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Copper in PDB 5wja: Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate

Enzymatic activity of Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate

All present enzymatic activity of Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate:
1.14.17.3; 4.3.2.5;

Protein crystallography data

The structure of Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate, PDB code: 5wja was solved by S.Maheshwari, K.Rudzka, S.B.Gabelli, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.77 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.544, 100.613, 101.582, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 27.3

Other elements in 5wja:

The structure of Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate also contains other interesting chemical elements:

Nickel (Ni) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate (pdb code 5wja). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate, PDB code: 5wja:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5wja

Go back to Copper Binding Sites List in 5wja
Copper binding site 1 out of 3 in the Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate


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 H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1001

b:73.3
occ:1.00
 ND1 A:HIS172 2.1 48.9 1.0
ND1 A:HIS108 2.2 67.0 1.0
O A:HOH1140 2.5 49.4 1.0
O A:HOH1178 2.8 57.5 1.0
CE1 A:HIS172 3.0 53.1 1.0
CG A:HIS108 3.0 57.9 1.0
CG A:HIS172 3.1 50.2 1.0
CE1 A:HIS108 3.2 62.9 1.0
CB A:HIS108 3.2 52.3 1.0
CB A:HIS172 3.5 47.4 1.0
O A:HOH1119 3.8 43.9 1.0
CB A:ALA107 4.0 52.6 1.0
OH A:TYR79 4.0 77.0 1.0
N A:HIS108 4.0 54.4 1.0
NE2 A:HIS172 4.1 53.0 1.0
CD2 A:HIS108 4.2 58.0 1.0
CD2 A:HIS172 4.2 50.8 1.0
CA A:HIS108 4.2 49.6 1.0
NE2 A:HIS108 4.2 59.1 1.0
C A:ALA107 4.3 54.0 1.0
CE1 A:TYR79 4.3 62.4 1.0
O A:ALA107 4.7 52.6 1.0
CZ A:TYR79 4.7 70.0 1.0
CA A:ALA107 4.8 52.2 1.0

Copper binding site 2 out of 3 in 5wja

Go back to Copper Binding Sites List in 5wja
Copper binding site 2 out of 3 in the Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate


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 H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1002

b:46.1
occ:1.00
 NE2 A:HIS242 2.0 36.0 1.0
SD A:MET314 2.1 37.4 1.0
OE1 A:GLU128 2.2 57.0 1.0
NE2 A:HIS244 2.3 40.3 1.0
CD A:GLU128 2.8 55.6 1.0
CD2 A:HIS242 2.9 32.7 1.0
OE2 A:GLU128 3.0 60.2 1.0
CE1 A:HIS242 3.1 34.6 1.0
CD2 A:HIS244 3.1 41.7 1.0
CE A:MET314 3.2 39.1 1.0
CE1 A:HIS244 3.2 42.7 1.0
CG A:MET314 3.2 41.9 1.0
CB A:MET314 3.6 39.9 1.0
CG A:GLU128 4.1 53.3 1.0
CG A:HIS242 4.1 32.6 1.0
ND1 A:HIS242 4.2 32.5 1.0
ND1 A:HIS244 4.2 43.3 1.0
CG A:HIS244 4.2 41.1 1.0
CA A:MET314 5.0 41.6 1.0

Copper binding site 3 out of 3 in 5wja

Go back to Copper Binding Sites List in 5wja
Copper binding site 3 out of 3 in the Crystal Structure of H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate


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 H107A Peptidylglycine Alpha-Hydroxylating Monooxygenase (Phm) in Complex with Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu1001

b:48.5
occ:1.00
 NE2 D:HIS242 2.1 37.2 1.0
SD D:MET314 2.1 51.2 1.0
NE2 D:HIS244 2.1 57.6 1.0
O D:HOH1113 2.4 70.6 1.0
CE D:MET314 2.8 50.7 1.0
CD2 D:HIS244 3.0 57.7 1.0
CD2 D:HIS242 3.0 33.7 1.0
CG D:MET314 3.1 50.7 1.0
CE1 D:HIS242 3.1 31.9 1.0
CE1 D:HIS244 3.2 56.3 1.0
OHB D:FLC1002 3.4 57.5 1.0
CB D:MET314 3.8 51.3 1.0
O D:HOH1127 4.1 54.9 1.0
CG D:HIS244 4.2 54.1 1.0
CG D:HIS242 4.2 35.8 1.0
ND1 D:HIS242 4.2 33.4 1.0
ND1 D:HIS244 4.2 55.0 1.0
OB1 D:FLC1002 4.2 66.1 1.0
OG1 D:FLC1002 4.4 65.8 1.0
CGC D:FLC1002 4.8 54.4 1.0
CB D:FLC1002 4.9 56.8 1.0
CG D:FLC1002 4.9 55.0 1.0

Reference:

S.Maheshwari, C.Shimokawa, K.Rudzka, C.D.Kline, B.A.Eipper, R.E.Mains, S.B.Gabelli, N.Blackburn, L.M.Amzel. Effects of Copper Occupancy on the Conformational Landscape of Peptidylglycine Alpha-Hydroxylating Monooxygenase. Commun Biol V. 1 74 2018.
ISSN: ESSN 2399-3642
PubMed: 30271955
DOI: 10.1038/S42003-018-0082-Y
Page generated: Wed Jul 31 05:21:10 2024

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