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Cadmium in PDB 6bmg: Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)

Protein crystallography data

The structure of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy), PDB code: 6bmg was solved by P.P.Samuel, M.D.Miller, W.Xu, S.Alvarado, G.N.Phillips Jr., J.S.Olson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 1.88
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.995, 85.995, 109.010, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19

Other elements in 6bmg:

The structure of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) (pdb code 6bmg). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy), PDB code: 6bmg:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 6bmg

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Cadmium binding site 1 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:27.3
occ:1.00
 O A:ACT214 2.2 39.3 1.0
NE2 A:HIS35 2.3 27.9 1.0
O B:HOH338 2.4 24.8 1.0
NE2 B:HIS116 2.4 28.7 1.0
O A:ACT213 2.4 32.5 1.0
OXT A:ACT213 2.5 34.4 1.0
C A:ACT213 2.7 31.6 1.0
C A:ACT214 2.9 49.6 1.0
OXT A:ACT214 3.2 59.4 1.0
CE1 A:HIS35 3.2 27.2 1.0
CE1 B:HIS116 3.3 28.1 1.0
HE1 A:HIS35 3.3 32.7 1.0
CD2 A:HIS35 3.4 27.4 1.0
CD2 B:HIS116 3.4 28.4 1.0
HE1 B:HIS116 3.4 33.8 1.0
HE22 B:GLN128 3.5 36.5 0.7
HD2 B:HIS116 3.5 34.1 1.0
HD2 A:HIS35 3.5 32.9 1.0
O A:HOH305 4.0 30.4 1.0
HH21 A:ARG31 4.1 32.7 1.0
HH22 A:ARG31 4.1 32.7 1.0
NE2 B:GLN128 4.2 30.4 0.7
HE21 B:GLN128 4.2 36.5 0.7
CH3 A:ACT213 4.3 35.7 1.0
CH3 A:ACT214 4.3 53.0 1.0
NH2 A:ARG31 4.3 27.2 1.0
ND1 A:HIS35 4.4 27.4 1.0
ND1 B:HIS116 4.4 27.9 1.0
CG A:HIS35 4.5 27.5 1.0
H3 A:ACT214 4.5 63.6 1.0
CG B:HIS116 4.5 27.6 1.0
O A:HOH334 4.6 48.1 1.0
H2 A:ACT214 4.6 63.6 1.0
H2 A:ACT213 4.7 42.9 1.0
O A:HOH313 4.7 27.8 1.0
H1 A:ACT213 4.7 42.9 1.0
H3 A:ACT213 4.7 42.9 1.0
O B:PHE123 4.7 28.2 1.0
HA B:PRO120 4.8 40.9 1.0
O B:PRO120 4.8 50.7 1.0
HB2 B:PRO120 4.8 38.4 1.0
HA2 B:GLY124 4.9 33.1 1.0
HB3 B:PRO120 4.9 38.4 1.0
H1 A:ACT214 5.0 63.6 1.0

Cadmium binding site 2 out of 9 in 6bmg

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Cadmium binding site 2 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:27.1
occ:1.00
 OD2 A:ASP126 2.3 25.4 1.0
OXT A:ACT210 2.4 32.2 1.0
OD1 A:ASP126 2.4 24.3 1.0
O A:ACT210 2.6 31.7 1.0
CG A:ASP126 2.7 25.3 1.0
C A:ACT210 2.8 31.1 1.0
O A:HOH335 4.0 39.6 1.0
CB A:ASP126 4.2 23.5 1.0
O A:HOH413 4.2 47.8 1.0
CH3 A:ACT210 4.3 35.8 1.0
O A:HOH390 4.5 33.0 1.0
HB3 A:ASP126 4.6 28.2 1.0
O A:HOH307 4.6 44.8 1.0
HB2 A:ASP126 4.6 28.2 1.0
H1 A:ACT210 4.6 43.0 1.0
H2 A:ACT210 4.7 43.0 1.0
HA A:ASP126 4.7 29.1 1.0
O A:HOH319 4.8 41.7 1.0
H3 A:ACT210 4.8 43.0 1.0
H A:ASP126 4.9 29.8 1.0
CA A:ASP126 5.0 24.2 1.0

