.8 1.0
CG K:HIS133 4.1 0.8 1.0
CD J:GLU200 4.2 0.8 1.0
CG J:GLU200 4.2 0.8 1.0
CB K:ASP129 4.3 0.8 1.0
NH2 J:ARG203 4.7 0.8 1.0
CB K:HIS146 4.7 0.8 1.0
NE K:ARG138 4.8 0.8 1.0
C K:ASP129 4.9 0.8 1.0
CD K:ARG138 4.9 0.8 1.0

Copper binding site 8 out of 9 in 3chx

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Copper binding site 8 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu731

b:0.3
occ:1.00
CD2 I:HIS144 2.7 0.8 1.0
CD2 I:HIS146 2.7 0.8 1.0
CB I:HIS40 3.0 0.8 1.0
CU I:CU732 3.1 0.7 1.0
CG I:HIS40 3.1 0.8 1.0
CG I:HIS146 3.3 0.8 1.0
CG I:HIS144 3.4 0.8 1.0
NE2 I:HIS146 3.5 0.8 1.0
CB I:HIS144 3.6 0.8 1.0
CD2 I:HIS40 3.6 0.8 1.0
N I:HIS146 3.6 0.8 1.0
ND1 I:HIS40 3.7 0.8 1.0
CB I:HIS146 3.7 0.8 1.0
NE2 I:HIS144 3.8 0.8 1.0
C I:HIS144 4.0 0.8 1.0
N I:VAL145 4.0 0.8 1.0
O I:HIS144 4.2 0.8 1.0
CA I:HIS146 4.2 0.8 1.0
C I:VAL145 4.3 0.8 1.0
NE2 I:HIS40 4.3 0.8 1.0
ND1 I:HIS146 4.3 0.8 1.0
CA I:VAL145 4.3 0.8 1.0
CA I:HIS40 4.3 0.8 1.0
CE1 I:HIS40 4.4 0.8 1.0
CE1 I:HIS146 4.4 0.8 1.0
CA I:HIS144 4.4 0.8 1.0
O I:HIS40 4.5 0.8 1.0
ND1 I:HIS144 4.7 0.8 1.0
C I:HIS40 4.7 0.8 1.0
OE2 I:GLU42 4.7 0.8 1.0
CE1 I:HIS144 4.8 0.8 1.0
N I:HIS40 4.9 0.8 1.0
O I:GLY99 4.9 0.8 1.0

Copper binding site 9 out of 9 in 3chx

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Copper binding site 9 out of 9 in the Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Methylosinus Trichosporium OB3B Particulate Methane Monooxygenase (Pmmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu732

b:0.7
occ:1.00
ND1 I:HIS40 2.7 0.8 1.0
OE2 I:GLU42 3.1 0.8 1.0
CU I:CU731 3.1 0.3 1.0
CG I:HIS40 3.3 0.8 1.0
N I:HIS40 3.5 0.8 1.0
CB I:HIS40 3.5 0.8 1.0
CE1 I:HIS40 3.5 0.8 1.0
NE2 I:HIS146 3.5 0.8 1.0
CD2 I:HIS146 3.6 0.8 1.0
CD I:GLU42 3.7 0.8 1.0
CD2 I:HIS144 3.8 0.8 1.0
CA I:HIS40 3.9 0.8 1.0
OE1 I:GLU42 4.1 0.8 1.0
CG I:HIS144 4.3 0.8 1.0
CD2 I:HIS40 4.3 0.8 1.0
C I:HIS40 4.3 0.8 1.0
NE2 I:HIS144 4.4 0.8 1.0
NE2 I:HIS40 4.4 0.8 1.0
CG I:GLU42 4.6 0.8 1.0
N I:GLY41 4.6 0.8 1.0
CB I:HIS144 4.6 0.8 1.0
CE1 I:HIS146 4.8 0.8 1.0
O I:HIS40 4.8 0.8 1.0
CG I:HIS146 4.9 0.8 1.0

Reference:

A.S.Hakemian, K.C.Kondapalli, J.Telser, B.M.Hoffman, T.L.Stemmler, A.C.Rosenzweig. The Metal Centers of Particulate Methane Monooxygenase From Methylosinus Trichosporium OB3B. Biochemistry V. 47 6793 2008.
ISSN: ISSN 0006-2960
PubMed: 18540635
DOI: 10.1021/BI800598H
Page generated: Sun Dec 13 11:09:18 2020

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