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Cadmium in PDB 6imj: The Crystal Structure of Se-Asfvlig:Dna Complex

Protein crystallography data

The structure of The Crystal Structure of Se-Asfvlig:Dna Complex, PDB code: 6imj was solved by Y.Q.Chen, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.828, 63.099, 119.265, 90.00, 89.93, 90.00
R / Rfree (%) 22.3 / 26.1

Other elements in 6imj:

The structure of The Crystal Structure of Se-Asfvlig:Dna Complex also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the The Crystal Structure of Se-Asfvlig:Dna Complex (pdb code 6imj). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the The Crystal Structure of Se-Asfvlig:Dna Complex, PDB code: 6imj:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 6imj

Go back to Cadmium Binding Sites List in 6imj
Cadmium binding site 1 out of 6 in the The Crystal Structure of Se-Asfvlig:Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of The Crystal Structure of Se-Asfvlig:Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:81.0
occ:1.00
NZ A:LYS380 2.6 74.3 1.0
OXT A:ILE419 2.7 91.7 1.0
O A:ILE419 2.9 83.8 1.0
CE A:LYS380 3.0 65.7 1.0
NE2 A:HIS381 3.0 48.9 1.0
C A:ILE419 3.2 81.5 1.0
CE1 A:HIS381 3.7 51.9 1.0
CD2 A:LEU377 3.8 41.9 1.0
CD2 A:HIS381 3.9 55.0 1.0
CD A:LYS380 4.4 58.7 1.0
CA A:ILE419 4.6 68.6 1.0
ND1 A:HIS381 4.7 57.5 1.0
CG A:HIS381 4.8 53.7 1.0

Cadmium binding site 2 out of 6 in 6imj

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Cadmium binding site 2 out of 6 in the The Crystal Structure of Se-Asfvlig:Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of The Crystal Structure of Se-Asfvlig:Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:0.5
occ:1.00
O2B A:ATP501 2.8 0.1 1.0
O1B A:ATP501 2.9 0.3 1.0
NE2 A:HIS310 3.1 54.5 1.0
PB A:ATP501 3.2 0.2 1.0
O1A A:ATP501 3.4 0.4 1.0
NH2 A:ARG172 3.7 84.7 1.0
PA A:ATP501 3.8 0.2 1.0
O3A A:ATP501 3.9 0.0 1.0
CD2 A:HIS310 3.9 53.3 1.0
O2A A:ATP501 3.9 0.3 1.0
CE1 A:HIS310 4.0 55.5 1.0
NZ A:LYS316 4.2 86.8 1.0
O3B A:ATP501 4.7 0.5 1.0
CZ A:ARG172 4.9 84.4 1.0
O A:VAL129 5.0 54.0 1.0

Cadmium binding site 3 out of 6 in 6imj

Go back to Cadmium Binding Sites List in 6imj
Cadmium binding site 3 out of 6 in the The Crystal Structure of Se-Asfvlig:Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of The Crystal Structure of Se-Asfvlig:Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:0.4
occ:1.00
O1G A:ATP501 2.8 0.4 1.0
NZ A:LYS151 3.5 55.9 1.0
OE1 A:GLU291 3.7 67.5 1.0
OE1 A:GLU203 3.9 76.5 1.0
O A:ARG152 3.9 37.1 1.0
C1' A:ATP501 4.0 46.4 1.0
PG A:ATP501 4.0 0.1 1.0
OD1 A:ASN153 4.0 51.8 1.0
O4' A:ATP501 4.1 51.0 1.0
O3G A:ATP501 4.1 0.2 1.0
O A:GLY154 4.2 46.4 1.0
CA A:ASN153 4.3 43.2 1.0
O2' A:ATP501 4.3 51.3 1.0
O A:HOH630 4.4 71.4 1.0
N A:GLY154 4.4 37.0 1.0
O3B A:ATP501 4.5 0.5 1.0
CE A:LYS151 4.5 52.6 1.0
C4' A:ATP501 4.5 58.5 1.0
CD A:GLU291 4.6 64.5 1.0
OE2 A:GLU291 4.6 76.7 1.0
C A:ASN153 4.8 45.2 1.0
C2' A:ATP501 4.8 49.5 1.0
CD A:LYS151 4.8 53.8 1.0
C A:ARG152 4.8 37.6 1.0
CG A:ASN153 4.9 46.1 1.0
CD A:GLU203 4.9 67.5 1.0

