Copper in PDB 8dsj: Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic

Enzymatic activity of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic

All present enzymatic activity of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic:
1.14.17.3; 4.3.2.5;

Protein crystallography data

The structure of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic, PDB code: 8dsj was solved by R.J.Arias, N.J.Blackburn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.40 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.14, 53.263, 86.424, 84.85, 89.96, 78.5
R / Rfree (%) 19.7 / 27.5

Copper Binding Sites:

The binding sites of Copper atom in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic (pdb code 8dsj). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic, PDB code: 8dsj:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8dsj

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Copper binding site 1 out of 6 in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:65.9
occ:1.00
 ND1 A:HIS108 2.0 61.7 1.0
ND1 A:HIS107 2.0 54.5 1.0
ND1 A:HIS172 2.0 44.1 1.0
CE1 A:HIS107 2.6 55.2 1.0
CE1 A:HIS108 2.6 62.8 1.0
CG A:HIS172 2.8 36.6 1.0
CG A:HIS108 2.9 53.3 1.0
CE1 A:HIS172 3.0 40.8 1.0
CG A:HIS107 3.0 47.6 1.0
CB A:HIS172 3.1 30.7 1.0
CB A:HIS108 3.5 44.7 1.0
NE2 A:HIS108 3.6 65.5 1.0
CB A:HIS107 3.7 41.1 1.0
NE2 A:HIS107 3.7 53.4 1.0
N A:HIS108 3.7 36.7 1.0
CD2 A:HIS108 3.8 60.9 1.0
CD2 A:HIS172 3.8 39.0 1.0
CD2 A:HIS107 3.9 50.5 1.0
NE2 A:HIS172 3.9 40.5 1.0
CA A:HIS108 4.2 37.7 1.0
C A:HIS107 4.2 36.9 1.0
CA A:HIS107 4.5 37.5 1.0
CA A:HIS172 4.5 27.1 1.0
OH A:TYR79 4.7 43.9 1.0
O A:HIS172 4.8 24.3 1.0
O A:HIS108 4.8 27.8 1.0
O A:HIS107 4.9 35.8 1.0
C A:HIS108 5.0 31.7 1.0

Copper binding site 2 out of 6 in 8dsj

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Copper binding site 2 out of 6 in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:61.3
occ:1.00
 NE2 A:HIS244 2.0 62.8 1.0
NE2 A:HIS242 2.0 49.5 1.0
SD A:MET314 2.3 62.9 1.0
CE1 A:HIS244 2.8 60.8 1.0
CD2 A:HIS242 3.0 46.9 1.0
CD2 A:HIS244 3.0 60.2 1.0
CE1 A:HIS242 3.1 45.8 1.0
CG A:MET314 3.4 61.6 1.0
CB A:MET314 3.6 59.8 1.0
CE A:MET314 3.8 62.7 1.0
ND1 A:HIS244 3.9 57.6 1.0
CG A:HIS244 4.0 58.7 1.0
CG A:HIS242 4.1 44.6 1.0
ND1 A:HIS242 4.2 42.4 1.0
O A:GLY308 4.9 85.2 1.0
CA A:MET314 5.0 57.1 1.0

Copper binding site 3 out of 6 in 8dsj

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Copper binding site 3 out of 6 in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:102.1
occ:1.00
 OD1 A:ASP282 3.3 32.6 1.0
CG A:ASP282 3.8 28.8 1.0
CB A:ASP282 4.0 24.9 1.0
CD2 A:HIS235 4.1 20.2 1.0
NE2 A:HIS235 4.2 20.8 1.0
OD2 A:ASP282 4.6 28.9 1.0

Copper binding site 4 out of 6 in 8dsj

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Copper binding site 4 out of 6 in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu401

b:79.8
occ:1.00
 ND1 K:HIS108 2.0 63.2 1.0
ND1 K:HIS172 2.0 58.1 1.0
ND1 K:HIS107 2.1 74.5 1.0
CE1 K:HIS108 2.7 63.1 1.0
CE1 K:HIS172 2.8 57.8 1.0
CG K:HIS107 2.9 63.3 1.0
CG K:HIS108 2.9 55.5 1.0
CE1 K:HIS107 3.1 73.3 1.0
CG K:HIS172 3.2 50.3 1.0
CB K:HIS107 3.2 54.0 1.0
CB K:HIS108 3.5 48.2 1.0
N K:HIS108 3.5 41.1 1.0
CB K:HIS172 3.6 41.8 1.0
NE2 K:HIS108 3.7 62.8 1.0
CD2 K:HIS108 3.8 58.2 1.0
C K:HIS107 3.8 43.9 1.0
NE2 K:HIS172 4.0 54.8 1.0
CD2 K:HIS107 4.1 65.3 1.0
CA K:HIS107 4.1 47.9 1.0
CA K:HIS108 4.1 40.8 1.0
NE2 K:HIS107 4.1 68.5 1.0
CD2 K:HIS172 4.2 52.7 1.0
O K:HIS107 4.6 42.3 1.0
O K:HIS172 4.7 31.4 1.0
OH K:TYR79 4.9 53.3 1.0
O K:HIS108 4.9 29.7 1.0
CA K:HIS172 5.0 34.8 1.0
C K:HIS108 5.0 33.0 1.0

Copper binding site 5 out of 6 in 8dsj

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Copper binding site 5 out of 6 in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu402

b:62.1
occ:1.00
 NE2 K:HIS242 2.0 54.8 1.0
NE2 K:HIS244 2.1 65.8 1.0
SD K:MET314 2.3 54.9 1.0
CE1 K:HIS242 2.8 51.5 1.0
CE1 K:HIS244 3.0 62.6 1.0
CD2 K:HIS244 3.1 64.2 1.0
CD2 K:HIS242 3.2 53.2 1.0
CG K:MET314 3.4 53.9 1.0
CB K:MET314 3.7 54.0 1.0
CE K:MET314 4.0 56.2 1.0
ND1 K:HIS242 4.0 48.7 1.0
ND1 K:HIS244 4.1 61.2 1.0
CG K:HIS242 4.2 48.8 1.0
CG K:HIS244 4.2 64.8 1.0
O K:GLY308 5.0 79.6 1.0

Copper binding site 6 out of 6 in 8dsj

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Copper binding site 6 out of 6 in the Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Peptidylglycine Alpha Hydroxylating Monooxygenase Anaerobic within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu403

b:124.4
occ:1.00
 CD2 K:HIS235 3.2 15.4 1.0
CB K:ASP282 4.0 31.3 1.0
NE2 K:HIS235 4.1 15.5 1.0
CG K:HIS235 4.2 15.6 1.0
N K:ASP282 4.3 27.7 1.0
O K:PRO280 4.3 47.7 1.0
CA K:ASP282 4.5 28.1 1.0
CB K:HIS235 4.7 14.9 1.0
C K:PRO280 4.7 47.4 1.0
OD1 K:ASP282 4.7 38.9 1.0
C K:VAL281 4.7 28.2 1.0
CB K:PRO280 4.7 58.3 1.0
CG K:ASP282 4.8 36.3 1.0

Reference:

R.J.Arias, E.F.Welch, N.J.Blackburn. New Structures Reveal Flexible Dynamics Between the Subdomains of Peptidylglycine Monooxygenase. Implications For An Open to Closed Mechanism. Protein Sci. E4615 2023.
ISSN: ESSN 1469-896X
PubMed: 36880254
DOI: 10.1002/PRO.4615
Page generated: Tue Apr 4 23:34:28 2023

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