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Copper in PDB 4fwy: F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound

Protein crystallography data

The structure of F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound, PDB code: 4fwy was solved by Y.-G.Gao, H.Robinson, I.D.Petrik, K.D.Miner, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.01 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.734, 48.286, 77.691, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 24.6

Copper Binding Sites:

The binding sites of Copper atom in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound (pdb code 4fwy). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound, PDB code: 4fwy:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 4fwy

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Copper binding site 1 out of 5 in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu202

b:38.4
occ:1.00
NE2 A:HIS29 2.1 33.9 1.0
NE2 A:HIS64 2.2 31.5 1.0
O A:HOH342 2.6 33.3 1.0
NE2 A:HIS43 2.7 78.8 1.0
CE1 A:HIS43 2.8 68.7 1.0
CD2 A:HIS29 3.0 30.3 1.0
CD2 A:HIS64 3.0 30.8 1.0
CE1 A:HIS29 3.2 35.5 1.0
CE1 A:HIS64 3.3 30.0 1.0
CD2 A:HIS43 3.8 79.9 1.0
OH A:TYR33 3.8 47.1 1.0
ND1 A:HIS43 3.9 75.0 1.0
CG2 A:VAL68 4.0 25.2 1.0
CG A:HIS64 4.2 27.8 1.0
CG A:HIS29 4.2 30.9 1.0
ND1 A:HIS29 4.3 34.6 1.0
ND1 A:HIS64 4.3 33.5 1.0
CG A:HIS43 4.4 77.2 1.0
NC A:HEM201 4.8 27.4 1.0
CZ A:TYR33 4.9 43.8 1.0
C4C A:HEM201 4.9 29.6 1.0

Copper binding site 2 out of 5 in 4fwy

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Copper binding site 2 out of 5 in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu203

b:35.6
occ:1.00
NE2 A:HIS119 1.7 34.0 1.0
NE2 A:HIS24 2.0 24.3 1.0
CD2 A:HIS119 2.6 35.0 1.0
CE1 A:HIS119 2.7 27.3 1.0
CE1 A:HIS24 3.0 28.0 1.0
CD2 A:HIS24 3.0 24.8 1.0
O A:HOH333 3.7 36.5 1.0
CB A:ARG118 3.7 23.9 1.0
CG A:HIS119 3.7 35.5 1.0
ND1 A:HIS119 3.8 35.4 1.0
CD A:ARG118 3.8 25.5 1.0
O A:LYS16 4.1 27.6 1.0
ND1 A:HIS24 4.2 23.8 1.0
C A:LYS16 4.2 25.4 1.0
CB A:LYS16 4.2 31.1 1.0
CG A:HIS24 4.2 26.5 1.0
CD2 A:LEU115 4.3 24.1 1.0
N A:VAL17 4.4 24.0 1.0
CG A:ARG118 4.4 26.9 1.0
CA A:VAL17 4.5 24.9 1.0
CA A:LYS16 4.9 27.1 1.0
CG2 A:VAL17 5.0 26.1 1.0
CA A:ARG118 5.0 26.5 1.0

Copper binding site 3 out of 5 in 4fwy

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Copper binding site 3 out of 5 in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu204

b:79.3
occ:1.00
OD2 A:ASP122 2.2 34.3 1.0
NE2 A:HIS12 2.5 33.2 1.0
OD1 A:ASP122 2.7 49.8 1.0
CG A:ASP122 2.8 48.2 1.0
CE1 A:HIS12 2.9 33.7 1.0
CD2 A:HIS12 3.7 32.1 1.0
ND1 A:HIS12 4.2 33.9 1.0
CB A:ASP122 4.3 52.3 1.0
CG A:HIS12 4.6 31.0 1.0
CE A:LYS16 4.9 54.6 1.0
CA A:ASP122 4.9 51.6 1.0

Copper binding site 4 out of 5 in 4fwy

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Copper binding site 4 out of 5 in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu205

b:47.4
occ:1.00
NE2 A:HIS116 2.1 40.0 1.0
O A:HOH324 2.5 42.7 1.0
CD2 A:HIS116 2.9 41.6 1.0
CE1 A:HIS116 3.2 42.4 1.0
CG A:HIS116 4.1 38.0 1.0
ND1 A:HIS116 4.3 38.4 1.0

Copper binding site 5 out of 5 in 4fwy

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Copper binding site 5 out of 5 in the F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of F33Y Cub Myoglobin (F33Y L29H F43H Sperm Whale Myoglobin) with Copper Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu206

b:82.9
occ:1.00
ND1 A:HIS81 2.6 44.6 1.0
CG A:HIS81 3.5 36.6 1.0
CB A:HIS81 3.6 33.5 1.0
CE1 A:HIS81 3.6 39.6 1.0
O A:HOH344 3.7 35.0 1.0
CA A:HIS81 4.0 27.5 1.0
CD2 A:HIS81 4.7 42.7 1.0
NE2 A:HIS81 4.8 42.7 1.0
C A:HIS81 4.9 25.2 1.0

Reference:

K.D.Miner, A.Mukherjee, Y.G.Gao, E.L.Null, I.D.Petrik, X.Zhao, N.Yeung, H.Robinson, Y.Lu. A Designed Functional Metalloenzyme That Reduces O(2) to H(2) O with Over One Thousand Turnovers. Angew.Chem.Int.Ed.Engl. V. 51 5589 2012.
ISSN: ISSN 1433-7851
PubMed: 22539151
DOI: 10.1002/ANIE.201201981
Page generated: Fri Sep 4 11:09:30 2020
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