Cadmium binding site 3 out of 9 in 6bmg

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Cadmium binding site 3 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:29.2
occ:0.69
 CD A:CD205 0.0 29.2 0.7
HE1 A:HIS12 1.8 50.9 1.0
CD A:CD205 2.3 36.0 0.3
OD1 A:ASP122 2.4 34.0 0.7
OD2 A:ASP122 2.5 39.1 0.7
CE1 A:HIS12 2.7 42.4 1.0
HZ1 A:LYS16 2.8 82.5 1.0
CG A:ASP122 2.8 33.4 0.7
NE2 A:HIS12 3.4 47.9 1.0
HB2 A:ASP122 3.6 33.8 0.3
NZ A:LYS16 3.6 68.8 1.0
HZ2 A:LYS16 3.8 82.5 1.0
ND1 A:HIS12 3.8 45.6 1.0
HD1 A:HIS12 4.0 54.7 1.0
HZ3 A:LYS16 4.0 82.5 1.0
CB A:ASP122 4.4 28.1 0.7
HE3 A:LYS16 4.4 72.2 1.0
HB3 A:ASP122 4.4 33.8 0.3
CB A:ASP122 4.4 28.2 0.3
CE A:LYS16 4.5 60.1 1.0
O A:HOH355 4.6 53.0 1.0
CD2 A:HIS12 4.6 43.7 1.0
HE2 A:LYS16 4.6 72.2 1.0
HB2 A:ASP122 4.7 33.8 0.7
HB3 A:ASP122 4.8 33.8 0.7
CG A:HIS12 4.8 42.6 1.0
HA A:ASP122 4.9 35.7 0.7
O A:ASP122 4.9 32.5 0.7
HA A:ASP122 5.0 34.8 0.3

Cadmium binding site 4 out of 9 in 6bmg

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Cadmium binding site 4 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:36.0
occ:0.31
 CD A:CD205 0.0 36.0 0.3
NE2 A:HIS12 2.1 47.9 1.0
CD A:CD205 2.3 29.2 0.7
HE1 A:HIS12 2.3 50.9 1.0
CE1 A:HIS12 2.5 42.4 1.0
CD2 A:HIS12 3.4 43.7 1.0
HZ1 A:LYS16 3.8 82.5 1.0
ND1 A:HIS12 3.8 45.6 1.0
OD2 A:ASP122 3.9 39.1 0.7
HD2 A:HIS12 3.9 52.4 1.0
HZ2 A:LYS16 4.0 82.5 1.0
CG A:HIS12 4.2 42.6 1.0
NZ A:LYS16 4.3 68.8 1.0
HD1 A:HIS12 4.4 54.7 1.0
O A:HOH405 4.4 48.1 1.0
OD1 A:ASP122 4.6 34.0 0.7
CG A:ASP122 4.7 33.4 0.7
HE3 A:LYS16 4.9 72.2 1.0
HZ3 A:LYS16 4.9 82.5 1.0

Cadmium binding site 5 out of 9 in 6bmg

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Cadmium binding site 5 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:37.2
occ:0.54
 O A:HOH412 2.2 36.1 0.5
OD2 A:ASP122 2.4 24.1 0.3
O A:HOH428 2.4 31.7 0.5
ND1 A:HIS119 2.4 24.9 1.0
O A:ACT212 2.6 37.5 0.5
OXT A:ACT212 2.6 39.6 0.5
C A:ACT212 2.9 35.4 0.5
OD1 A:ASP122 3.0 24.7 0.3
CG A:ASP122 3.0 25.7 0.3
HB3 A:HIS119 3.1 30.0 1.0
CG A:HIS119 3.3 25.0 1.0
CE1 A:HIS119 3.4 25.9 1.0
HA A:HIS119 3.4 29.9 1.0
HD3 A:LYS16 3.5 50.1 1.0
HE1 A:HIS119 3.5 31.1 1.0
CB A:HIS119 3.6 25.0 1.0
HB3 A:ASP122 3.7 33.8 0.7
HE3 A:LYS16 3.7 72.2 1.0
HE2 A:LYS16 3.8 72.2 1.0
CA A:HIS119 4.0 24.9 1.0
CE A:LYS16 4.1 60.1 1.0
CD A:LYS16 4.2 41.8 1.0
O A:ARG118 4.4 27.9 1.0
CH3 A:ACT212 4.4 30.9 0.5
HB2 A:ASP122 4.4 33.8 0.7
O A:HOH371 4.4 34.2 1.0
HB2 A:HIS119 4.5 30.0 1.0
NE2 A:HIS119 4.5 25.6 1.0
HG2 A:LYS16 4.5 40.7 1.0
CD2 A:HIS119 4.5 25.2 1.0
CB A:ASP122 4.5 28.1 0.7
CB A:ASP122 4.5 28.2 0.3
HB3 A:LYS16 4.5 37.2 1.0
H1 A:ACT212 4.7 37.1 0.5
HB2 A:ASP122 4.8 33.8 0.3
H2 A:ACT212 4.8 37.1 0.5
HB3 A:ASP122 4.8 33.8 0.3
CG A:LYS16 4.9 33.9 1.0
N A:HIS119 4.9 24.5 1.0
H3 A:ACT212 4.9 37.1 0.5
O A:HOH433 4.9 54.1 1.0
OD2 A:ASP122 5.0 39.1 0.7
HD2 A:LYS16 5.0 50.1 1.0

