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Copper 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:

Zinc (Zn) 9 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M, PDB code: 3rfr:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 3rfr

Go back to Copper Binding Sites List in 3rfr
Copper binding site 1 out of 4 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu420

b:93.3
occ:1.00
CU1 A:CUA420 0.0 93.3 1.0
ND1 A:HIS29 2.5 74.9 1.0
CA A:HIS29 2.6 71.9 1.0
CU2 A:CUA420 2.7 72.6 1.0
N A:HIS29 2.7 72.6 1.0
OE1 A:GLU31 3.0 72.3 1.0
CE1 A:HIS135 3.1 52.0 1.0
NE2 A:HIS135 3.1 49.6 1.0
CG A:HIS29 3.3 74.3 1.0
CE1 A:HIS29 3.4 75.5 1.0
OE2 A:GLU31 3.5 73.7 1.0
CB A:HIS29 3.5 72.5 1.0
ND1 A:HIS133 3.5 61.8 1.0
CD A:GLU31 3.7 71.6 1.0
C A:HIS29 3.8 71.0 1.0
CE1 A:HIS133 3.9 62.7 1.0
N A:GLY30 4.2 70.0 1.0
CD2 A:HIS29 4.4 75.8 1.0
ND1 A:HIS135 4.4 50.4 1.0
NE2 A:HIS29 4.4 76.8 1.0
CD2 A:HIS135 4.5 51.1 1.0
OH A:TYR341 4.6 71.7 1.0
O A:HIS29 4.6 71.0 1.0
CG A:HIS133 4.7 60.5 1.0
CZ A:TYR341 4.9 70.3 1.0
CE1 A:TYR341 5.0 69.5 1.0

Copper binding site 2 out of 4 in 3rfr

Go back to Copper Binding Sites List in 3rfr
Copper binding site 2 out of 4 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu420

b:72.6
occ:1.00
CU2 A:CUA420 0.0 72.6 1.0
NE2 A:HIS135 1.8 49.6 1.0
ND1 A:HIS133 2.1 61.8 1.0
ND1 A:HIS29 2.5 74.9 1.0
N A:HIS29 2.6 72.6 1.0
CU1 A:CUA420 2.7 93.3 1.0
CD2 A:HIS135 2.7 51.1 1.0
CE1 A:HIS135 2.8 52.0 1.0
CG A:HIS133 2.9 60.5 1.0
CB A:HIS133 3.0 57.4 1.0
CE1 A:HIS133 3.2 62.7 1.0
CE1 A:HIS29 3.3 75.5 1.0
CG A:HIS29 3.5 74.3 1.0
CA A:HIS29 3.5 71.9 1.0
O A:HIS133 3.7 56.3 1.0
CB A:HIS29 3.9 72.5 1.0
CG A:HIS135 3.9 52.3 1.0
ND1 A:HIS135 3.9 50.4 1.0
C A:HIS133 4.0 56.7 1.0
CA A:HIS133 4.1 57.7 1.0
CD2 A:HIS133 4.1 62.9 1.0
NE2 A:HIS133 4.2 63.6 1.0
NE2 A:HIS29 4.4 76.8 1.0
CD2 A:HIS29 4.5 75.8 1.0
N A:VAL134 4.8 56.6 1.0
C A:HIS29 4.9 71.0 1.0
OE1 A:GLU31 5.0 72.3 1.0

Copper binding site 3 out of 4 in 3rfr

Go back to Copper Binding Sites List in 3rfr
Copper binding site 3 out of 4 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu420

b:63.1
occ:1.00
ND1 E:HIS29 2.0 76.6 1.0
ND1 E:HIS133 2.1 63.3 1.0
NE2 E:HIS135 2.2 50.7 1.0
N E:HIS29 2.6 73.7 1.0
CE1 E:HIS29 2.8 78.2 1.0
CG E:HIS133 2.9 62.2 1.0
CG E:HIS29 3.0 76.3 1.0
CB E:HIS133 3.1 59.2 1.0
CE1 E:HIS135 3.1 52.7 1.0
CE1 E:HIS133 3.2 64.5 1.0
CD2 E:HIS135 3.2 51.6 1.0
CA E:HIS29 3.3 73.5 1.0
CB E:HIS29 3.5 74.4 1.0
O E:HIS133 3.9 57.0 1.0
NE2 E:HIS29 3.9 79.8 1.0
CD2 E:HIS29 4.0 78.4 1.0
CD2 E:HIS133 4.1 65.3 1.0
NE2 E:HIS133 4.2 65.7 1.0
ND1 E:HIS135 4.2 51.4 1.0
CA E:HIS133 4.3 59.2 1.0
C E:HIS133 4.3 57.8 1.0
CG E:HIS135 4.3 52.9 1.0
C E:HIS29 4.7 72.3 1.0
OE1 E:GLU31 5.0 72.8 1.0

Copper binding site 4 out of 4 in 3rfr

Go back to Copper Binding Sites List in 3rfr
Copper binding site 4 out of 4 in the Crystal Structure of Particulate Methane Monooxygenase (Pmmo) From Methylocystis Sp. Strain M


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 (Pmmo) From Methylocystis Sp. Strain M within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cu420

b:76.6
occ:1.00
NE2 I:HIS135 1.9 34.4 1.0
ND1 I:HIS29 2.2 60.0 1.0
N I:HIS29 2.2 58.1 1.0
ND1 I:HIS133 2.3 46.3 1.0
CE1 I:HIS135 2.8 37.4 1.0
CG I:HIS133 3.0 44.9 1.0
CE1 I:HIS29 3.1 59.5 1.0
CD2 I:HIS135 3.1 36.4 1.0
CG I:HIS29 3.1 59.2 1.0
CA I:HIS29 3.2 57.4 1.0
CB I:HIS133 3.2 41.6 1.0
CE1 I:HIS133 3.3 47.2 1.0
CB I:HIS29 3.5 57.5 1.0
ND1 I:HIS135 4.0 36.1 1.0
NE2 I:HIS29 4.1 60.2 1.0
CG I:HIS135 4.1 37.9 1.0
CD2 I:HIS29 4.2 59.9 1.0
O I:HIS133 4.2 41.7 1.0
CD2 I:HIS133 4.3 46.7 1.0
NE2 I:HIS133 4.4 47.4 1.0
CA I:HIS133 4.4 41.4 1.0
C I:HIS133 4.5 41.3 1.0
C I:HIS29 4.6 57.0 1.0
OE1 I:GLU31 4.7 58.5 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: Sun Dec 13 11:11:39 2020

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