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Copper in PDB 4phz: Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)

Enzymatic activity of Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)

All present enzymatic activity of Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell):
1.14.18.3;

Protein crystallography data

The structure of Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell), PDB code: 4phz was solved by S.Sirajuddin, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.462, 184.531, 189.417, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) (pdb code 4phz). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell), PDB code: 4phz:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4phz

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Copper binding site 1 out of 6 in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)


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 Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu301

b:62.6
occ:0.81
 OD2 K:ASP129 1.7 49.5 1.0
NE2 K:HIS146 2.2 48.0 1.0
NE2 K:HIS133 2.3 66.2 1.0
CG K:ASP129 2.8 45.7 1.0
CD2 K:HIS146 3.1 46.0 1.0
CE1 K:HIS133 3.1 67.4 1.0
CE1 K:HIS146 3.2 45.3 1.0
CD2 K:HIS133 3.3 62.8 1.0
OD1 K:ASP129 3.3 50.9 1.0
CB K:ASP129 4.1 41.2 1.0
CG K:HIS146 4.2 44.0 1.0
ND1 K:HIS146 4.3 44.3 1.0
ND1 K:HIS133 4.3 64.7 1.0
OE2 K:GLU149 4.4 53.7 1.0
CZ K:PHE150 4.4 50.5 1.0
CE2 K:PHE150 4.4 49.0 1.0
CG K:HIS133 4.4 59.0 1.0
O K:ASP129 4.9 33.4 1.0

Copper binding site 2 out of 6 in 4phz

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Copper binding site 2 out of 6 in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)


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 Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:49.7
occ:0.76
 NE2 A:HIS135 2.1 29.9 1.0
ND1 A:HIS133 2.4 68.6 1.0
CG A:HIS29 2.8 76.1 1.0
CE1 A:HIS135 2.9 30.8 1.0
ND1 A:HIS29 2.9 77.6 1.0
CD2 A:HIS29 3.0 74.8 1.0
CE1 A:HIS29 3.1 71.3 1.0
NE2 A:HIS29 3.1 73.3 1.0
CE1 A:HIS133 3.3 68.3 1.0
CD2 A:HIS135 3.3 29.8 1.0
CA A:HIS29 3.4 69.3 1.0
CG A:HIS133 3.4 63.6 1.0
CB A:HIS29 3.6 70.3 1.0
N A:HIS29 3.6 62.9 1.0
CB A:HIS133 3.8 57.7 1.0
ND1 A:HIS135 4.1 32.4 1.0
CG A:HIS135 4.3 31.5 1.0
O A:HIS133 4.3 56.8 1.0
OE2 A:GLU31 4.4 94.1 1.0
OE1 A:GLU31 4.4 83.4 1.0
NE2 A:HIS133 4.5 66.7 1.0
CD2 A:HIS133 4.6 66.1 1.0
C A:HIS29 4.7 68.6 1.0
C A:HIS133 4.8 54.0 1.0
CD A:GLU31 4.8 82.0 1.0
CA A:HIS133 4.9 56.9 1.0

Copper binding site 3 out of 6 in 4phz

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Copper binding site 3 out of 6 in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)


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 Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:24.7
occ:0.74
 NE2 E:HIS135 1.9 12.7 1.0
ND1 E:HIS133 2.3 27.3 1.0
CE1 E:HIS135 2.7 13.0 1.0
CD2 E:HIS135 3.0 12.9 1.0
CE1 E:HIS133 3.1 25.9 1.0
CG E:HIS29 3.1 45.7 1.0
ND1 E:HIS29 3.1 47.3 1.0
CD2 E:HIS29 3.3 47.4 1.0
CE1 E:HIS29 3.3 46.7 1.0
CG E:HIS133 3.3 25.9 1.0
NE2 E:HIS29 3.4 46.5 1.0
CA E:HIS29 3.5 47.6 1.0
N E:HIS29 3.7 46.8 1.0
CB E:HIS133 3.7 25.0 1.0
CB E:HIS29 3.8 48.1 1.0
ND1 E:HIS135 3.9 13.3 1.0
CG E:HIS135 4.1 13.6 1.0
O E:HIS133 4.2 26.4 1.0
NE2 E:HIS133 4.3 27.9 1.0
OE2 E:GLU31 4.3 56.3 1.0
OE1 E:GLU31 4.4 53.4 1.0
CD2 E:HIS133 4.4 26.5 1.0
C E:HIS133 4.7 23.3 1.0
CD E:GLU31 4.8 53.3 1.0
C E:HIS29 4.8 50.4 1.0
CA E:HIS133 4.8 25.1 1.0