Cadmium binding site 6 out of 9 in 6bmg

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Cadmium binding site 6 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:26.4
occ:1.00
 NE2 B:HIS35 2.3 24.3 1.0
NE2 A:HIS116 2.3 27.3 1.0
O A:ACT211 2.3 34.4 1.0
OXT A:ACT209 2.4 28.6 1.0
O A:ACT209 2.4 31.4 1.0
O A:HOH357 2.4 23.9 1.0
C A:ACT209 2.7 32.1 1.0
OXT A:ACT211 2.8 60.8 1.0
C A:ACT211 2.8 46.2 1.0
CE1 B:HIS35 3.2 24.9 1.0
CE1 A:HIS116 3.3 25.9 1.0
CD2 B:HIS35 3.3 26.0 1.0
CD2 A:HIS116 3.3 26.2 1.0
HE1 B:HIS35 3.3 29.9 1.0
HE1 A:HIS116 3.4 31.2 1.0
HD2 A:HIS116 3.5 31.5 1.0
HD2 B:HIS35 3.5 31.3 1.0
HE22 A:GLN128 3.8 37.2 1.0
O A:HOH308 4.0 25.4 1.0
CH3 A:ACT209 4.2 37.7 1.0
HH21 B:ARG31 4.2 31.6 1.0
HH22 B:ARG31 4.3 31.6 1.0
CH3 A:ACT211 4.3 44.3 1.0
O A:HOH384 4.3 48.8 1.0
ND1 B:HIS35 4.4 24.4 1.0
ND1 A:HIS116 4.4 26.8 1.0
CG B:HIS35 4.4 24.4 1.0
CG A:HIS116 4.5 25.5 1.0
NE2 A:GLN128 4.5 31.0 1.0
NH2 B:ARG31 4.5 26.3 1.0
H1 A:ACT209 4.5 45.2 1.0
O A:PRO120 4.6 25.9 1.0
H3 A:ACT209 4.6 45.2 1.0
H2 A:ACT209 4.6 45.2 1.0
H2 A:ACT211 4.6 53.2 1.0
H1 A:ACT211 4.6 53.2 1.0
HE21 A:GLN128 4.7 37.2 1.0
HA A:PRO120 4.7 29.3 1.0
O A:PHE123 4.7 26.2 1.0
O B:HOH303 4.8 31.2 1.0
O A:HOH383 4.8 54.8 1.0
H3 A:ACT211 5.0 53.2 1.0

Cadmium binding site 7 out of 9 in 6bmg

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Cadmium binding site 7 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:49.1
occ:0.65
 H1 A:MET0 2.4 83.8 1.0
O A:HOH425 2.4 42.0 0.7
H2 A:MET0 2.4 83.8 1.0
NE2 A:HIS81 2.5 57.8 1.0
N A:MET0 2.8 69.8 1.0
HB3 A:MET0 2.8 94.9 1.0
O A:HOH438 2.9 52.4 0.7
CE1 A:HIS81 3.4 58.9 1.0
CA A:MET0 3.4 74.4 1.0
HA A:MET0 3.4 89.3 1.0
CB A:MET0 3.4 79.1 1.0
HE1 A:HIS81 3.5 70.7 1.0
HG2 A:MET0 3.5 0.4 1.0
H3 A:MET0 3.5 83.8 1.0
CD2 A:HIS81 3.6 57.3 1.0
HD2 A:HIS81 3.8 68.8 1.0
CG A:MET0 4.0 84.5 1.0
O A:HOH324 4.1 50.4 1.0
O A:HOH303 4.1 48.4 1.0
HB2 A:MET0 4.3 94.9 1.0
O A:LYS79 4.5 32.8 1.0
HE2 A:MET0 4.5 0.6 1.0
ND1 A:HIS81 4.6 57.6 1.0
HG3 A:MET0 4.6 0.4 1.0
CG A:HIS81 4.7 55.9 1.0
HE3 A:MET0 4.8 0.6 1.0
C A:MET0 4.9 65.2 1.0

