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Copper in PDB 8dsn: Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A

Enzymatic activity of Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A

All present enzymatic activity of Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A:
1.14.17.3; 4.3.2.5;

Protein crystallography data

The structure of Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A, PDB code: 8dsn 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) 38.05 / 2.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.878, 53.488, 86.056, 84.71, 89.82, 77.96
R / Rfree (%) 19.8 / 29.6

Copper Binding Sites:

The binding sites of Copper atom in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A (pdb code 8dsn). 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 Monoxygenase, Q272A, PDB code: 8dsn:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 8dsn

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Copper binding site 1 out of 6 in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A


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 Monoxygenase, Q272A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:122.5
occ:1.00
 ND1 A:HIS108 2.0 80.0 1.0
ND1 A:HIS107 2.0 81.3 1.0
ND1 A:HIS172 2.1 66.0 1.0
CE1 A:HIS108 2.8 75.9 1.0
CG A:HIS107 2.9 65.2 1.0
CE1 A:HIS172 2.9 63.8 1.0
CE1 A:HIS107 3.1 75.1 1.0
CG A:HIS108 3.1 62.2 1.0
CB A:HIS107 3.1 53.0 1.0
CG A:HIS172 3.2 50.0 1.0
CB A:HIS172 3.6 38.4 1.0
CB A:HIS108 3.6 50.8 1.0
N A:HIS108 3.6 40.9 1.0
C A:HIS107 3.7 44.0 1.0
NE2 A:HIS108 3.9 73.4 1.0
CA A:HIS107 4.0 45.1 1.0
CD2 A:HIS107 4.0 69.0 1.0
O A:HIS107 4.0 41.4 1.0
CD2 A:HIS108 4.1 68.8 1.0
NE2 A:HIS107 4.1 76.4 1.0
NE2 A:HIS172 4.1 62.1 1.0
CD2 A:HIS172 4.2 55.0 1.0
CA A:HIS108 4.2 42.7 1.0
O A:HIS172 4.9 25.7 1.0
CA A:HIS172 5.0 31.7 1.0

Copper binding site 2 out of 6 in 8dsn

Go back to Copper Binding Sites List in 8dsn
Copper binding site 2 out of 6 in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A


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 Monoxygenase, Q272A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:119.0
occ:1.00
 NE2 A:HIS242 2.0 68.1 1.0
SD A:MET314 2.3 54.2 1.0
NE2 A:HIS244 2.7 92.6 1.0
CE1 A:HIS242 2.9 59.0 1.0
CE A:MET314 2.9 55.8 1.0
CD2 A:HIS242 3.1 54.0 1.0
CD2 A:HIS244 3.3 82.2 1.0
CE1 A:HIS244 3.5 81.5 1.0
O A:GLY308 3.8 137.7 1.0
ND1 A:HIS242 4.0 54.4 1.0
CG A:MET314 4.1 58.0 1.0
CG A:HIS242 4.2 51.3 1.0
CG A:HIS244 4.2 76.2 1.0
ND1 A:HIS244 4.3 73.6 1.0
CB A:MET314 4.6 59.1 1.0
O A:THR243 4.8 44.6 1.0
C A:GLY308 4.9 151.7 1.0
O A:THR309 4.9 172.1 1.0
O A:GLY307 5.0 141.8 1.0

Copper binding site 3 out of 6 in 8dsn

Go back to Copper Binding Sites List in 8dsn
Copper binding site 3 out of 6 in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A


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 Monoxygenase, Q272A within 5.0Å range:

Copper binding site 4 out of 6 in 8dsn

Go back to Copper Binding Sites List in 8dsn
Copper binding site 4 out of 6 in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A


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 Monoxygenase, Q272A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu401

b:136.4
occ:1.00
 ND1 K:HIS107 2.0 85.7 1.0
ND1 K:HIS172 2.1 65.6 1.0
ND1 K:HIS108 2.1 79.5 1.0
CE1 K:HIS172 2.8 60.7 1.0
CE1 K:HIS108 2.8 73.9 1.0
CG K:HIS107 2.9 72.2 1.0
CB K:HIS107 3.0 61.3 1.0
CG K:HIS108 3.1 60.2 1.0
CE1 K:HIS107 3.1 80.6 1.0
CG K:HIS172 3.3 50.7 1.0
CB K:HIS108 3.6 51.3 1.0
N K:HIS108 3.7 42.4 1.0
C K:HIS107 3.8 48.0 1.0
CB K:HIS172 3.8 40.4 1.0
NE2 K:HIS108 4.0 68.4 1.0
NE2 K:HIS172 4.0 59.0 1.0
CA K:HIS107 4.0 51.9 1.0
CD2 K:HIS107 4.0 75.0 1.0
CD2 K:HIS108 4.1 63.9 1.0
NE2 K:HIS107 4.2 78.0 1.0
CD2 K:HIS172 4.2 53.6 1.0
CA K:HIS108 4.2 41.6 1.0
O K:HIS107 4.3 49.4 1.0
O K:HIS172 4.7 32.7 1.0

Copper binding site 5 out of 6 in 8dsn

Go back to Copper Binding Sites List in 8dsn
Copper binding site 5 out of 6 in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A


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 Monoxygenase, Q272A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu402

b:76.0
occ:1.00
 NE2 K:HIS244 2.0 82.3 1.0
NE2 K:HIS242 2.1 71.5 1.0
SD K:MET314 2.3 70.0 1.0
CD2 K:HIS242 2.6 61.3 1.0
CE1 K:HIS244 3.0 79.0 1.0
CD2 K:HIS244 3.1 81.4 1.0
CE1 K:HIS242 3.3 66.5 1.0
O K:HOH513 3.5 22.0 1.0
CG K:MET314 3.6 66.0 1.0
CB K:MET314 3.7 65.5 1.0
CE K:MET314 3.8 69.8 1.0
CG K:HIS242 3.9 56.2 1.0
ND1 K:HIS244 4.1 82.3 1.0
CG K:HIS244 4.2 81.5 1.0
ND1 K:HIS242 4.2 58.4 1.0
OD1 K:ASN316 4.7 49.5 1.0

Copper binding site 6 out of 6 in 8dsn

Go back to Copper Binding Sites List in 8dsn
Copper binding site 6 out of 6 in the Peptidylglycine Alpha Hydroxylating Monoxygenase, Q272A


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 Monoxygenase, Q272A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cu403

b:106.6
occ:1.00
 CD2 K:HIS235 2.9 32.7 1.0
CB K:HIS235 3.5 23.4 1.0
CG K:HIS235 3.5 30.5 1.0
C K:VAL281 4.0 30.9 1.0
N K:ASP282 4.0 32.2 1.0
CB K:ASP282 4.0 40.3 1.0
O K:VAL281 4.0 27.9 1.0
CA K:HIS235 4.1 21.8 1.0
NE2 K:HIS235 4.2 34.3 1.0
CA K:ASP282 4.2 33.7 1.0
O K:PRO280 4.2 43.9 1.0
C K:PRO280 4.3 46.5 1.0
N K:VAL281 4.5 40.2 1.0
CB K:PRO280 4.6 63.8 1.0
CA K:VAL281 4.6 35.0 1.0
OH K:TYR322 4.7 30.5 1.0
C K:HIS235 4.8 20.7 1.0
ND1 K:HIS235 4.9 35.6 1.0
N K:VAL236 4.9 23.2 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: Wed Jul 31 09:39:25 2024

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