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Copper in PDB 5n4l: Rat Ceruloplasmin Trigonal Form

Protein crystallography data

The structure of Rat Ceruloplasmin Trigonal Form, PDB code: 5n4l was solved by V.R.Samygina, A.V.Sokolov, G.Bourenkov, V.B.Vasilyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.99 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.230, 128.230, 407.660, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 26.5

Other elements in 5n4l:

The structure of Rat Ceruloplasmin Trigonal Form also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Copper atom in the Rat Ceruloplasmin Trigonal Form (pdb code 5n4l). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 11 binding sites of Copper where determined in the Rat Ceruloplasmin Trigonal Form, PDB code: 5n4l:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 11 in 5n4l

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Copper binding site 1 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1101

b:0.3
occ:1.00
NE2 A:HIS974 2.0 0.3 1.0
O A:HOH1209 2.1 0.4 1.0
NE2 A:HIS1014 2.1 0.9 1.0
NE2 A:HIS162 2.4 0.2 1.0
CE1 A:HIS1014 2.5 0.9 1.0
CD2 A:HIS162 2.6 0.5 1.0
CE1 A:HIS974 2.9 0.8 1.0
CD2 A:HIS974 3.1 1.0 1.0
CD2 A:HIS1014 3.4 0.3 1.0
CE1 A:HIS162 3.7 0.2 1.0
CD2 A:HIS972 3.8 0.2 1.0
ND1 A:HIS1014 3.8 0.2 1.0
CG A:HIS162 3.9 0.9 1.0
ND1 A:HIS974 4.0 0.6 1.0
NE2 A:HIS101 4.1 0.3 1.0
NE2 A:HIS972 4.2 98.8 1.0
CG A:HIS974 4.2 1.0 1.0
CG A:HIS1014 4.2 0.1 1.0
CU A:CU1105 4.2 0.8 1.0
CD2 A:LEU1012 4.3 0.1 1.0
CE1 A:HIS1016 4.4 0.4 1.0
ND1 A:HIS162 4.4 0.6 1.0
CU A:CU1104 4.6 0.8 1.0
CD2 A:HIS101 4.6 0.1 1.0
NE2 A:HIS1016 4.7 1.0 1.0
CE1 A:HIS101 4.7 0.3 1.0
CE1 A:HIS160 4.9 0.9 1.0

Copper binding site 2 out of 11 in 5n4l

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Copper binding site 2 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1102

b:0.6
occ:1.00
SG A:CYS1015 2.0 0.4 1.0
ND1 A:HIS969 2.0 0.1 1.0
ND1 A:HIS1020 2.1 0.0 1.0
CG A:HIS969 2.9 0.2 1.0
CE1 A:HIS1020 3.0 0.4 1.0
CE1 A:HIS969 3.0 0.2 1.0
CB A:HIS969 3.2 0.1 1.0
CG A:HIS1020 3.2 0.1 1.0
CA A:HIS969 3.2 0.5 1.0
CB A:CYS1015 3.2 0.8 1.0
SD A:MET1025 3.3 0.5 1.0
O A:LEU968 3.4 0.9 1.0
CB A:HIS1020 3.6 0.1 1.0
CG2 A:VAL1017 3.8 0.8 1.0
CD2 A:HIS969 4.0 0.4 1.0
NE2 A:HIS969 4.0 0.1 1.0
N A:HIS969 4.1 1.0 1.0
CG1 A:VAL1017 4.1 0.3 1.0
C A:LEU968 4.1 0.4 1.0
NE2 A:HIS1020 4.2 0.3 1.0
N A:THR970 4.2 0.3 1.0
C A:HIS969 4.3 0.0 1.0
CD2 A:HIS1020 4.3 0.6 1.0
CA A:CYS1015 4.5 0.8 1.0
CB A:VAL1017 4.6 0.6 1.0
CG A:MET1025 4.6 0.5 1.0
CE A:MET1025 4.7 1.0 1.0

Copper binding site 3 out of 11 in 5n4l

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Copper binding site 3 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1103

