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Zinc in PDB 3rgb: Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)

Enzymatic activity of Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)

All present enzymatic activity of Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath):
1.14.13.25;

Protein crystallography data

The structure of Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath), PDB code: 3rgb 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) 29.46 / 2.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 264.140, 264.140, 150.010, 90.00, 90.00, 90.00
R / Rfree (%) 26.9 / 29.6

Other elements in 3rgb:

The structure of Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath) 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 From Methylococcus Capsulatus (Bath) (pdb code 3rgb). 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 From Methylococcus Capsulatus (Bath), PDB code: 3rgb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 3rgb

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Zinc binding site 1 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:74.9
occ:1.00
 OE1 A:GLU57 2.2 69.1 1.0
OE2 A:GLU57 2.5 71.2 1.0
CD A:GLU57 2.7 68.5 1.0
CG A:GLU57 4.2 63.7 1.0
NZ A:LYS155 4.3 53.2 1.0
CE A:LYS155 4.8 51.9 1.0
CA A:GLY335 4.9 61.8 1.0
O A:GLY335 5.0 60.0 1.0

Zinc binding site 2 out of 9 in 3rgb

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Zinc binding site 2 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn664

b:48.5
occ:0.50
 CD2 B:HIS11 2.7 0.1 1.0
NE2 B:HIS11 2.9 0.7 1.0
OE1 C:GLU284 3.2 0.2 1.0
CG B:HIS11 4.0 0.7 1.0
CE1 B:HIS11 4.1 0.2 1.0
CD C:GLU284 4.3 0.6 1.0
ND1 B:HIS11 4.6 0.0 1.0
OE2 C:GLU284 4.7 0.1 1.0
CB B:HIS11 5.0 100.0 1.0

Zinc binding site 3 out of 9 in 3rgb

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Zinc binding site 3 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn663

b:56.5
occ:1.00
 NE2 C:HIS160 2.1 79.5 1.0
NE2 C:HIS173 2.2 78.0 1.0
OD2 C:ASP156 2.5 70.2 1.0
OD1 C:ASP156 2.7 72.3 1.0
O C:HOH290 2.8 3.1 1.0
CG C:ASP156 2.9 71.6 1.0
CE1 C:HIS160 3.0 80.3 1.0
CD2 C:HIS160 3.0 79.9 1.0
CD2 C:HIS173 3.2 77.5 1.0
CE1 C:HIS173 3.2 78.3 1.0
ND1 C:HIS160 4.1 81.5 1.0
CG C:HIS160 4.1 80.5 1.0
ND1 C:HIS173 4.3 78.4 1.0
CG C:HIS173 4.3 77.2 1.0
OE1 C:GLU176 4.4 74.1 1.0
CE1 C:PHE177 4.4 75.8 1.0
CB C:ASP156 4.5 72.1 1.0
CZ C:PHE177 4.5 76.0 1.0
O C:ASP156 4.9 74.8 1.0

Zinc binding site 4 out of 9 in 3rgb

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Zinc binding site 4 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn800

b:0.6
occ:1.00
 CA E:GLY335 3.3 60.8 1.0
N E:GLY335 4.0 61.0 1.0
C E:GLY335 4.5 59.3 1.0
OE1 E:GLU57 4.5 70.3 1.0
O E:THR333 4.7 63.9 1.0
O E:GLY335 4.7 59.4 1.0
C E:THR334 5.0 60.7 1.0

Zinc binding site 5 out of 9 in 3rgb

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Zinc binding site 5 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn800

b:0.8
occ:1.00
 OE2 I:GLU57 3.8 81.5 1.0
OE1 I:GLU57 3.9 79.0 1.0
CD I:GLU57 4.2 78.5 1.0

Zinc binding site 6 out of 9 in 3rgb

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Zinc binding site 6 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn664

b:0.8
occ:0.50
 NE2 J:HIS11 2.2 0.6 1.0
CE1 J:HIS11 3.0 0.3 1.0
CD2 J:HIS11 3.0 0.3 1.0
OE1 K:GLU284 3.7 0.8 1.0
ND1 J:HIS11 3.9 0.6 1.0
CG J:HIS11 4.0 0.5 1.0
OE2 K:GLU284 4.3 0.1 1.0
CD K:GLU284 4.4 0.1 1.0