Cadmium binding site 8 out of 9 in 6bmg

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Cadmium binding site 8 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:27.9
occ:1.00
 OE2 B:GLU38 2.2 31.1 1.0
O B:ACT205 2.3 28.7 1.0
ND1 B:HIS36 2.4 25.3 1.0
OXT B:ACT205 2.5 29.1 1.0
C B:ACT205 2.7 29.7 1.0
CD B:GLU38 2.9 31.8 1.0
OE1 B:GLU38 3.0 28.1 1.0
HB3 B:HIS36 3.1 28.3 1.0
HA B:HIS36 3.3 26.0 1.0
CE1 B:HIS36 3.3 23.5 1.0
CG B:HIS36 3.3 24.7 1.0
HE1 B:HIS36 3.4 28.2 1.0
CB B:HIS36 3.6 23.6 1.0
HZ B:PHE106 3.8 35.4 1.0
HE2 B:PHE106 3.9 32.5 1.0
CA B:HIS36 3.9 21.8 1.0
CZ B:PHE106 3.9 29.5 1.0
CE2 B:PHE106 4.0 27.0 1.0
O B:HOH350 4.1 29.8 1.0
CH3 B:ACT205 4.3 40.9 1.0
O B:HOH397 4.4 41.2 1.0
HD2 B:PRO37 4.4 36.2 1.0
O B:HOH352 4.4 29.7 1.0
CG B:GLU38 4.4 29.4 1.0
NE2 B:HIS36 4.4 25.5 1.0
CD2 B:HIS36 4.5 24.2 1.0
HB2 B:HIS36 4.5 28.3 1.0
O B:HIS35 4.5 22.5 1.0
HG3 B:GLU38 4.6 35.3 1.0
H2 B:ACT205 4.7 49.1 1.0
CE1 B:PHE106 4.7 28.5 1.0
H3 B:ACT205 4.7 49.1 1.0
O B:HOH314 4.7 42.2 1.0
H1 B:ACT205 4.7 49.1 1.0
C B:HIS36 4.8 23.5 1.0
CD2 B:PHE106 4.8 24.3 1.0
H B:GLU38 4.8 32.4 1.0
HG2 B:GLU38 4.9 35.3 1.0
HE1 B:PHE106 5.0 34.2 1.0

Cadmium binding site 9 out of 9 in 6bmg

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Cadmium binding site 9 out of 9 in the Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:45.7
occ:0.59
 H1 B:MET0 2.4 82.6 1.0
NE2 B:HIS81 2.5 40.9 1.0
H2 B:MET0 2.5 82.6 1.0
O B:HOH383 2.6 29.4 0.6
N B:MET0 2.8 68.8 1.0
HB3 B:MET0 2.9 91.0 1.0
CE1 B:HIS81 3.3 43.4 1.0
HE1 B:HIS81 3.4 52.0 1.0
CD2 B:HIS81 3.5 40.3 1.0
CA B:MET0 3.5 67.0 1.0
HG2 B:MET0 3.5 97.8 1.0
H3 B:MET0 3.5 82.6 1.0
CB B:MET0 3.6 75.8 1.0
HA B:MET0 3.6 80.5 1.0
HD2 B:HIS81 3.7 48.4 1.0
CG B:MET0 4.1 81.5 1.0
O B:LYS79 4.3 25.4 1.0
O B:HOH311 4.4 40.0 1.0
O B:HOH323 4.4 49.0 1.0
HB2 B:MET0 4.4 91.0 1.0
ND1 B:HIS81 4.5 40.9 1.0
CG B:HIS81 4.6 39.4 1.0
HG3 B:MET0 4.6 97.8 1.0
HE2 B:MET0 4.8 0.5 1.0
HE3 B:MET0 4.9 0.5 1.0
C B:MET0 5.0 53.5 1.0

Reference:

P.P.Samuel, M.D.Miller, W.Xu, S.Alvarado, G.N.Phillips Jr., J.S.Olson. Structure of Recombinant Dwarf Sperm Whale Myoglobin (Oxy) To Be Published.
Page generated: Sat Dec 12 08:28:05 2020

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