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Cadmium in PDB 5an6: Crystal Structure of Thermotoga Maritima CSM2

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima CSM2, PDB code: 5an6 was solved by G.Gallo, G.Augusto, G.Rangel, A.Zelanis, M.A.Mori, C.B.Campos, M.Wurtele, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.651 / 2.4
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 77.000, 77.000, 160.000, 90.00, 90.00, 120.00
R / Rfree (%) 20.98 / 24.88

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Thermotoga Maritima CSM2 (pdb code 5an6). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of Thermotoga Maritima CSM2, PDB code: 5an6:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 5an6

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Cadmium binding site 1 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1129

b:54.8
occ:1.00
OE1 B:GLU88 2.6 44.5 1.0
O B:HOH2040 2.6 31.5 1.0
OE2 B:GLU88 2.6 48.5 1.0
CD B:GLU88 2.9 53.2 1.0
NZ C:LYS30 4.2 62.6 1.0
NH1 B:ARG85 4.2 66.9 1.0
CG B:GLU88 4.4 47.7 1.0
CG B:ARG85 4.7 39.9 1.0
CE C:LYS30 4.7 56.3 1.0
O B:HOH2024 4.8 51.1 1.0

Cadmium binding site 2 out of 7 in 5an6

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Cadmium binding site 2 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1130

b:73.6
occ:1.00
O B:HOH2041 2.7 43.3 1.0
O B:HOH2036 2.7 48.6 1.0
O C:THR33 3.5 73.2 1.0
CD2 B:LEU121 3.5 42.9 1.0
ND1 B:HIS124 3.9 54.0 1.0
N C:GLN35 4.1 61.2 1.0
C C:THR33 4.1 72.3 1.0
CE1 B:HIS124 4.2 56.0 1.0
CA C:ASN34 4.3 59.3 1.0
N C:LEU36 4.4 48.6 1.0
N C:ASN34 4.5 64.0 1.0
CB C:LEU36 4.6 54.3 1.0
C C:ASN34 4.7 60.8 1.0
OH B:TYR117 4.9 63.4 1.0
CG C:LEU36 4.9 58.4 1.0
CG B:LEU121 4.9 52.1 1.0
CD2 B:LEU93 5.0 50.5 1.0

Cadmium binding site 3 out of 7 in 5an6

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Cadmium binding site 3 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1131

b:0.7
occ:1.00
O B:HOH2042 2.9 67.1 1.0
O B:HOH2009 3.2 74.6 1.0
CD1 C:LEU121 3.7 70.4 1.0
N B:ASN34 3.7 87.7 1.0
CA B:ASN34 3.8 90.0 1.0
CD2 C:HIS124 4.0 75.4 1.0
N B:GLN35 4.2 79.9 1.0
N B:LEU36 4.3 88.2 1.0
NE2 C:HIS124 4.3 77.2 1.0
CB B:LEU36 4.3 72.8 1.0
OD1 B:ASN34 4.4 97.5 1.0
C B:ASN34 4.5 86.8 1.0
CA B:LEU36 4.7 79.8 1.0
C B:THR33 4.9 89.2 1.0
CD2 C:LEU93 4.9 48.3 1.0
C B:LEU36 5.0 78.8 1.0
CB B:ASN34 5.0 87.7 1.0

Cadmium binding site 4 out of 7 in 5an6

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Cadmium binding site 4 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1132

b:61.5
occ:1.00
OE2 B:GLU95 2.5 46.0 1.0
OE2 A:GLU88 2.5 56.8 1.0
OE1 A:GLU88 2.6 49.9 1.0
O B:HOH2027 2.7 33.5 1.0
CD A:GLU88 2.9 54.7 1.0
OE1 B:GLU95 2.9 64.0 1.0
CD B:GLU95 3.1 55.1 1.0
NZ B:LYS94 3.1 55.6 1.0
CG B:GLU98 4.3 36.7 1.0
CB B:GLU98 4.3 33.8 1.0
CG A:GLU88 4.4 51.6 1.0
CE B:LYS94 4.5 44.0 1.0
CG B:GLU95 4.6 43.8 1.0
CG A:ARG85 4.9 39.2 1.0

Cadmium binding site 5 out of 7 in 5an6

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Cadmium binding site 5 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1133

b:0.5
occ:1.00
O B:HOH2002 2.9 65.3 1.0
CB B:LYS14 3.9 68.4 1.0
N B:LYS14 4.1 65.7 1.0
CA B:LYS14 4.3 69.6 1.0
CG B:LYS14 4.6 68.1 1.0
CB B:LEU13 4.7 57.8 1.0

Cadmium binding site 6 out of 7 in 5an6

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Cadmium binding site 6 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1129

b:0.6
occ:1.00
OD1 C:ASP59 2.6 49.5 1.0
O C:HOH2019 2.8 51.3 1.0
NZ C:LYS55 3.0 58.7 1.0
O C:HOH2031 3.2 73.4 1.0
OD2 C:ASP59 3.4 50.0 1.0
CG C:ASP59 3.4 51.2 1.0
O C:HOH2017 4.2 41.4 1.0
CE C:LYS55 4.4 63.5 1.0
CG C:LYS55 4.5 47.9 1.0
CB C:ASP59 4.8 47.4 1.0
CD C:LYS55 4.9 53.4 1.0

Cadmium binding site 7 out of 7 in 5an6

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Cadmium binding site 7 out of 7 in the Crystal Structure of Thermotoga Maritima CSM2


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Thermotoga Maritima CSM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd1130

b:71.3
occ:1.00
OE1 C:GLU88 2.6 67.9 1.0
O B:HOH2008 2.7 42.0 1.0
OE2 C:GLU88 2.8 71.4 1.0
CD C:GLU88 3.0 66.1 1.0
NZ B:LYS30 4.2 69.9 1.0
O C:HOH2026 4.4 58.7 1.0
CG C:GLU88 4.5 51.0 1.0
CE B:LYS30 4.7 60.6 1.0

Reference:

G.Gallo, G.Augusto, G.Rangel, A.Zelanis, M.A.Mori, C.B.Campos, M.Wurtele. Structural Basis For Dimer Formation of the Crispr- Associated Protein CSM2 of Thermotoga Maritima. Febs J. V. 283 694 2016.
ISSN: ISSN 1742-464X
PubMed: 26663887
DOI: 10.1111/FEBS.13621
Page generated: Sat Dec 12 08:26:15 2020

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