Cadmium binding site 4 out of 6 in 6imj

Go back to Cadmium Binding Sites List in 6imj
Cadmium binding site 4 out of 6 in the The Crystal Structure of Se-Asfvlig:Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of The Crystal Structure of Se-Asfvlig:Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:83.0
occ:1.00
NE2 B:HIS381 2.8 55.7 1.0
OXT B:ILE419 2.8 89.1 1.0
O B:ILE419 2.9 0.8 1.0
C B:ILE419 3.2 86.9 1.0
CE1 B:HIS381 3.4 54.5 1.0
CD2 B:LEU377 3.5 60.9 1.0
CD2 B:HIS381 3.8 50.7 1.0
ND1 B:HIS381 4.5 50.0 1.0
CG B:LEU377 4.5 51.0 1.0
CA B:ILE419 4.6 68.1 1.0
CG B:HIS381 4.7 48.7 1.0
CB B:LEU377 4.7 39.7 1.0
CA B:LEU377 4.9 42.0 1.0
CD1 B:LEU377 4.9 52.5 1.0

Cadmium binding site 5 out of 6 in 6imj

Go back to Cadmium Binding Sites List in 6imj
Cadmium binding site 5 out of 6 in the The Crystal Structure of Se-Asfvlig:Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of The Crystal Structure of Se-Asfvlig:Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd503

b:0.5
occ:1.00
O1B B:ATP501 2.9 0.9 1.0
O2B B:ATP501 3.1 0.3 1.0
NE2 B:HIS310 3.2 54.8 1.0
O2A B:ATP501 3.2 0.6 1.0
O B:HOH602 3.3 76.2 1.0
PB B:ATP501 3.3 0.6 1.0
PA B:ATP501 3.7 0.8 1.0
O3A B:ATP501 3.9 0.7 1.0
O1A B:ATP501 3.9 0.2 1.0
CD2 B:HIS310 3.9 51.8 1.0
NZ B:LYS316 4.0 73.1 1.0
CE1 B:HIS310 4.0 60.6 1.0
NH2 B:ARG172 4.0 77.8 1.0
OE2 B:GLU393 4.3 74.8 1.0
O B:VAL129 4.7 53.7 1.0
O3B B:ATP501 4.8 0.0 1.0

Cadmium binding site 6 out of 6 in 6imj

Go back to Cadmium Binding Sites List in 6imj
Cadmium binding site 6 out of 6 in the The Crystal Structure of Se-Asfvlig:Dna Complex


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of The Crystal Structure of Se-Asfvlig:Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd504

b:0.6
occ:1.00
O3G B:ATP501 2.8 0.6 1.0
PG B:ATP501 3.9 0.9 1.0
O B:GLY154 4.0 54.2 1.0
OD1 B:ASN153 4.0 47.0 1.0
NZ B:LYS151 4.0 58.7 1.0
C1' B:ATP501 4.0 53.0 1.0
OE1 B:GLU203 4.1 59.1 1.0
O2' B:ATP501 4.1 61.5 1.0
OE1 B:GLU291 4.1 68.8 1.0
O3B B:ATP501 4.2 0.0 1.0
O4' B:ATP501 4.2 57.8 1.0
O1G B:ATP501 4.3 0.4 1.0
O B:ARG152 4.3 36.6 1.0
C4' B:ATP501 4.5 64.7 1.0
CA B:ASN153 4.5 42.7 1.0
N B:GLY154 4.6 34.5 1.0
C2' B:ATP501 4.7 57.4 1.0
OE2 B:GLU291 4.8 73.6 1.0
C B:GLY154 4.9 44.3 1.0
O3' B:ATP501 4.9 59.9 1.0
CD B:GLU291 4.9 66.3 1.0
C B:ASN153 4.9 42.2 1.0
CG B:ASN153 5.0 48.0 1.0

Reference:

Y.Chen, H.Liu, C.Yang, Y.Gao, X.Yu, X.Chen, R.Cui, L.Zheng, S.Li, X.Li, J.Ma, Z.Huang, J.Li, J.Gan. Structure of the Error-Prone Dna Ligase of African Swine Fever Virus Identifies Critical Active Site Residues. Nat Commun V. 10 387 2019.
ISSN: ESSN 2041-1723
PubMed: 30674878
DOI: 10.1038/S41467-019-08296-W
Page generated: Sat Dec 12 08:28:44 2020

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