b:0.7
occ:1.00
ND1 A:HIS323 1.9 99.1 1.0
SG A:CYS318 2.1 0.3 1.0
ND1 A:HIS275 2.4 0.2 1.0
CG A:HIS323 2.9 0.2 1.0
CE1 A:HIS323 3.0 96.8 1.0
CB A:HIS323 3.1 0.4 1.0
CG A:HIS275 3.2 0.2 1.0
CE1 A:HIS275 3.3 0.0 1.0
CD1 A:LEU328 3.3 0.1 1.0
CB A:CYS318 3.4 95.8 1.0
CA A:HIS275 3.4 0.4 1.0
CB A:HIS275 3.5 0.9 1.0
CB A:ASN320 3.7 0.1 1.0
CD2 A:HIS323 4.0 0.4 1.0
NE2 A:HIS323 4.0 0.4 1.0
CD2 A:HIS275 4.2 99.6 1.0
NE2 A:HIS275 4.2 0.0 1.0
N A:HIS275 4.3 0.1 1.0
N A:SER276 4.3 91.4 1.0
O A:VAL274 4.4 0.1 1.0
C A:HIS275 4.4 1.0 1.0
CG A:LEU328 4.6 0.7 1.0
C A:VAL274 4.6 97.6 1.0
CG A:ASN320 4.6 0.6 1.0
N A:ASN320 4.7 0.4 1.0
CA A:CYS318 4.7 96.7 1.0
CA A:HIS323 4.7 0.7 1.0
CA A:ASN320 4.7 0.3 1.0
C A:CYS318 4.8 88.8 1.0
O A:CYS318 4.9 0.7 1.0
CD2 A:PHE201 4.9 93.5 1.0
CD2 A:LEU328 4.9 0.1 1.0
ND2 A:ASN320 4.9 0.4 1.0
O A:ASN320 5.0 0.9 1.0

Copper binding site 4 out of 11 in 5n4l

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Copper binding site 4 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1104

b:0.8
occ:1.00
NE2 A:HIS1016 1.9 1.0 1.0
NE2 A:HIS103 2.4 0.1 1.0
NE2 A:HIS160 2.4 0.2 1.0
O A:HOH1209 2.5 0.4 1.0
CE1 A:HIS1016 2.9 0.4 1.0
CD2 A:HIS1016 2.9 0.9 1.0
CE1 A:HIS103 3.1 0.2 1.0
CD2 A:HIS160 3.3 97.3 1.0
CE1 A:HIS160 3.4 0.9 1.0
CD2 A:HIS103 3.5 0.9 1.0
CD1 A:ILE158 3.9 0.3 1.0
ND1 A:HIS1016 4.0 0.8 1.0
NE2 A:HIS972 4.0 98.8 1.0
CG A:HIS1016 4.1 0.8 1.0
ND1 A:HIS103 4.3 0.3 1.0
CD2 A:HIS972 4.3 0.2 1.0
ND1 A:HIS160 4.5 0.8 1.0
CG A:HIS160 4.5 96.1 1.0
CG A:HIS103 4.5 0.2 1.0
CG1 A:ILE158 4.5 0.4 1.0
CU A:CU1105 4.6 0.8 1.0
CU A:CU1101 4.6 0.3 1.0
CE1 A:HIS972 4.6 0.9 1.0
CD2 A:HIS101 4.8 0.1 1.0
CG A:HIS972 5.0 0.5 1.0

Copper binding site 5 out of 11 in 5n4l

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Copper binding site 5 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1105

b:0.8
occ:1.00
NE2 A:HIS101 1.9 0.3 1.0
NE2 A:HIS972 2.2 98.8 1.0
CD2 A:HIS101 2.9 0.1 1.0
CE1 A:HIS101 2.9 0.3 1.0
CE1 A:HIS972 3.0 0.9 1.0
CD2 A:HIS974 3.1 1.0 1.0
CD2 A:HIS972 3.3 0.2 1.0
NE2 A:HIS974 3.3 0.3 1.0
CD2 A:HIS103 3.3 0.9 1.0
NE2 A:HIS103 3.5 0.1 1.0
O A:ALA102 3.5 0.1 1.0
O A:HOH1209 3.8 0.4 1.0
OH A:TYR107 3.8 0.3 1.0
CG A:HIS974 3.9 1.0 1.0
ND1 A:HIS101 4.0 0.7 1.0
CG A:HIS101 4.0 0.1 1.0
ND1 A:HIS972 4.2 0.3 1.0
CG A:HIS103 4.2 0.2 1.0
CU A:CU1101 4.2 0.3 1.0
CE1 A:HIS974 4.2 0.8 1.0
CE1 A:HIS103 4.3 0.2 1.0
CG A:HIS972 4.3 0.5 1.0
CA A:HIS974 4.5 0.4 1.0
ND1 A:HIS974 4.5 0.6 1.0
CU A:CU1104 4.6 0.8 1.0
C A:ALA102 4.6 0.7 1.0
CA A:HIS103 4.7 0.8 1.0
OD2 A:ASP989 4.7 0.4 1.0
ND1 A:HIS103 4.7 0.3 1.0
CB A:HIS974 4.7 0.8 1.0
O A:PHE973 4.8 0.1 1.0

