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Cadmium in PDB 2fcs: X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group

Protein crystallography data

The structure of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group, PDB code: 2fcs was solved by D.Bang, A.V.Gribenko, V.Tereshko, A.A.Kossiakoff, S.B.Kent, G.I.Makhatadze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 106.578, 106.578, 106.578, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group (pdb code 2fcs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group, PDB code: 2fcs:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 2fcs

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Cadmium binding site 1 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd100

b:33.5
occ:1.00
OE2 A:GLU64 2.2 37.5 1.0
OXT A:ACT101 2.2 37.1 1.0
OXT A:ACT102 2.3 40.3 1.0
O A:HOH103 2.5 29.4 1.0
OE1 A:GLU64 2.5 33.0 1.0
O A:ACT101 2.6 39.1 1.0
CD A:GLU64 2.7 34.2 1.0
C A:ACT101 2.8 39.4 1.0
C A:ACT102 3.3 42.9 1.0
O A:ACT102 3.6 41.8 1.0
CG A:GLU64 4.2 32.2 1.0
CH3 A:ACT101 4.3 38.8 1.0
CH3 A:ACT102 4.5 43.0 1.0
O A:HOH1025 4.5 45.9 1.0
NZ A:LYS63 4.7 40.8 1.0
CE A:LYS63 4.7 36.4 1.0

Cadmium binding site 2 out of 9 in 2fcs

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Cadmium binding site 2 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd200

b:24.8
occ:0.50
CD A:CD200 0.0 24.8 0.5
CD A:CD200 1.6 33.4 0.5
OD1 A:ASP21 2.2 31.5 1.0
O A:HOH201 2.3 52.7 1.0
OD2 A:ASP21 2.4 26.2 1.0
CG A:ASP21 2.7 28.2 1.0
NZ A:LYS29 2.8 35.8 1.0
CE A:LYS29 3.3 30.7 1.0
OE1 A:GLU18 3.9 33.5 1.0
CB A:ASP21 4.2 27.8 1.0
ND2 A:ASN25 4.3 22.5 1.0
CG A:GLU18 4.3 27.2 1.0
N A:GLU18 4.5 25.5 1.0
CB A:ASN25 4.6 23.1 1.0
CD A:GLU18 4.6 31.1 1.0
CD A:LYS29 4.8 28.3 1.0
CB A:GLU18 4.8 26.1 1.0
CG A:ASN25 4.8 24.4 1.0
CA A:VAL17 4.9 26.0 1.0

Cadmium binding site 3 out of 9 in 2fcs

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Cadmium binding site 3 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd200

b:33.4
occ:0.50
CD A:CD200 0.0 33.4 0.5
CD A:CD200 1.6 24.8 0.5
OD1 A:ASP21 2.4 31.5 1.0
OE1 A:GLU18 2.6 33.5 1.0
O A:HOH201 2.8 52.7 1.0
CG A:ASP21 3.2 28.2 1.0
OD2 A:ASP21 3.3 26.2 1.0
CD A:GLU18 3.5 31.1 1.0
CG A:GLU18 3.7 27.2 1.0
CB A:GLU18 4.2 26.1 1.0
ND2 A:ASN25 4.3 22.5 1.0
NZ A:LYS29 4.3 35.8 1.0
CB A:ASP21 4.7 27.8 1.0
OE2 A:GLU18 4.7 34.9 1.0
O A:HOH1012 4.7 32.5 1.0
N A:GLU18 4.8 25.5 1.0
CE A:LYS29 4.9 30.7 1.0

Cadmium binding site 4 out of 9 in 2fcs

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Cadmium binding site 4 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd300

b:38.8
occ:1.00
N A:LEU1 2.1 35.2 1.0
O A:ACT301 2.2 42.4 1.0
OXT A:ACT301 2.2 43.1 1.0
OE1 A:GLU16 2.2 37.8 1.0
OE2 A:GLU16 2.5 32.4 1.0
C A:ACT301 2.6 43.5 1.0
CD A:GLU16 2.7 32.5 1.0
CA A:LEU1 3.1 33.7 1.0
C A:LEU1 3.4 32.8 1.0
O A:LEU1 3.5 31.6 1.0
CH3 A:ACT301 4.1 43.9 1.0
N A:GLN2 4.2 30.6 1.0
CG A:GLU16 4.2 30.8 1.0
O A:HOH1047 4.4 46.3 1.0
O A:HOH302 4.4 45.2 1.0
CB A:LEU1 4.4 35.0 1.0
O A:HOH1042 4.7 47.4 1.0
O A:HOH1052 4.8 53.6 1.0
O A:HOH1009 4.9 34.2 1.0
CA A:GLN2 5.0 30.8 1.0
CB A:GLN2 5.0 31.6 1.0