Zinc binding site 7 out of 9 in 3rgb

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Zinc binding site 7 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn664

b:0.6
occ:0.50
 OE1 G:GLU284 2.2 0.2 1.0
CD2 F:HIS11 2.5 0.8 1.0
NE2 F:HIS11 2.6 0.1 1.0
CD G:GLU284 3.0 0.9 1.0
CG F:HIS11 3.3 0.4 1.0
CB G:GLU284 3.4 0.8 1.0
CE1 F:HIS11 3.4 0.3 1.0
OE2 G:GLU284 3.8 0.7 1.0
CG G:GLU284 3.8 0.0 1.0
ND1 F:HIS11 3.8 0.3 1.0
CB F:HIS11 4.3 0.6 1.0
CB G:ALA281 4.4 0.6 1.0
CA G:GLU284 4.8 0.1 1.0
N G:GLY285 5.0 1.0 1.0

Zinc binding site 8 out of 9 in 3rgb

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Zinc binding site 8 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn663

b:66.7
occ:1.00
 NE2 K:HIS160 2.2 85.0 1.0
NE2 K:HIS173 2.3 83.2 1.0
OD2 K:ASP156 2.5 75.7 1.0
O K:HOH290 2.8 16.8 1.0
OD1 K:ASP156 2.8 77.7 1.0
CG K:ASP156 3.0 77.0 1.0
CE1 K:HIS160 3.0 86.0 1.0
CD2 K:HIS160 3.1 85.3 1.0
CE1 K:HIS173 3.1 83.5 1.0
CD2 K:HIS173 3.3 82.4 1.0
ND1 K:HIS160 4.1 87.2 1.0
CG K:HIS160 4.2 86.2 1.0
ND1 K:HIS173 4.2 83.5 1.0
CE1 K:PHE177 4.3 81.2 1.0
CG K:HIS173 4.4 82.2 1.0
CZ K:PHE177 4.4 81.3 1.0
OE1 K:GLU176 4.4 79.5 1.0
CB K:ASP156 4.5 77.4 1.0
O K:ASP156 5.0 80.3 1.0

Zinc binding site 9 out of 9 in 3rgb

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Zinc binding site 9 out of 9 in the Crystal Structure of Particulate Methane Monooxygenase From Methylococcus Capsulatus (Bath)


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 From Methylococcus Capsulatus (Bath) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn663

b:65.5
occ:1.00
 NE2 G:HIS160 2.1 89.7 1.0
NE2 G:HIS173 2.3 87.9 1.0
O G:HOH290 2.3 11.6 1.0
OD2 G:ASP156 2.5 80.6 1.0
OD1 G:ASP156 2.7 82.6 1.0
CG G:ASP156 3.0 81.8 1.0
CD2 G:HIS160 3.0 90.0 1.0
CE1 G:HIS173 3.1 88.2 1.0
CE1 G:HIS160 3.1 90.5 1.0
CD2 G:HIS173 3.3 87.1 1.0
CG G:HIS160 4.1 90.7 1.0
ND1 G:HIS160 4.1 91.9 1.0
ND1 G:HIS173 4.2 88.1 1.0
CG G:HIS173 4.3 86.8 1.0
CE1 G:PHE177 4.3 86.2 1.0
OE1 G:GLU176 4.4 84.5 1.0
CZ G:PHE177 4.4 86.2 1.0
CB G:ASP156 4.4 82.0 1.0
O G:ASP156 4.8 84.5 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: Sat Oct 26 14:46:27 2024

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