Copper binding site 6 out of 11 in 5n4l

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Copper binding site 6 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1101

b:0.3
occ:1.00
SG B:CYS1015 1.9 0.4 1.0
ND1 B:HIS969 2.0 0.8 1.0
ND1 B:HIS1020 2.3 0.4 1.0
CG B:HIS969 2.9 0.1 1.0
CE1 B:HIS969 3.0 0.1 1.0
SD B:MET1025 3.1 0.0 1.0
CB B:HIS969 3.2 0.4 1.0
CE1 B:HIS1020 3.2 0.2 1.0
CA B:HIS969 3.3 0.4 1.0
CG B:HIS1020 3.3 0.9 1.0
CB B:CYS1015 3.3 97.1 1.0
CG1 B:VAL1017 3.5 0.1 1.0
O B:LEU968 3.5 0.4 1.0
CB B:HIS1020 3.6 0.3 1.0
CD2 B:HIS969 3.9 0.1 1.0
NE2 B:HIS969 4.0 0.1 1.0
N B:HIS969 4.2 0.1 1.0
N B:THR970 4.2 0.2 1.0
C B:LEU968 4.2 0.4 1.0
C B:HIS969 4.3 0.4 1.0
NE2 B:HIS1020 4.4 0.7 1.0
CE B:MET1025 4.4 85.7 1.0
CD2 B:HIS1020 4.4 0.7 1.0
CG2 B:VAL1017 4.4 0.2 1.0
CB B:VAL1017 4.5 0.7 1.0
O B:CYS1015 4.5 0.2 1.0
CA B:CYS1015 4.5 0.3 1.0
CG B:MET1025 4.6 0.2 1.0
C B:CYS1015 4.8 0.4 1.0

Copper binding site 7 out of 11 in 5n4l

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Copper binding site 7 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1102

b:0.5
occ:1.00
SG B:CYS318 1.9 0.1 1.0
ND1 B:HIS323 2.1 0.4 1.0
ND1 B:HIS275 2.3 98.8 1.0
CG B:HIS323 3.0 0.3 1.0
CE1 B:HIS275 3.0 0.5 1.0
CE1 B:HIS323 3.1 0.3 1.0
CG B:HIS275 3.1 0.1 1.0
CB B:HIS323 3.2 0.0 1.0
CB B:CYS318 3.2 0.1 1.0
CD1 B:LEU328 3.3 0.9 1.0
CA B:HIS275 3.5 0.3 1.0
CB B:HIS275 3.5 0.8 1.0
CB B:ASN320 3.6 0.4 1.0
NE2 B:HIS275 3.9 0.3 1.0
CD2 B:HIS275 4.0 99.5 1.0
CD2 B:HIS323 4.1 0.4 1.0
NE2 B:HIS323 4.1 0.8 1.0
O B:VAL274 4.2 0.5 1.0
N B:SER276 4.3 0.5 1.0
N B:HIS275 4.4 0.1 1.0
C B:HIS275 4.5 0.2 1.0
CA B:CYS318 4.5 0.1 1.0
C B:VAL274 4.6 0.5 1.0
CG B:ASN320 4.6 0.5 1.0
CG B:LEU328 4.6 0.3 1.0
ND2 B:ASN320 4.6 0.5 1.0
N B:ASN320 4.7 0.9 1.0
O B:CYS318 4.7 99.0 1.0
CA B:ASN320 4.7 0.6 1.0
C B:CYS318 4.7 0.7 1.0
CA B:HIS323 4.8 0.8 1.0
CD2 B:PHE201 4.9 92.6 1.0
CB B:LEU328 4.9 0.9 1.0

Copper binding site 8 out of 11 in 5n4l

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Copper binding site 8 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1103

b:0.7
occ:1.00
NE2 B:HIS1016 1.7 0.8 1.0
NE2 B:HIS160 2.1 0.6 1.0
CE1 B:HIS1016 2.4 0.2 1.0
NE2 B:HIS103 2.5 0.1 1.0
CD2 B:HIS1016 2.9 0.1 1.0
CD2 B:HIS160 3.1 0.7 1.0
CE1 B:HIS160 3.1 0.6 1.0
CE1 B:HIS103 3.2 0.2 1.0
CU B:CU1106 3.4 0.2 1.0
ND1 B:HIS1016 3.5 0.1 1.0
CD2 B:HIS103 3.6 0.5 1.0
CG B:HIS1016 3.8 0.8 1.0
ND1 B:HIS160 4.2 0.1 1.0
CG B:HIS160 4.2 0.1 1.0
CD2 B:HIS101 4.4 1.0 1.0
CU B:CU1105 4.4 0.7 1.0
ND1 B:HIS103 4.4 0.8 1.0
CD2 B:HIS972 4.6 0.5 1.0
CG B:HIS103 4.7 0.2 1.0
CD1 B:ILE158 4.7 94.0 1.0
NE2 B:HIS972 4.7 0.4 1.0
NE2 B:HIS101 4.7 0.4 1.0
CG1 B:ILE158 5.0 88.9 1.0
CG B:HIS972 5.0 0.9 1.0