Cadmium binding site 5 out of 9 in 2fcs

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Cadmium binding site 5 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd400

b:52.2
occ:0.25
OD1 A:ASP52 2.2 46.0 1.0
O A:HOH1023 2.9 39.7 1.0
O A:HOH1029 3.2 46.3 1.0
CG A:ASP52 3.3 37.7 1.0
OD2 A:ASP52 3.5 40.4 1.0
NZ A:LYS27 3.8 32.9 1.0
CD A:LYS27 3.9 28.2 1.0
O A:PRO38 4.2 28.2 1.0
CB A:PRO38 4.3 29.3 1.0
C A:PRO38 4.4 29.3 1.0
CE A:LYS27 4.5 32.4 1.0
CB A:ASP52 4.6 35.0 1.0
N A:ASP39 4.7 29.3 1.0
O A:HOH1001 4.8 27.3 1.0
O A:HOH1056 4.8 32.8 0.5
CA A:ASP39 4.8 30.7 1.0
CG A:GLU24 4.9 35.3 1.0
CA A:PRO38 4.9 29.1 1.0

Cadmium binding site 6 out of 9 in 2fcs

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Cadmium binding site 6 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd600

b:31.6
occ:0.50
CD B:CD600 0.0 31.6 0.5
CD B:CD600 1.6 37.8 0.5
OD1 B:ASP21 2.1 36.4 1.0
OD2 B:ASP21 2.3 30.8 1.0
O B:HOH601 2.3 53.5 1.0
CG B:ASP21 2.6 34.2 1.0
NZ B:LYS29 2.9 41.8 1.0
CE B:LYS29 3.3 36.8 1.0
OE1 B:GLU18 3.8 35.8 1.0
CB B:ASP21 4.1 32.3 1.0
CG B:GLU18 4.2 34.6 1.0
ND2 B:ASN25 4.3 30.6 1.0
CD B:GLU18 4.4 36.0 1.0
N B:GLU18 4.5 33.1 1.0
CB B:GLU18 4.6 33.7 1.0
CB B:ASN25 4.8 30.6 1.0
O B:HOH2009 4.8 34.7 1.0
CD B:LYS29 4.9 35.0 1.0
CA B:VAL17 4.9 33.4 1.0
CA B:ASP21 4.9 32.5 1.0
CG B:ASN25 4.9 29.5 1.0

Cadmium binding site 7 out of 9 in 2fcs

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Cadmium binding site 7 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd600

b:37.8
occ:0.50
CD B:CD600 0.0 37.8 0.5
CD B:CD600 1.6 31.6 0.5
OD1 B:ASP21 2.2 36.4 1.0
OE1 B:GLU18 2.5 35.8 1.0
O B:HOH601 3.0 53.5 1.0
CG B:ASP21 3.1 34.2 1.0
OD2 B:ASP21 3.2 30.8 1.0
CD B:GLU18 3.4 36.0 1.0
CG B:GLU18 3.7 34.6 1.0
CB B:GLU18 4.2 33.7 1.0
ND2 B:ASN25 4.2 30.6 1.0
NZ B:LYS29 4.4 41.8 1.0
CB B:ASP21 4.5 32.3 1.0
OE2 B:GLU18 4.6 38.7 1.0
N B:GLU18 4.9 33.1 1.0
CA B:ASP21 4.9 32.5 1.0
CE B:LYS29 4.9 36.8 1.0

Cadmium binding site 8 out of 9 in 2fcs

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Cadmium binding site 8 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd700

b:49.9
occ:1.00
N B:LEU1 2.1 39.8 1.0
OE2 B:GLU16 2.2 45.1 1.0
O B:HOH701 2.3 47.0 1.0
OE1 B:GLU16 2.7 45.7 1.0
CD B:GLU16 2.8 44.3 1.0
CA B:LEU1 3.1 40.7 1.0
C B:LEU1 3.5 39.6 1.0
O B:LEU1 3.7 41.2 1.0
O B:HOH2018 3.9 40.1 1.0
O B:HOH2037 4.1 53.9 1.0
N B:GLN2 4.2 37.9 1.0
CG B:GLU16 4.2 38.6 1.0
O B:HOH2020 4.3 43.8 1.0
CB B:LEU1 4.4 41.8 1.0
O B:VAL17 4.8 33.1 1.0
O B:HOH2016 4.8 40.7 1.0

Cadmium binding site 9 out of 9 in 2fcs

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Cadmium binding site 9 out of 9 in the X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Crystal Structure of A Chemically Synthesized [L-GLN35]Ubiquitin with A Cubic Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd800

b:48.4
occ:0.25
ND1 B:HIS68 2.2 41.7 1.0
CE1 B:HIS68 3.2 42.2 1.0
CG B:HIS68 3.2 37.8 1.0
O B:HOH2021 3.4 42.4 1.0
CB B:HIS68 3.5 34.9 1.0
O B:HOH2054 4.0 38.9 0.5
CD B:LYS6 4.1 35.4 0.5
NE2 B:HIS68 4.3 39.4 1.0
CD2 B:HIS68 4.3 42.2 1.0
CG B:LYS6 4.3 35.4 1.0
CA B:HIS68 4.5 33.3 1.0
CB B:LYS6 4.7 35.2 1.0

Reference:

D.Bang, A.V.Gribenko, V.Tereshko, A.A.Kossiakoff, S.B.Kent, G.I.Makhatadze. Dissecting the Energetics of Protein Alpha-Helix C-Cap Termination Through Chemical Protein Synthesis. Nat.Chem.Biol. V. 2 139 2006.
ISSN: ISSN 1552-4450
PubMed: 16446709
DOI: 10.1038/NCHEMBIO766
Page generated: Sat Dec 12 08:17:05 2020

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