Copper binding site 4 out of 6 in 4phz

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Copper binding site 4 out of 6 in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)


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 Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu501

b:60.4
occ:0.98
 NE2 I:HIS135 1.9 36.3 1.0
ND1 I:HIS133 2.2 42.6 1.0
O I:HOH607 2.4 29.6 1.0
CD2 I:HIS135 2.8 34.4 1.0
CE1 I:HIS135 3.0 34.2 1.0
ND1 I:HIS29 3.1 75.2 1.0
CE1 I:HIS133 3.2 48.0 1.0
CG I:HIS29 3.2 78.0 1.0
CG I:HIS133 3.2 38.8 1.0
CE1 I:HIS29 3.3 79.4 1.0
CD2 I:HIS29 3.4 83.7 1.0
NE2 I:HIS29 3.5 85.1 1.0
CB I:HIS133 3.5 34.8 1.0
CA I:HIS29 3.6 65.4 1.0
N I:HIS29 3.8 59.2 1.0
O I:HIS133 3.8 36.6 1.0
CB I:HIS29 3.9 68.4 1.0
CG I:HIS135 4.0 33.5 1.0
ND1 I:HIS135 4.1 32.4 1.0
NE2 I:HIS133 4.3 48.5 1.0
C I:HIS133 4.3 38.1 1.0
CD2 I:HIS133 4.4 44.0 1.0
CA I:HIS133 4.6 36.4 1.0
OE1 I:GLU31 4.6 62.3 1.0
OE2 I:GLU31 4.8 71.6 1.0
C I:HIS29 5.0 67.3 1.0

Copper binding site 5 out of 6 in 4phz

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Copper binding site 5 out of 6 in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)


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 Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu301

b:62.2
occ:0.85
 NE2 C:HIS146 1.9 49.1 1.0
NE2 C:HIS133 2.2 53.2 1.0
OD2 C:ASP129 2.3 45.6 1.0
CE1 C:HIS146 2.7 52.7 1.0
CE1 C:HIS133 2.8 55.6 1.0
CD2 C:HIS146 3.0 48.3 1.0
CG C:ASP129 3.3 45.5 1.0
CD2 C:HIS133 3.5 52.0 1.0
OD1 C:ASP129 3.6 49.6 1.0
ND1 C:HIS146 3.9 47.3 1.0
CG C:HIS146 4.1 46.7 1.0
ND1 C:HIS133 4.1 53.1 1.0
CG C:HIS133 4.4 51.8 1.0
CE2 C:PHE150 4.5 55.0 1.0
CZ C:PHE150 4.6 53.7 1.0
CB C:ASP129 4.7 42.5 1.0
OE2 C:GLU149 4.9 48.1 1.0
NE C:ARG138 4.9 92.9 1.0

Copper binding site 6 out of 6 in 4phz

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Copper binding site 6 out of 6 in the Crystal Structure of Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell)


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 Particulate Methane Monooxygenase From Methylocystis Sp. Atcc 49242 (Rockwell) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cu301

b:70.3
occ:0.74
 NE2 G:HIS146 1.9 59.7 1.0
NE2 G:HIS133 2.3 68.1 1.0
OD2 G:ASP129 2.4 46.8 1.0
CE1 G:HIS146 2.7 60.3 1.0
CE1 G:HIS133 2.9 71.2 1.0
CD2 G:HIS146 3.1 54.4 1.0
O G:HOH407 3.3 33.1 1.0
CG G:ASP129 3.4 48.0 1.0
CD2 G:HIS133 3.5 66.0 1.0
OD1 G:ASP129 3.7 51.3 1.0
ND1 G:HIS146 3.9 55.6 1.0
CG G:HIS146 4.1 50.5 1.0
ND1 G:HIS133 4.2 69.0 1.0
O G:HOH402 4.3 34.9 1.0
CE2 G:PHE150 4.4 45.2 1.0
CZ G:PHE150 4.5 47.3 1.0
CG G:HIS133 4.5 61.5 1.0
CB G:ASP129 4.7 45.3 1.0
OE2 G:GLU149 4.8 46.4 1.0
NE G:ARG138 4.9 91.7 1.0
NH1 G:ARG138 5.0 98.9 1.0

Reference:

S.Sirajuddin, D.Barupala, S.Helling, K.Marcus, T.L.Stemmler, A.C.Rosenzweig. Effects of Zinc on Particulate Methane Monooxygenase Activity and Structure. J.Biol.Chem. V. 289 21782 2014.
ISSN: ESSN 1083-351X
PubMed: 24942740
DOI: 10.1074/JBC.M114.581363
Page generated: Wed Jul 31 03:22:34 2024

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