Copper binding site 9 out of 11 in 5n4l

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Copper binding site 9 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1104

b:0.5
occ:1.00
ND1 B:HIS631 2.2 0.6 1.0
SG B:CYS674 2.4 0.0 1.0
CD2 B:HIS679 2.7 0.8 1.0
CE1 B:HIS631 3.0 0.4 1.0
CG B:HIS679 3.1 0.3 1.0
CG B:HIS631 3.1 0.8 1.0
CB B:CYS674 3.2 0.0 1.0
NE2 B:HIS679 3.3 0.9 1.0
OG1 B:THR676 3.3 0.0 1.0
SD B:MET684 3.4 0.7 1.0
O B:VAL630 3.4 0.8 1.0
CA B:HIS631 3.5 0.9 1.0
CB B:HIS679 3.6 1.0 1.0
CB B:HIS631 3.6 0.3 1.0
ND1 B:HIS679 3.7 0.3 1.0
CE1 B:HIS679 3.8 0.7 1.0
NE2 B:HIS631 4.0 0.5 1.0
CD2 B:HIS631 4.1 0.5 1.0
C B:VAL630 4.2 0.3 1.0
N B:HIS631 4.3 0.7 1.0
CG2 B:THR676 4.4 0.0 1.0
N B:GLY632 4.4 0.9 1.0
CB B:THR676 4.4 0.5 1.0
C B:HIS631 4.5 0.2 1.0
CE B:MET684 4.6 0.6 1.0
CA B:CYS674 4.6 0.6 1.0
CG B:MET684 4.7 0.1 1.0
CD1 B:ILE633 4.9 0.0 1.0

Copper binding site 10 out of 11 in 5n4l

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Copper binding site 10 out of 11 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Rat Ceruloplasmin Trigonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu1105

b:0.7
occ:1.00
NE2 B:HIS1014 1.9 93.0 1.0
NE2 B:HIS974 2.3 0.5 1.0
CE1 B:HIS1014 2.3 0.7 1.0
NE2 B:HIS162 2.7 0.9 1.0
CD2 B:HIS1014 2.9 89.8 1.0
CD2 B:HIS162 2.9 0.3 1.0
CE1 B:HIS974 3.1 0.9 1.0
ND1 B:HIS1014 3.3 0.7 1.0
CD2 B:HIS974 3.4 0.6 1.0
CU B:CU1106 3.6 0.2 1.0
CG B:HIS1014 3.6 0.2 1.0
CE1 B:HIS1016 3.6 0.2 1.0
CD2 B:HIS972 3.9 0.5 1.0
CE1 B:HIS162 4.0 0.0 1.0
NE2 B:HIS101 4.2 0.4 1.0
CG B:HIS162 4.2 0.8 1.0
ND1 B:HIS974 4.3 0.1 1.0
NE2 B:HIS972 4.3 0.4 1.0
ND1 B:HIS1016 4.4 0.1 1.0
CD2 B:HIS101 4.4 1.0 1.0
CU B:CU1103 4.4 0.7 1.0
CG B:HIS974 4.4 0.8 1.0
CE1 B:HIS101 4.5 0.9 1.0
CD2 B:LEU1012 4.6 0.8 1.0
CE1 B:HIS160 4.6 0.6 1.0
NE2 B:HIS1016 4.6 0.8 1.0
ND1 B:HIS162 4.8 0.3 1.0
ND1 B:HIS101 4.9 0.7 1.0
CG B:HIS101 4.9 0.7 1.0
CB B:HIS1014 4.9 0.1 1.0
NE2 B:HIS160 5.0 0.6 1.0

Reference:

V.R.Samygina, A.V.Sokolov, G.Bourenkov, T.R.Schneider, V.A.Anashkin, S.O.Kozlov, N.N.Kolmakov, V.B.Vasilyev. Rat Ceruloplasmin: A New Labile Copper Binding Site and Zinc/Copper Mosaic. Metallomics V. 9 1828 2017.
ISSN: ESSN 1756-591X
PubMed: 29177316
DOI: 10.1039/C7MT00157F
Page generated: Sun Dec 13 11:18:53 2020

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